diff --git a/R/callback-itm.R b/R/callback-itm.R
index 89bd1abe..941470b7 100644
--- a/R/callback-itm.R
+++ b/R/callback-itm.R
@@ -43,6 +43,25 @@ mimic_sampling <- function(x, val_var, aux_time, ...) {
set(x, j = val_var, value = !is.na(x[[val_var]]))
}
+picdb_sampling <- function(x, val_var, aux_time, ...) {
+ x <- combine_date_time(x, aux_time, hours(12L))
+
+ # These identifiers indicate that the culture showed no growth
+ # of the respective organism
+ no_growth_identifiers <- c('MIC1008', 'MIC2123', 'MIC2287', 'MIC2291', 'MIC2293',
+ 'MIC2370', 'MIC2408', 'MIC2421', 'MIC575',
+ 'MIC585', 'MIC593', 'MIC629', 'MIC631',
+ 'MIC635', 'MIC637', 'MIC645', 'MIC648',
+ 'MIC874', 'MIC941', 'MIC979'
+ )
+
+ # Assign:
+ # - 0 if NA or in no_growth_identifiers
+ # - 1 otherwise, indicating growth
+ bool_value <- !is.na(x[[val_var]]) & !(x[[val_var]] %in% no_growth_identifiers)
+ set(x, j = val_var, value = bool_value)
+}
+
#' Item callback utilities
#'
#' For concept loading, item callback functions are used in order to handle
@@ -610,18 +629,24 @@ aumc_rate_units <- function(mcg_to_units) {
}
sic_dur <- function (x, val_var, stop_var, grp_var = NULL, ...) {
-
calc_dur(x, val_var, index_var(x), stop_var, grp_var)
}
-sic_rate_kg <- function (x, val_var, stop_var, env, ...) {
-
- res <- add_weight(x, env, "weight")
- wgh_var <- "weight"
- res[, c(val_var) := get(val_var) * 10^3 / get(wgh_var)]
- expand(res, index_var(x), stop_var, keep_vars = c(id_vars(x), val_var))
+sic_rate_kg <- function(x, val_var, unit_var, stop_var, env, ...) {
+
+ g_to_mcg <- convert_unit(binary_op(`*`, 1000000), "mcg", "g")
+
+ res <- g_to_mcg(x, val_var, unit_var)
+ res <- add_weight(res, env, "weight")
+
+ res <- res[, c(val_var) := get(val_var) / get("weight")]
+ res <- res[, c(unit_var) := paste(get(unit_var), "min", sep = "/kg/")]
+
+ expand(res, index_var(x), stop_var,
+ keep_vars = c(id_vars(x), val_var, unit_var))
}
+
eicu_duration <- function(gap_length) {
assert_that(is_interval(gap_length), is_scalar(gap_length))
@@ -643,6 +668,15 @@ aumc_dur <- function(x, val_var, stop_var, grp_var, ...) {
calc_dur(x, val_var, index_var(x), stop_var, grp_var)
}
+default_duration <- function(x, val_var, stop_var, grp_var, ...) {
+ calc_dur(x, val_var, index_var(x), stop_var, grp_var)
+}
+
+no_duration <- function(x, val_var, grp_var, ...) {
+ calc_dur(x, val_var, index_var(x), index_var(x), grp_var)
+}
+
+
#' Used for determining vasopressor durations, `calc_dur()` will calculate
#' durations by taking either per ID or per combination of ID and `grp_var`
#' the minimum for `min_var` and the maximum of `max_var` and returning the
@@ -759,6 +793,13 @@ aumc_death <- function(x, val_var, ...) {
x
}
+sic_death <- function(x, val_var, adm_time, ...) {
+ idx <- index_var(x)
+
+ x <- x[, c(val_var) := is_true(get(idx) - (get(adm_time) + secs(get(val_var))) < hours(72L))]
+ x
+}
+
aumc_bxs <- function(x, val_var, dir_var, ...) {
x <- x[get(dir_var) == "-", c(val_var) := -1L * get(val_var)]
x
diff --git a/R/callback-tbl.R b/R/callback-tbl.R
new file mode 100644
index 00000000..6088230b
--- /dev/null
+++ b/R/callback-tbl.R
@@ -0,0 +1,36 @@
+
+sic_data_float_h <- function(dat, ...) {
+
+ hexstring_to_float <- function(x) {
+ if (is.na(x)) {
+ return(NA_real_)
+ }
+ hexstring <- substring(x, seq(1, 482, 2), seq(2, 482, 2))
+ bytes <- as.raw(strtoi(hexstring[-1], base = 16))
+ floats <- readBin(bytes, numeric(), length(bytes) %/% 4, 4, endian = "little")
+ ifelse(floats == 0, NA_real_, floats)
+ }
+
+ setDT(dat)
+
+ # TODO: remove hard coding of rawdata and derive from JSON config
+ dat[, c("rawdata") := lapply(get("rawdata"), hexstring_to_float)]
+ dat <- dat[, .(
+ Offset = Offset + 60 * (0:(sapply(rawdata, length)-1)),
+ Val = Val,
+ cnt = cnt,
+ rawdata = unlist(rawdata),
+ rawdata_present = !is.na(rawdata)
+ ),
+ by = .(id, CaseID, DataID)
+ ]
+
+ # Fix measurements that only have one value
+ dat[rawdata_present == FALSE, rawdata := Val]
+ dat[, rawdata_present := NULL]
+
+ return(dat)
+
+}
+
+
diff --git a/R/concept-utils.R b/R/concept-utils.R
index 47f7d96b..734ff707 100644
--- a/R/concept-utils.R
+++ b/R/concept-utils.R
@@ -199,6 +199,30 @@ get_hirid_ids <- function(x, ids) {
load_id("variables", x, .data$id %in% .env$ids, cols = "unit", id_var = "id")
}
+#' @rdname data_items
+#' @export
+init_itm.sic_itm <- function(x, table, sub_var, ids,
+ callback = "identity_callback", ...) {
+
+ assert_that(is.string(table), has_length(ids),
+ is.character(ids) || is_intish(ids))
+
+ x[["table"]] <- table
+
+ units <- get_sic_ids(x, ids)
+ units <- rename_cols(rm_na(units), sub_var, "referenceglobalid")
+
+ todo <- c("ids", "units")
+ x[todo] <- mget(todo)
+
+ complete_tbl_itm(x, callback, sub_var, ...)
+}
+
+get_sic_ids <- function(x, ids) {
+ load_id("d_references", x, .data$referenceglobalid %in% .env$ids, cols = "referenceunit", id_var = "referenceglobalid")
+}
+
+
#' @param unit_val String valued unit to be used in case no `unit_var` is
#' available for the given table
#'
@@ -330,6 +354,10 @@ prepare_query.sel_itm <- prep_sel
#' @export
prepare_query.hrd_itm <- prep_sel
+#' @keywords internal
+#' @export
+prepare_query.sic_itm <- prep_sel
+
#' @keywords internal
#' @export
prepare_query.rgx_itm <- function(x) {
@@ -546,6 +574,28 @@ do_callback.hrd_itm <- function(x, ...) {
NextMethod()
}
+#' @keywords internal
+ #' @export
+ do_callback.sic_itm <- function(x, ...) {
+ # TODO: generalise and combine with do_callback.hrd_itm
+ if (is.null(get_itm_var(x, "unit_var"))) {
+ x <- try_add_vars(x, unit_var = "referenceunit")
+ }
+
+ NextMethod()
+}
+
+#' @keywords internal
+#' @export
+do_callback.sic_itm <- function(x, ...) {
+ # TODO: generalise and combine with do_callback.hrd_itm
+ if (is.null(get_itm_var(x, "unit_var"))) {
+ x <- try_add_vars(x, unit_var = "referenceunit")
+ }
+
+ NextMethod()
+}
+
#' @keywords internal
#' @export
do_callback.col_itm <- function(x, ...) {
@@ -604,6 +654,19 @@ do_itm_load.hrd_itm <- function(x, id_type = "icustay", interval = hours(1L)) {
res
}
+#' @export
+do_itm_load.sic_itm <- function(x, id_type = "icustay", interval = hours(1L)) {
+
+ res <- NextMethod()
+
+ if (is.null(get_itm_var(x, "unit_var"))) {
+ unt <- x[["units"]]
+ res <- merge(res, unt, by = get_itm_var(x, "sub_var"), all.x = TRUE)
+ }
+
+ res
+}
+
#' @export
do_itm_load.col_itm <- function(x, id_type = "icustay", interval = hours(1L)) {
diff --git a/R/config-utils.R b/R/config-utils.R
index ca9e6a49..4b036943 100644
--- a/R/config-utils.R
+++ b/R/config-utils.R
@@ -386,6 +386,34 @@ partition_col <- function(x, orig_names = FALSE) {
col
}
+tbl_callback <- function(x){
+ x <- as_tbl_cfg(x)
+ assert_that(length(x) == 1L)
+
+ if (!("callback" %in% vctrs::fields(x))) {
+ return(identity_callback)
+ }
+
+ callback_field <- vctrs::field(x, "callback")
+ if (is.character(callback_field)) {
+ msg_ricu(paste("[tbl_callback] Using callback function: ", callback_field))
+ return(str_to_fun(callback_field))
+ }
+
+ if (!is.null(callback_field) && !is.list(callback_field)) {
+ return(identity_callback)
+ }
+
+ callback_value <- callback_field[[1]]
+ if (is.character(callback_value)) {
+ msg_ricu(paste("[tbl_callback] Using callback function: ", callback_value))
+ return(str_to_fun(callback_value))
+ }
+
+ return(identity_callback)
+ }
+
+
#' @export
n_tick.tbl_cfg <- function(x) {
diff --git a/R/data-load.R b/R/data-load.R
index 80b57ee4..113b32dc 100644
--- a/R/data-load.R
+++ b/R/data-load.R
@@ -178,6 +178,17 @@ load_difftime.sic_tbl <- function(x, rows, cols = colnames(x),
load_eiau(x, {{ rows }}, cols, id_hint, time_vars, sec_as_mins)
}
+#' @rdname load_src
+#' @export
+# copy-pasted from mimic_tbl
+load_difftime.picdb_tbl <- function(x, rows, cols = colnames(x),
+ id_hint = id_vars(x),
+ time_vars = ricu::time_vars(x), ...) {
+
+ warn_dots(...)
+ load_mihi(x, {{ rows }}, cols, id_hint, time_vars)
+}
+
#' @rdname load_src
#' @export
load_difftime.character <- function(x, src, ...) {
diff --git a/R/data-utils.R b/R/data-utils.R
index 0d2b73cc..d3941c0f 100644
--- a/R/data-utils.R
+++ b/R/data-utils.R
@@ -128,6 +128,28 @@ id_orig_helper.miiv_env <- function(x, id) {
as_id_tbl(res, id, by_ref = TRUE)
}
+#' @rdname data_utils
+#' @export
+id_orig_helper.sic_env <- function(x, id) {
+
+ if (!identical(id, "patientid")) {
+ return(NextMethod())
+ }
+
+ cfg <- as_id_cfg(x)[id == id_var_opts(x)]
+
+ assert_that(length(cfg) == 1L)
+
+ sta <- field(cfg, "start")
+ age <- "admissionyear"
+
+ res <- as_src_tbl(x, field(cfg, "table"))
+ res <- res[, c(id, sta, age)]
+ res <- res[, c(sta, age) := shift_year(get(sta), get(age))]
+
+ as_id_tbl(res, id, by_ref = TRUE)
+}
+
#' @export
id_orig_helper.default <- function(x, ...) stop_generic(x, .Generic)
@@ -228,33 +250,32 @@ id_win_helper.eicu_env <- function(x) {
order_rename(res, ids, sta, end)
}
-#' @rdname data_utils
-#' @export
-id_win_helper.sic_env <- function(x) {
-
- sec_as_mins <- function(x) min_as_mins(as.integer(x / 60))
-
+
+ #' @rdname data_utils
+ #' @export
+ id_win_helper.sic_env <- function(x) {
cfg <- sort(as_id_cfg(x), decreasing = TRUE)
-
+
ids <- field(cfg, "id")
- sta <- c(unique(field(cfg, "start")), "HospAdmTime")
+ sta <- field(cfg, "start")
end <- field(cfg, "end")
-
+
tbl <- as_src_tbl(x, unique(field(cfg, "table")))
-
+
mis <- setdiff(sta, colnames(tbl))
-
+
res <- load_src(tbl, cols = c(ids, intersect(sta, colnames(tbl)), end))
-
- if (length(mis) > 0L) {
- res[, c(mis) := 0L]
- }
-
- res <- res[, c(sta, end) := lapply(.SD, sec_as_mins), .SDcols = c(sta, end)]
+
+ assert_that(length(mis) == 1L)
+ res[, firstadmission := 0L]
+
+ res <- res[, c(sta, end) := lapply(.SD, s_as_mins), .SDcols = c(sta, end)]
+ res[, timeofstay := offsetafterfirstadmission + timeofstay]
+
res <- setcolorder(res, c(ids, sta, end))
res <- rename_cols(res, c(ids, paste0(ids, "_start"),
paste0(ids, "_end")), by_ref = TRUE)
-
+
as_id_tbl(res, ids[2L], by_ref = TRUE)
}
@@ -361,6 +382,35 @@ id_win_helper.miiv_env <- function(x) {
order_rename(res, ids, sta, end)
}
+#' @rdname data_utils
+#' @export
+# copy-pasted from mimic
+id_win_helper.picdb_env <- function(x) {
+
+ merge_inter <- function(x, y) {
+ merge(x, y, by = intersect(colnames(x), colnames(y)))
+ }
+
+ get_id_tbl <- function(tbl, id, start, end, aux) {
+ as_src_tbl(x, tbl)[, c(id, start, end, aux)]
+ }
+
+ cfg <- sort(as_id_cfg(x), decreasing = TRUE)
+
+ ids <- field(cfg, "id")
+ sta <- field(cfg, "start")
+ end <- field(cfg, "end")
+
+ res <- Map(get_id_tbl, field(cfg, "table"), ids, sta,
+ end, c(as.list(ids[-1L]), list(NULL)))
+ res <- Reduce(merge_inter, res)
+
+ res <- res[, c(sta, end) := lapply(.SD, as_dt_min, get(sta[1L])),
+ .SDcols = c(sta, end)]
+
+ order_rename(res, ids, sta, end)
+}
+
#' @export
id_win_helper.default <- function(x) stop_generic(x, .Generic)
diff --git a/R/setup-import.R b/R/setup-import.R
index 0d2e536d..ab6388ec 100644
--- a/R/setup-import.R
+++ b/R/setup-import.R
@@ -184,6 +184,8 @@ import_tbl.tbl_cfg <- function(x, data_dir = src_data_dir(x), progress = NULL,
assert_that(is.dir(data_dir), is.flag(cleanup))
+ msg_ricu(paste("[import_tbl] Import table ", tbl_name(x)))
+ msg_ricu(paste("[import_tbl] Number of parts: ", n_part(x)))
if (n_part(x) > 1L) {
partition_table(x, data_dir, progress, ...)
} else {
@@ -218,8 +220,8 @@ merge_fst_chunks <- function(src, targ, new, old, sort_col, prog, nme, tick) {
fst::write_fst(dat, new_file, compress = 100L)
- progress_tick(paste(nme, "part", part_no), prog,
- coalesce(tick, floor(nrow(dat) / 2)))
+ # progress_tick(paste(nme, "part", part_no), prog,
+ # coalesce(tick, floor(nrow(dat) / 2)))
invisible(NULL)
}
@@ -227,7 +229,7 @@ merge_fst_chunks <- function(src, targ, new, old, sort_col, prog, nme, tick) {
split_write <- function(x, part_fun, dir, chunk_no, prog, nme, tick) {
n_row <- nrow(x)
-
+
x <- split(x, part_fun(x))
tmp_nme <- file.path(dir, paste0("part_", names(x)),
@@ -238,16 +240,21 @@ split_write <- function(x, part_fun, dir, chunk_no, prog, nme, tick) {
Map(fst::write_fst, x, tmp_nme)
- progress_tick(paste(nme, "chunk", chunk_no), prog,
- coalesce(tick, floor(n_row / 2)))
+ # progress_tick(paste(nme, "chunk", chunk_no), prog,
+ # coalesce(tick, floor(n_row / 2)))
invisible(NULL)
}
-partition_table <- function(x, dir, progress = NULL, chunk_length = 10 ^ 7,
+partition_table <- function(x, dir, progress = NULL, chunk_length = 10 ^ 7, tempdir = NULL,
...) {
- tempdir <- ensure_dirs(tempfile())
+ # tempdir <- ensure_dirs(tempfile())
+ if (is.null(tempdir)) {
+ # tempdir <- ensure_dirs(file.path(dir, "tempdir"))
+ tempdir <- ensure_dirs(tempfile())
+ }
+ msg_ricu(paste("[partition_table] tempdir: ", tempdir))
on.exit(unlink(tempdir, recursive = TRUE))
spec <- col_spec(x)
@@ -257,6 +264,8 @@ partition_table <- function(x, dir, progress = NULL, chunk_length = 10 ^ 7,
file <- file.path(dir, rawf)
name <- tbl_name(x)
+ callback <- tbl_callback(x)
+
exp_row <- n_row(x)
if (is.na(exp_row)) {
@@ -267,17 +276,18 @@ partition_table <- function(x, dir, progress = NULL, chunk_length = 10 ^ 7,
if (length(file) == 1L) {
- callback <- function(x, pos, ...) {
- report_problems(x, rawf)
- split_write(x, pfun, tempdir, ((pos - 1L) / chunk_length) + 1L,
- progress, name, tick)
- }
+ process_chunk <- function(x, pos, ...) {
+ report_problems(x, rawf)
+ split_write(callback(x), pfun, tempdir, ((pos - 1L) / chunk_length) + 1L,
+ progress, name, tick)
+ }
if (grepl("\\.gz$", file)) {
+ msg_ricu(paste("[partition_table] gunzip: ", file))
file <- gunzip(file, tempdir)
}
- readr::read_csv_chunked(file, callback, chunk_length, col_types = spec,
+ readr::read_csv_chunked(file, process_chunk, chunk_length, col_types = spec,
progress = FALSE, ...)
if (is.na(exp_row)) {
@@ -287,11 +297,9 @@ partition_table <- function(x, dir, progress = NULL, chunk_length = 10 ^ 7,
} else {
for (i in seq_along(file)) {
-
dat <- readr::read_csv(file[i], col_types = spec, progress = FALSE, ...)
report_problems(dat, rawf[i])
-
- split_write(dat, pfun, tempdir, i, progress, name, tick)
+ split_write(callback(data), pfun, tempdir, i, progress, name, tick)
}
}
@@ -350,11 +358,12 @@ gunzip <- function(file, exdir) {
return(dest)
}
-csv_to_fst <- function(x, dir, progress = NULL, ...) {
+csv_to_fst <- function(x, dir, progress = NULL, tempdir = NULL, ...) {
raw <- raw_file_name(x)
src <- file.path(dir, raw)
dst <- file.path(dir, fst_file_name(x))
+ callback <- tbl_callback(x)
assert_that(length(x) == 1L, length(src) == 1L, length(dst) == 1L)
@@ -364,6 +373,7 @@ csv_to_fst <- function(x, dir, progress = NULL, ...) {
report_problems(dat, raw)
+ dat <- callback(dat)
dat <- rename_cols(setDT(dat), ricu_cols(x), orig_cols(x))
fst::write_fst(dat, dst, compress = 100L)
@@ -421,25 +431,3 @@ report_problems <- function(x, file) {
invisible(NULL)
}
-
-report_problems <- function(x, file) {
-
- prob_to_str <- function(x) {
- paste0("[", x[1L], ", ", x[2L], "]: got '", x[4L], "' instead of ", x[3L])
- }
-
- probs <- readr::problems(x)
-
- if (nrow(probs)) {
-
- probs <- bullet(apply(probs, 1L, prob_to_str))
-
- warn_ricu(
- c("Encountered parsing problems for file {basename(file)}:", probs),
- class = "csv_parsing_error", indent = c(0L, rep_along(2L, probs)),
- exdent = c(0L, rep_along(2L, probs))
- )
- }
-
- invisible(NULL)
-}
diff --git a/R/utils-file.R b/R/utils-file.R
index 18c49cba..e83393a1 100644
--- a/R/utils-file.R
+++ b/R/utils-file.R
@@ -193,7 +193,7 @@ auto_attach_srcs <- function() {
res <- sys_env("RICU_SRC_LOAD", unset = NA_character_)
if (is.na(res)) {
- c("mimic", "mimic_demo", "eicu", "eicu_demo", "hirid", "aumc", "miiv", "sic")
+ c("mimic", "mimic_demo", "eicu", "eicu_demo", "hirid", "aumc", "miiv", "sic", "picdb")
} else {
strsplit(res, ",")[[1L]]
}
diff --git a/R/utils-misc.R b/R/utils-misc.R
index 0a708290..18481bb9 100644
--- a/R/utils-misc.R
+++ b/R/utils-misc.R
@@ -244,6 +244,8 @@ cat_line <- function(...) {
ms_as_mins <- function(x) min_as_mins(as.integer(x / 6e4))
+s_as_mins <- function(x) min_as_mins(as.integer(x / 60))
+
min_as_mins <- function(x) as.difftime(x, units = "mins")
digest_lst <- function(x) as.character(openssl::md5(serialize(x, NULL)))
diff --git a/environment.yaml b/environment.yaml
new file mode 100644
index 00000000..f8cb700d
--- /dev/null
+++ b/environment.yaml
@@ -0,0 +1,21 @@
+name: ricu
+channels:
+ - nodefaults
+ - conda-forge
+dependencies:
+ - r-base
+ - r-data.table
+ - r-curl
+ - r-assertthat
+ - r-fst
+ - r-readr
+ - r-jsonlite
+ - r-prt>=0.1.2
+ - r-tibble
+ - r-backports
+ - r-rlang
+ - r-vctrs
+ - r-cli>=2.1.0
+ - r-fansi
+ - r-openssl
+ - r-utils
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict.R b/inst/extdata/config/concept-dict.R
deleted file mode 100644
index 5a51be41..00000000
--- a/inst/extdata/config/concept-dict.R
+++ /dev/null
@@ -1,3275 +0,0 @@
-
-strip_ws <- function(x) gsub("\\s+", " ", x)
-
-cfg <- list(
- hr = list(
- unit = c("bpm", "/min"),
- min = 0,
- max = 300,
- description = "heart rate",
- omopid = 4239408L,
- category = "vitals",
- sources = list(
- mimic = list(
- list(ids = c(211L, 220045L), table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(table = "vitalperiodic", val_var = "heartrate",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = 200L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6640L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 220045L, table = "chartevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 708L, table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- sbp = list(
- unit = c("mmHg", "mm Hg"),
- min = 0,
- max = 300,
- description = "systolic blood pressure",
- omopid = 4152194L,
- category = "vitals",
- sources = list(
- mimic = list(
- list(ids = c(51L, 455L, 6701L, 220050L, 220179L),
- table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(table = "vitalperiodic", val_var = "systemicsystolic",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = 100L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6641L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = c(220050L, 220179L), table = "chartevents",
- sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(701L, 704L), table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- dbp = list(
- unit = c("mmHg", "mm Hg"),
- min = 0,
- max = 200,
- description = "diastolic blood pressure",
- omopid = 4154790L,
- category = "vitals",
- sources = list(
- mimic = list(
- list(ids = c(8368L, 8441L, 8555L, 220051L, 220180L),
- table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(table = "vitalperiodic", val_var = "systemicdiastolic",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = 120L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6643L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = c(220051L, 220180L), table = "chartevents",
- sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(702L, 705L), table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- map = list(
- unit = c("mmHg", "mm Hg"),
- min = 0,
- max = 250,
- description = "mean arterial pressure",
- omopid = 4239021L,
- category = "vitals",
- sources = list(
- mimic = list(
- list(ids = c(52L, 443L, 456L, 6072L, 220052L, 220181L, 225312L),
- table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(table = "vitalperiodic", val_var = "systemicmean",
- class = "col_itm"),
- list(table = "vitalaperiodic", val_var = "noninvasivemean",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = c(110L, 610L), table = "observations",
- sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6642L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = c(220052L, 220181L, 225312L), table = "chartevents",
- sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(703L, 706L), table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- resp = list(
- unit = c("insp/min", "/min"),
- min = 0,
- max = 120,
- description = "respiratory rate",
- omopid = 4313591L,
- category = "respiratory",
- sources = list(
- mimic = list(
- list(ids = c(618L, 619L, 220210L, 224688L, 224689L, 224690L),
- table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(table = "vitalperiodic", val_var = "respiration",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = c(300L, 310L), table = "observations",
- sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(8874L, 12266L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = c(220210L, 224688L, 224689L, 224690L),
- table = "chartevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 719L, table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- o2sat = list(
- unit = c("%", "% Sat."),
- min = 50,
- max = 100,
- description = "oxygen saturation",
- omopid = 40483579L,
- category = "respiratory",
- sources = list(
- mimic = list(
- list(ids = c(646L, 220277L, 226253L, 50817L), table = "chartevents",
- sub_var = "itemid")
- ),
- eicu = list(
- list(table = "vitalperiodic", val_var = "sao2", unit_val = "%",
- class = "col_itm"),
- list(ids = "O2 Sat (%)", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = c(4000L, 8280L, 20000800L), table = "observations",
- sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6709L, 8903L), table = "numericitems",
- sub_var = "itemid"),
- list(ids = 12311L, table = "numericitems", sub_var = "itemid",
- callback = "transform_fun(binary_op(`*`, 100))")
- ),
- miiv = list(
- list(ids = c(220277L, 226253L, 50817L), table = "chartevents",
- sub_var = "itemid")
- ),
- sic = list(
- list(ids = 710L, table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- fio2 = list(
- unit = "%",
- min = 21,
- max = 100,
- description = "fraction of inspired oxygen",
- omopid = 4353936L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = c(3420L, 223835L), table = "chartevents",
- sub_var = "itemid"),
- list(ids = 50816L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "FiO2", table = "respiratorycharting",
- sub_var = "respchartvaluelabel",
- callback = "transform_fun(percent_as_numeric)"),
- list(ids = "FiO2", table = "lab", sub_var = "labname",
- callback = "convert_unit(set_val(NA), '%', 'mm\\\\(hg\\\\)')")
- ),
- hirid = list(
- list(ids = 2010L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 12279L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 223835L, table = "chartevents", sub_var = "itemid"),
- list(ids = 50816L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 2283L, table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- tco2 = list(
- unit = "mEq/L",
- min = 5,
- max = 60,
- description = "totcal CO2",
- omopid = 4193415L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = 50804L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Total CO2", table = "lab", sub_var = "labname",
- callback = "convert_unit(set_val(NA), 'mEq/L', 'lpm')")
- ),
- miiv = list(
- list(ids = 50804L, table = "labevents", sub_var = "itemid")
- )
- )
- ),
- alt = list(
- unit = c("IU/L", "U/l"),
- min = 0,
- description = "alanine aminotransferase",
- omopid = 4146380L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50861L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "ALT (SGPT)", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20002600L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6800L, 11978L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50861L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 617L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- ast = list(
- unit = c("IU/L", "U/l"),
- min = 0,
- description = "aspartate aminotransferase",
- omopid = 4263457L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50878L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "AST (SGOT)", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000330L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6806L, 11990L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50878L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 616L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- phos = list(
- unit = "mg/dL",
- min = 0,
- max = 40,
- description = "phosphate",
- omopid = 4017907L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50970L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "phosphate", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20002500L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 3.097521), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6828L, 9935L), table = "numericitems",
- sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 3.097521), 'mg/dL')")
- ),
- miiv = list(
- list(ids = 50970L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 471L, table = "laboratory", sub_var = "LaboratoryID",
- callback = "transform_fun(binary_op(`*`, 3.097521))")
- )
- )
- ),
- bun = list(
- unit = "mg/dL",
- min = 0,
- max = 200,
- description = "blood urea nitrogen",
- omopid = 4017361L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 51006L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "BUN", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20004100L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 2.8), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6850L, 9943L), table = "numericitems",
- sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 2.8), 'mg/dL')")
- ),
- miiv = list(
- list(ids = 51006L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 355L, table = "laboratory", sub_var = "LaboratoryID",
- callback = "transform_fun(binary_op(`*`, 2.14))")
- )
- )
- ),
- ph = list(
- min = 6.8,
- max = 8,
- description = "pH of blood",
- omopid = 4097822L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = 50820L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "pH", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20000300L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6848L, 12310L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50820L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 688L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- bili = list(
- unit = "mg/dL",
- min = 0,
- max = 100,
- description = "total bilirubin",
- omopid = 4118986L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50885L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "total bilirubin", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20004300L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6813L, 9945L), table = "numericitems",
- sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')")
- ),
- miiv = list(
- list(ids = 50885L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 333L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- inr_pt = list(
- description = "prothrombin time/international normalized ratio",
- omopid = 4306239L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51237L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "PT - INR", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000567L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 11893L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51237L, table = "labevents", sub_var = "itemid")
- )
- )
- ),
- plt = list(
- unit = c("K/uL", "G/l"),
- min = 5,
- max = 1200,
- description = "platelet count",
- omopid = 4267147L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51265L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "platelets x 1000", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20000110L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6797L, 9964L, 10409L, 14252L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51265L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 314L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- lact = list(
- unit = "mmol/L",
- min = 0,
- max = 50,
- description = "lactate",
- omopid = 4191725L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = 50813L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "lactate", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000524L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6837L, 9580L, 10053L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50813L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(657L, 454L), table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- lymph = list(
- unit = "%",
- min = 0,
- max = 100,
- description = "lymphocytes",
- omopid = 4254663L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51244L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "-lymphs", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000480L, table = "observations", sub_var = "variableid",
- callback = "blood_cell_ratio", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 11846L, table = "numericitems", sub_var = "itemid"),
- list(ids = 14258L, table = "numericitems", sub_var = "itemid",
- callback = "blood_cell_ratio")
- ),
- miiv = list(
- list(ids = 51244L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 223L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- bicar = list(
- unit = c("mEq/L", "mmol/l"),
- min = 5,
- max = 50,
- description = "bicarbonate",
- omopid = 4194291L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50882L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "bicarbonate", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20004200L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6810L, 9992L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50882L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 456L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- crea = list(
- unit = "mg/dL",
- min = 0,
- max = 15,
- description = "creatinine",
- omopid = 4013964L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50912L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "creatinine", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20000600L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 0.011312), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6836L, 9941L, 14216L), table = "numericitems",
- sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 0.011309), 'mg/dL')")
- ),
- miiv = list(
- list(ids = 50912L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 367L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- pt = list(
- unit = "sec",
- min = 0,
- description = "prothrombine time",
- omopid = 4245261L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51274L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "PT", table = "lab", sub_var = "labname")
- ),
- aumc = list(
- list(ids = 6789L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51274L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 598L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- rdw = list(
- unit = "%",
- min = 0,
- max = 100,
- description = "erythrocyte distribution width",
- omopid = 4281085L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51277L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "RDW", table = "lab", sub_var = "labname")
- ),
- aumc = list(
- list(ids = 18952L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51277L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 3319L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- alp = list(
- unit = c("IU/L", "U/l"),
- min = 0,
- description = "alkaline phosphatase",
- omopid = 4275206L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50863L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "alkaline phos.", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20002700L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6803L, 11984L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50863L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 609L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- wbc = list(
- unit = c("K/uL", "G/l"),
- min = 0,
- description = "white blood cell count",
- omopid = 4298431L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51301L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "WBC x 1000", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20000700L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6779L, 9965L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51301L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 301L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- hgb = list(
- unit = "g/dL",
- min = 4,
- max = 18,
- description = "hemoglobin",
- omopid = 4118981L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51222L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Hgb", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = c(24000548L, 24000836L, 20000900L), table = "observations",
- sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL', 'g/l')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6778L, 9553L, 9960L, 10286L, 19703L),
- table = "numericitems", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 1.611344), 'g/dL')")
- ),
- miiv = list(
- list(ids = 51222L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(658L, 289L), table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- hct = list(
- unit = "%",
- min = 15,
- max = 60,
- description = "hematocrit",
- omopid = 4151358L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51221L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Hct", table = "lab", sub_var = "labname")
- ),
- aumc = list(
- list(ids = c(6777L, 11423L, 11545L), table = "numericitems",
- sub_var = "itemid",
- callback = "transform_fun(binary_op(`*`, 100))")
- ),
- miiv = list(
- list(ids = 51221L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(217L, 682L), table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- pco2 = list(
- unit = c("mmHg", "mm Hg"),
- min = 10,
- max = 150,
- description = "CO2 partial pressure",
- omopid = 4097882L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = 50818L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "paCO2", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20001200L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6846L, 9990L, 21213L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50818L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 687L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- po2 = list(
- unit = c("mmHg", "mm Hg"),
- min = 40,
- max = 600,
- description = "O2 partial pressure",
- omopid = 4094581L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = 50821L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "paO2", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20000200L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(7433L, 9996L, 21214L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50821L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(664L, 689L), table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- mch = list(
- unit = "pg",
- min = 0,
- description = "mean corpuscular hemoglobin",
- omopid = 4182871L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51248L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "MCH", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000160L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 11679L, table = "numericitems", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 0.016113), 'pg')")
- ),
- miiv = list(
- list(ids = 51248L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 566L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- mchc = list(
- unit = "%",
- min = 20,
- max = 50,
- description = "mean corpuscular hemoglobin concentration",
- omopid = 4290193L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51249L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "MCHC", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000170L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 0.16114), '%')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 18666L, table = "numericitems", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 1.611), '%')")
- ),
- miiv = list(
- list(ids = 51249L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 290L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- mcv = list(
- unit = "fL",
- min = 50,
- max = 150,
- description = "mean corpuscular volume",
- omopid = 4016239L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51250L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "MCV", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000150L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 9968L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51250L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 286L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- ptt = list(
- unit = "sec",
- min = 0,
- description = "partial thromboplastin time",
- omopid = 4175016L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51275L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "PTT", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20004410L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 17982L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51275L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 597L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- ca = list(
- unit = "mg/dL",
- min = 4,
- max = 20,
- description = "calcium",
- omopid = 4216722L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50893L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "calcium", table = "lab", sub_var = "labname",
- callback = "convert_unit(binary_op(`*`, 4), 'mg/dL', 'mmol/l')")
- ),
- hirid = list(
- list(ids = 20005100L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 4.008), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6817L, 9933L), table = "numericitems", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 4.008), 'mg/dL')")
- ),
- miiv = list(
- list(ids = 50893L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 457L, table = "laboratory", sub_var = "LaboratoryID",
- callback = "transform_fun(binary_op(`*`, 4.008))")
- )
- )
- ),
- cl = list(
- unit = c("mEq/L", "mmol/l"),
- min = 80,
- max = 130,
- description = "chloride",
- omopid = 4188066L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50902L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "chloride", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = c(24000439L, 24000521L), table = "observations",
- sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 9930L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50902L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(683L, 450L), table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- mg = list(
- unit = "mg/dL",
- min = 0.5,
- max = 5,
- description = "magnesium",
- omopid = 4243005L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50960L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "magnesium", table = "lab", sub_var = "labname",
- callback = "convert_unit(binary_op(`/`, 1.215), 'mg/dL', 'mEq/L')"
- )
- ),
- hirid = list(
- list(ids = 24000230L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 2.431), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6839L, 9952L), table = "numericitems", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 2.431), 'mg/dL')")
- ),
- miiv = list(
- list(ids = 50960L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 468L, table = "laboratory", sub_var = "LaboratoryID",
- callback = "transform_fun(binary_op(`*`, 2.431))")
- )
- )
- ),
- k = list(
- unit = c("mEq/L", "mmol/l"),
- min = 0,
- max = 10,
- description = "potassium",
- omopid = 4207483L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50971L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "potassium", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = c(20000500L, 24000520L, 24000833L, 24000867L),
- table = "observations", sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6835, 9556, 9927, 10285), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50971L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(463L, 685L), table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- na = list(
- unit = c("mEq/L", "mmol/l"),
- min = 110,
- max = 165,
- description = "sodium",
- omopid = 4208938L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50983L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "sodium", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = c(20000400L, 24000519L, 24000658L, 24000835L, 24000866L),
- table = "observations", sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6840, 9555, 9924, 10284), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50983L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(469L, 686L), table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- basos = list(
- unit = "%",
- min = 0,
- max = 50,
- description = "basophils",
- omopid = 4172647L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51146L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "-basos", table = "lab", sub_var = "labname")
- ),
- aumc = list(
- list(ids = 11710L, table = "numericitems", sub_var = "itemid"),
- list(ids = 14256L, table = "numericitems", sub_var = "itemid",
- callback = "blood_cell_ratio")
- ),
- miiv = list(
- list(ids = 51146L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 174L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- eos = list(
- unit = "%",
- min = 0,
- max = 50,
- description = "eosinophils",
- omopid = 4216098L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51200L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "-eos", table = "lab", sub_var = "labname")
- ),
- aumc = list(
- list(ids = 6773L, table = "numericitems", sub_var = "itemid"),
- list(ids = 9967L, table = "numericitems", sub_var = "itemid",
- callback = "blood_cell_ratio")
- ),
- miiv = list(
- list(ids = 51200L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 197L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- neut = list(
- unit = "%",
- min = 0,
- max = 100,
- description = "neutrophils",
- omopid = 4148615L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51256L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "-polys", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000550L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6786L, 11856L), table = "numericitems",
- sub_var = "itemid"),
- list(ids = 14254L, table = "numericitems", sub_var = "itemid",
- callback = "blood_cell_ratio")
- ),
- miiv = list(
- list(ids = 51256L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 230L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- glu = list(
- unit = "mg/dL",
- min = 0,
- max = 1000,
- description = "glucose",
- omopid = 4144235L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = c(50809L, 50931L), table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "glucose", table = "lab", sub_var = "labname"),
- list(ids = "bedside glucose", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = c(20005110L, 24000523L, 24000585L), table = "observations",
- sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 18.016), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6833L, 9557L, 9947L), table = "numericitems",
- sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 18.016), 'mg/dL')")
- ),
- miiv = list(
- list(ids = c(50809L, 50931L), table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = c(348L, 656L), table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- cai = list(
- unit = "mmol/L",
- min = 0.5,
- max = 2,
- description = "calcium ionized",
- omopid = 46272910L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = 50808L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "ionized calcium", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000522L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6815L, 8915L, 9560L, 9561L, 10267L),
- table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50808L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 655L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- crp = list(
- unit = "mg/L",
- min = 0,
- description = "C-reactive protein",
- omopid = 4208414L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50889L, table = "labevents", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
- ),
- eicu = list(
- list(ids = "CRP", table = "lab", sub_var = "labname",
- callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
- ),
- hirid = list(
- list(ids = 20002200L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6825L, 10079L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50889L, table = "labevents", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
- )
- )
- ),
- esr = list(
- unit = c("mm/hr", "mm/1h"),
- min = 0,
- max = 200,
- description = "erythrocyte sedimentation rate",
- omopid = 4212065L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51288L, table = "labevents", sub_var = "itemid")
- ),
- hirid = list(
- list(ids = 24000668L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6808L, 11902L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51288L, table = "labevents", sub_var = "itemid")
- )
- )
- ),
- hbco = list(
- description = "carboxyhemoglobin",
- omopid = 4056787L,
- category = "blood gas",
- sources = list(
- eicu = list(
- list(ids = "Carboxyhemoglobin", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000526L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 11690L, table = "numericitems", sub_var = "itemid")
- )
- )
- ),
- methb = list(
- unit = "%",
- min = 0,
- max = 100,
- description = "methemoglobin",
- omopid = 4204561L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = 50814L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Methemoglobin", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000549L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 11692L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50814L, table = "labevents", sub_var = "itemid")
- )
- )
- ),
- tnt = list(
- unit = "ng/mL",
- min = 0,
- description = "troponin t",
- omopid = 4005525L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 51003L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "troponin - T", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000806L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`/`, 1000), 'ng/mL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 10407L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51003L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 481L, table = "laboratory", sub_var = "LaboratoryID",
- callback = "transform_fun(binary_op(`/`, 1000))")
- )
- )
- ),
- alb = list(
- unit = "g/dL",
- min = 0,
- max = 6,
- description = "albumin",
- omopid = 4017497L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50862L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "albumin", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000605L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6801L, 9937L), table = "numericitems",
- sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL')")
- ),
- miiv = list(
- list(ids = 50862L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 287L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- fgn = list(
- unit = "mg/dL",
- min = 0,
- max = 1500,
- description = "fibrinogen",
- omopid = 4094436L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51214L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "fibrinogen", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000536L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 100), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6776L, 9989L, 10175L), table = "numericitems",
- sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 100), 'mg/dL')")
- ),
- miiv = list(
- list(ids = 51214L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 344L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- be = list(
- unit = c("mEq/L", "mmol/l"),
- min = -25,
- max = 25,
- description = "base excess",
- omopid = 4284393L,
- category = "blood gas",
- sources = list(
- mimic = list(
- list(ids = 50802L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Base Excess", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 20001300L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6807L, 9994L), table = "numericitems",
- sub_var = "itemid", dir_var = "tag", callback = "aumc_bxs")
- ),
- miiv = list(
- list(ids = 50802L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 668L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- rbc = list(
- unit = "m/uL",
- min = 0,
- max = 20,
- description = "red blood cell count",
- omopid = 4030871L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51279L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "RBC", table = "lab", sub_var = "labname")
- ),
- aumc = list(
- list(ids = c(6774L, 9962L), table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51279L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 599L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- ck = list(
- unit = c("IU/L", "U/l"),
- min = 0,
- description = "creatine kinase",
- omopid = 4265595L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50910L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "CPK", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000210L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6822L, 11998L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50910L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 611L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- ckmb = list(
- unit = "ng/mL",
- min = 0,
- description = "creatine kinase MB",
- omopid = 4017058L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50911L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "CPK-MB", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000220L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6824L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50911L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 253L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- egcs = list(
- min = 1,
- max = 4,
- description = "GCS eye",
- omopid = 4084277L,
- category = "neurological",
- sources = list(
- mimic = list(
- list(ids = c(184L, 220739L), table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Eyes", table = "nursecharting",
- sub_var = "nursingchartcelltypevalname")
- ),
- hirid = list(
- list(ids = 10000300L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6732L, table = "listitems", sub_var = "itemid",
- callback = strip_ws("apply_map(
- c(`Geen reactie` = 1,
- `Reactie op pijnprikkel` = 2,
- `Reactie op verbale prikkel` = 3,
- `Spontane reactie` = 4)
- )")),
- list(ids = 13077L, table = "listitems", sub_var = "itemid",
- callback = strip_ws("apply_map(
- c(`Niet` = 1,
- `Op pijn` = 2,
- `Op aanspreken` = 3,
- `Spontaan` = 4)
- )"))
- ),
- miiv = list(
- list(ids = 220739L, table = "chartevents", sub_var = "itemid")
- )
- )
- ),
- vgcs = list(
- min = 1,
- max = 5,
- description = "GCS verbal",
- omopid = 4084912L,
- category = "neurological",
- sources = list(
- mimic = list(
- list(ids = c(723L, 223900L), table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Verbal", table = "nursecharting",
- sub_var = "nursingchartcelltypevalname")
- ),
- hirid = list(
- list(ids = 10000100L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6735L, table = "listitems", sub_var = "itemid",
- callback = strip_ws("apply_map(
- c(`Geen reactie (geen zichtbare poging tot praten)` = 1,
- `Onbegrijpelijke geluiden` = 2,
- `Onduidelijke woorden (pogingen tot communicatie,
- maar onduidelijk)` = 3,
- `Verwarde conversatie` = 4,
- `Helder en adequaat (communicatie mogelijk)` = 5)
- )")),
- list(ids = 13066L, table = "listitems", sub_var = "itemid",
- callback = strip_ws("apply_map(
- c(`Geen geluid` = 1,
- `Onverstaanbare woorden` = 2,
- `Onjuiste woorden` = 3,
- `Verwarde taal` = 4,
- `Georiënteerd` = 5)
- )"))
- ),
- miiv = list(
- list(ids = 223900L, table = "chartevents", sub_var = "itemid")
- )
- )
- ),
- mgcs = list(
- min = 1,
- max = 6,
- description = "GCS motor",
- omopid = 4083352L,
- category = "neurological",
- sources = list(
- mimic = list(
- list(ids = c(454L, 223901L), table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Motor", table = "nursecharting",
- sub_var = "nursingchartcelltypevalname")
- ),
- hirid = list(
- list(ids = 10000200L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6734L, table = "listitems", sub_var = "itemid",
- callback = strip_ws("apply_map(
- c(`Geen reactie` = 1,
- `Strekken` = 2,
- `Decortatie reflex (abnormaal buigen)` = 3,
- `Spastische reactie (terugtrekken)` = 4,
- `Localiseert pijn` = 5,
- `Volgt verbale commando's op` = 6)
- )")),
- list(ids = 13072L, table = "listitems", sub_var = "itemid",
- callback = strip_ws("apply_map(
- c(`Geen reactie` = 1,
- `Strekken op pijn` = 2,
- `Abnormaal buigen bij pijn` = 3,
- `Terugtrekken bij pijn` = 4,
- `Localiseren pijn` = 5,
- `Voert opdrachten uit` = 6)
- )"))
- ),
- miiv = list(
- list(ids = 223901L, table = "chartevents", sub_var = "itemid")
- )
- )
- ),
- tgcs = list(
- min = 3,
- max = 15,
- description = "GCS total",
- omopid = 4093836L,
- category = "neurological",
- sources = list(
- mimic = list(
- list(ids = 198L, table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "GCS Total", table = "nursecharting",
- sub_var = "nursingchartcelltypevalname")
- )
- )
- ),
- urine = list(
- unit = "mL",
- min = 0,
- max = 2000,
- aggregate = "sum",
- description = "urine output",
- omopid = 4264378L,
- category = "output",
- sources = list(
- mimic = list(
- list(ids = c(40055L, 40056L, 40057L, 40065L, 40069L, 40085L,
- 40086L, 40094L, 40096L, 40405L, 40428L, 40473L,
- 40715L, 43175L, 226557L, 226558L, 226559L, 226560L,
- 226561L, 226563L, 226564L, 226565L, 226566L, 226567L,
- 226584L, 227510L),
- table = "outputevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = c("Urine", "URINE CATHETER"), table = "intakeoutput",
- sub_var = "celllabel"),
- list(regex = c("catheter.+output|output.+catheter"),
- table = "intakeoutput", sub_var = "celllabel", class = "rgx_itm")
- ),
- hirid = list(
- list(ids = 30005110L, table = "observations", sub_var = "variableid",
- callback = "hirid_urine", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 8794L, table = "numericitems", sub_var = "itemid")
- ),
- miiv = list(
- list(ids = c(226557L, 226558L, 226559L, 226560L, 226561L, 226563L,
- 226564L, 226565L, 226566L, 226567L, 226584L, 227510L),
- table = "outputevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 725L, table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- dobu_rate = list(
- unit = c("mcg/kg/min", "mcgkgmin"),
- min = 0,
- max = 50,
- description = "dobutamine rate",
- omopid = 1337720L,
- category = "medications",
- sources = list(
- mimic = list(
- list(ids = c(30042L, 30306L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid",
- callback = "mimic_rate_cv"),
- list(ids = 221653L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- eicu = list(
- list(regex = "^dobu.*\\(.+\\)$", table = "infusiondrug",
- sub_var = "drugname", weight_var = "patientweight",
- callback = "eicu_rate_kg(ml_to_mcg = 2000)", class = "rgx_itm")
- ),
- hirid = list(
- list(ids = 426L, table = "pharma", sub_var = "pharmaid",
- grp_var = "infusionid", callback = "hirid_rate_kg")
- ),
- aumc = list(
- list(ids = 7178L, table = "drugitems", sub_var = "itemid",
- rel_weight = "doserateperkg", rate_uom = "doserateunit",
- stop_var = "stop", callback = "aumc_rate_kg")
- ),
- miiv = list(
- list(ids = 221653L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- sic = list(
- list(ids = 1559L, table = "medication", sub_var = "DrugID",
- val_var = "AmountPerMinute", stop_var = "OffsetDrugEnd",
- callback = "sic_rate_kg")
- )
- )
- ),
- dobu_dur = list(
- description = "dobutamine duration",
- category = "medications",
- aggregate = "max",
- sources = list(
- mimic = list(
- list(ids = c(30042L, 30306L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid",
- callback = "mimic_dur_incv"),
- list(ids = 221653L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", grp_var = "linkorderid",
- callback = "mimic_dur_inmv")
- ),
- eicu = list(
- list(regex = "^dobu", table = "infusiondrug", sub_var = "drugname",
- callback = "eicu_duration(gap_length = hours(5L))",
- class = "rgx_itm")
- ),
- hirid = list(
- list(ids = 426L, table = "pharma", sub_var = "pharmaid",
- grp_var = "infusionid", callback = "hirid_duration")
- ),
- aumc = list(
- list(ids = 7178L, table = "drugitems", sub_var = "itemid",
- stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
- ),
- miiv = list(
- list(ids = 221653L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", grp_var = "linkorderid",
- callback = "mimic_dur_inmv")
- ),
- sic = list(
- list(ids = list(1559L), table = "medication",
- sub_var = "DrugID", stop_var = "OffsetDrugEnd",
- callback = "sic_dur")
- )
- )
- ),
- dobu60 = list(
- concepts = c("dobu_rate", "dobu_dur"),
- description = "dobutamine administration for min 1h",
- category = "medications",
- interval = "00:01:00",
- callback = "vaso60",
- class = "rec_cncpt"
- ),
- dopa_rate = list(
- unit = c("mcg/kg/min", "mcgkgmin"),
- min = 0,
- max = 50,
- description = "dopamine rate",
- omopid = 1337860L,
- category = "medications",
- sources = list(
- mimic = list(
- list(ids = c(30043L, 30125L, 30307L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid",
- callback = "mimic_rate_cv"),
- list(ids = 221662L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- eicu = list(
- list(regex = "^dopa.*\\(.+\\)$", table = "infusiondrug",
- sub_var = "drugname", weight_var = "patientweight",
- callback = "eicu_rate_kg(ml_to_mcg = 1600)", class = "rgx_itm")
- ),
- aumc = list(
- list(ids = 7179L, table = "drugitems", sub_var = "itemid",
- rel_weight = "doserateperkg", rate_uom = "doserateunit",
- stop_var = "stop", callback = "aumc_rate_kg")
- ),
- miiv = list(
- list(ids = 221662L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- sic = list(
- list(ids = 1618L, table = "medication", sub_var = "DrugID",
- val_var = "AmountPerMinute", stop_var = "OffsetDrugEnd",
- callback = "sic_rate_kg")
- )
- )
- ),
- dopa_dur = list(
- description = "dopamine duration",
- category = "medications",
- aggregate = "max",
- sources = list(
- mimic = list(
- list(ids = c(30043L, 30125L, 30307L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid",
- callback = "mimic_dur_incv"),
- list(ids = 221662L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", grp_var = "linkorderid",
- callback = "mimic_dur_inmv")
- ),
- eicu = list(
- list(regex = "^dopa", table = "infusiondrug", sub_var = "drugname",
- callback = "eicu_duration(gap_length = hours(5L))",
- class = "rgx_itm")
- ),
- aumc = list(
- list(ids = 7179L, table = "drugitems", sub_var = "itemid",
- stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
- ),
- miiv = list(
- list(ids = 221662L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", grp_var = "linkorderid",
- callback = "mimic_dur_inmv")
- ),
- sic = list(
- list(ids = 1618L, table = "medication",
- sub_var = "DrugID", stop_var = "OffsetDrugEnd",
- callback = "sic_dur")
- )
- )
- ),
- dopa60 = list(
- concepts = c("dopa_rate", "dopa_dur"),
- description = "dopamine administration for min 1h",
- category = "outcome",
- interval = "00:01:00",
- callback = "vaso60",
- class = "rec_cncpt"
- ),
- norepi_rate = list(
- unit = c("mcg/kg/min", "mcgkgmin"),
- min = 0,
- max = 3,
- description = "norepinephrine rate",
- omopid = 1321341,
- category = "medications",
- sources = list(
- mimic = list(
- list(ids = c(30047L, 30120L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid",
- callback = "mimic_rate_cv"),
- list(ids = 221906L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- eicu = list(
- list(regex = "^norepi.*\\(.+\\)$", table = "infusiondrug",
- sub_var = "drugname", weight_var = "patientweight",
- callback = "eicu_rate_kg(ml_to_mcg = 32)", class = "rgx_itm")
- ),
- hirid = list(
- list(ids = c(1000462L, 1000656L, 1000657L, 1000658L), table = "pharma",
- sub_var = "pharmaid", grp_var = "infusionid",
- callback = "hirid_rate_kg")
- ),
- aumc = list(
- list(ids = 7229L, table = "drugitems", sub_var = "itemid",
- rel_weight = "doserateperkg", rate_uom = "doserateunit",
- stop_var = "stop", callback = "aumc_rate_kg")
- ),
- miiv = list(
- list(ids = 221906L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- sic = list(
- list(ids = 1562L, table = "medication", sub_var = "DrugID",
- val_var = "AmountPerMinute", stop_var = "OffsetDrugEnd",
- callback = "sic_rate_kg")
- )
- )
- ),
- norepi_dur = list(
- description = "norepinephrine duration",
- category = "medications",
- aggregate = "max",
- sources = list(
- mimic = list(
- list(ids = c(30047L, 30120L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid",
- callback = "mimic_dur_incv"),
- list(ids = 221906L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", grp_var = "linkorderid",
- callback = "mimic_dur_inmv")
- ),
- eicu = list(
- list(regex = "^norepi", table = "infusiondrug", sub_var = "drugname",
- callback = "eicu_duration(gap_length = hours(5L))",
- class = "rgx_itm")
- ),
- hirid = list(
- list(ids = c(1000462L, 1000656L, 1000657L, 1000658L), table = "pharma",
- sub_var = "pharmaid", grp_var = "infusionid",
- callback = "hirid_duration")
- ),
- aumc = list(
- list(ids = 7229L, table = "drugitems", sub_var = "itemid",
- stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
- ),
- miiv = list(
- list(ids = 221906L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", grp_var = "linkorderid",
- callback = "mimic_dur_inmv")
- ),
- sic = list(
- list(ids = list(1562L), table = "medication",
- sub_var = "DrugID", stop_var = "OffsetDrugEnd",
- callback = "sic_dur")
- )
- )
- ),
- norepi60 = list(
- concepts = c("norepi_rate", "norepi_dur"),
- description = "norepinephrine administration for min 1h",
- category = "outcome",
- interval = "00:01:00",
- callback = "vaso60",
- class = "rec_cncpt"
- ),
- epi_rate = list(
- unit = c("mcg/kg/min", "mcgkgmin"),
- min = 0,
- max = 1.5,
- description = "epinephrine rate",
- omopid = 1343916L,
- category = "medications",
- sources = list(
- mimic = list(
- list(ids = c(30044L, 30119L, 30309L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid",
- callback = "mimic_rate_cv"),
- list(ids = 221289L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- eicu = list(
- list(regex = "^epi( |n).*\\(.+\\)$", table = "infusiondrug",
- sub_var = "drugname", weight_var = "patientweight",
- callback = "eicu_rate_kg(ml_to_mcg = 40)", class = "rgx_itm")
- ),
- hirid = list(
- list(ids = c(71L, 1000649L, 1000650L, 1000655L, 1000750L),
- table = "pharma", sub_var = "pharmaid",
- grp_var = "infusionid", callback = "hirid_rate_kg")
- ),
- aumc = list(
- list(ids = 6818L, table = "drugitems", sub_var = "itemid",
- rel_weight = "doserateperkg", rate_uom = "doserateunit",
- stop_var = "stop", callback = "aumc_rate_kg")
- ),
- miiv = list(
- list(ids = 221289L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- sic = list(
- list(ids = 1502L, table = "medication", sub_var = "DrugID",
- val_var = "AmountPerMinute", stop_var = "OffsetDrugEnd",
- callback = "sic_rate_kg")
- )
- )
- ),
- epi_dur = list(
- description = "epinephrine duration",
- category = "medications",
- aggregate = "max",
- sources = list(
- mimic = list(
- list(ids = c(30044L, 30119L, 30309L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid",
- callback = "mimic_dur_incv"),
- list(ids = 221289L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", grp_var = "linkorderid",
- callback = "mimic_dur_inmv")
- ),
- eicu = list(
- list(regex = "^epi( |n)", table = "infusiondrug", sub_var = "drugname",
- callback = "eicu_duration(gap_length = hours(5L))",
- class = "rgx_itm")
- ),
- hirid = list(
- list(ids = c(71L, 1000649L, 1000650L, 1000655L, 1000750L),
- table = "pharma", sub_var = "pharmaid", grp_var = "infusionid",
- callback = "hirid_duration")
- ),
- aumc = list(
- list(ids = 6818L, table = "drugitems", sub_var = "itemid",
- stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
- ),
- miiv = list(
- list(ids = 221289L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", grp_var = "linkorderid",
- callback = "mimic_dur_inmv")
- ),
- sic = list(
- list(ids = list(1502L), table = "medication",
- sub_var = "DrugID", stop_var = "OffsetDrugEnd",
- callback = "sic_dur")
- )
- )
- ),
- epi60 = list(
- concepts = c("epi_rate", "epi_dur"),
- description = "epinephrine administration for min 1h",
- category = "outcome",
- interval = "00:01:00",
- callback = "vaso60",
- class = "rec_cncpt"
- ),
- vent_start = list(
- class = "lgl_cncpt",
- description = "ventilation start",
- category = "respiratory",
- sources = list(
- mimic = list(
- list(
- ids = c(
- 1L, 60L, 218L, 221L, 223L, 436L, 437L,
- 444L, 445L, 448L, 449L, 450L, 459L, 501L,
- 502L, 503L, 505L, 506L, 535L, 543L, 639L,
- 654L, 667L, 668L, 669L, 670L, 671L, 672L,
- 681L, 682L, 683L, 684L, 686L, 1211L, 1340L,
- 1486L, 1600L, 1655L, 2000L, 3459L, 5865L, 5866L,
- 220339L, 223848L, 223849L, 224419L, 224684L, 224685L, 224686L,
- 224687L, 224695L, 224696L, 224697L, 224700L, 224701L, 224702L,
- 224703L, 224704L, 224705L, 224706L, 224707L, 224709L, 224738L,
- 224746L, 224747L, 224750L, 226873L, 227187L),
- table = "chartevents", sub_var = "itemid",
- callback = "transform_fun(set_val(TRUE))"
- )
- ),
- eicu = list(
- list(table = "respiratorycare", val_var = "ventstartoffset",
- callback = "vent_flag", class = "col_itm"),
- list(table = "respiratorycare", val_var = "priorventstartoffset",
- callback = "vent_flag", class = "col_itm"),
- list(ids = c("Start", "Continued", "respFlowPtVentData"),
- table = "respiratorycharting", sub_var = "respcharttypecat",
- callback = "transform_fun(set_val(TRUE))")
- )
- )
- ),
- vent_end = list(
- class = "lgl_cncpt",
- description = "ventilation end",
- category = "respiratory",
- sources = list(
- mimic = list(
- list(ids = c(225468L, 225477L, 227194L), table = "procedureevents_mv",
- sub_var = "itemid", callback = "transform_fun(set_val(TRUE))"),
- list(ids = c(467L, 469L, 226732L), table = "chartevents",
- sub_var = "itemid", callback = "transform_fun(set_val(TRUE))")
- ),
- eicu = list(
- list(table = "respiratorycare", val_var = "ventendoffset",
- callback = "vent_flag", class = "col_itm"),
- list(table = "respiratorycare", val_var = "priorventendoffset",
- callback = "vent_flag", class = "col_itm"),
- list(ids = c("off", "Off", "Suspended"), table = "respiratorycharting",
- sub_var = "respchartvalue", val_var = "respchartvaluelabel",
- callback = "transform_fun(set_val(TRUE))")
- )
- )
- ),
- mech_vent = list(
- class = "fct_cncpt",
- target = "win_tbl",
- levels = c("invasive", "noninvasive"),
- description = "mechanical ventilation windows",
- omopid = 4230167L,
- category = "respiratory",
- sources = list(
- aumc = list(
- list(ids = c(9328L, 10740L, 12635L), table = "processitems",
- sub_var = "itemid", dur_var = "stop",
- callback = "apply_map(c(`Beademen` = 'invasive',
- `Beademen non-invasief` = 'noninvasive',
- `Tracheostoma` = 'invasive'))"
- )
- ),
- miiv = list(
- list(ids = c(225792L, 225794L), table = "procedureevents",
- sub_var = "itemid", dur_var = "endtime",
- callback = "apply_map(c(`225792` = 'invasive',
- `225794` = 'noninvasive'),
- var = 'sub_var')")
- ),
- hirid = list(
- list(ids = 15001552L, table = "observations", sub_var = "variableid",
- target = "ts_tbl", interval = "00:01:00", class = "hrd_itm",
- callback = "combine_callbacks(hirid_vent,
- apply_map(c(`1` = 'invasive',
- `2` = 'invasive',
- `3` = 'noninvasive',
- `4` = 'noninvasive',
- `5` = 'noninvasive',
- `6` = 'noninvasive')))")
- )
- )
- ),
- ett_gcs = list(
- class = "lgl_cncpt",
- description = "tracheostomy",
- omopid = 4097216L,
- category = "respiratory",
- target = "win_tbl",
- sources = list(
- mimic = list(
- list(ids = c("1.0 ET/Trach", "No Response-ETT"), table = "chartevents",
- sub_var = "value", target = "ts_tbl",
- callback = "combine_callbacks(
- transform_fun(set_val(TRUE)),
- ts_to_win_tbl(mins(1L))
- )")
- ),
- hirid = list(
- list(class = "fun_itm", callback = "combine_callbacks(
- fwd_concept('mech_vent'),
- transform_fun(comp_na(`==`, 'invasive'))
- )")
- ),
- aumc = list(
- list(ids = 6735L, table = "listitems", sub_var = "itemid",
- target = "ts_tbl", callback = "combine_callbacks(
- transform_fun(comp_na(`==`, 'Geïntubeerd')),
- ts_to_win_tbl(mins(1L))
- )")
- ),
- miiv = list(
- list(ids = "No Response-ETT", table = "chartevents", sub_var = "value",
- target = "ts_tbl", callback = "combine_callbacks(
- transform_fun(set_val(TRUE)),
- ts_to_win_tbl(mins(1L))
- )")
- ),
- eicu = list(
- list(class = "fun_itm", callback = "combine_callbacks(
- fwd_concept('rass'),
- transform_fun(comp_na(`<=`, -3)),
- ts_to_win_tbl(mins(360L))
- )")
- )
- )
- ),
- rass = list(
- min = -5,
- max = 4,
- description = "Richmond agitation sedation scale",
- omopid = 36684829L,
- category = "neurological",
- sources = list(
- mimic = list(
- list(ids = 228096L, table = "chartevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "Sedation Score", table = "nursecharting",
- sub_var = "nursingchartcelltypevalname")
- ),
- hirid = list(
- list(ids = 15001565L, table = "observations", sub_var = "variableid",
- callback = "transform_fun(floor)", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 14444L, sub_var = "itemid", table = "listitems",
- callback = "transform_fun(aumc_rass)")
- ),
- miiv = list(
- list(ids = 228096L, table = "chartevents", sub_var = "itemid")
- )
- )
- ),
- abx = list(
- class = "lgl_cncpt",
- description = "antibiotics",
- omopid = 4085730L,
- category = "medications",
- sources = list(
- mimic = list(
- list(regex = paste(
- "aztreonam", "bactrim", "cephalexin", "chloramphenicol", "cipro",
- "flagyl", "metronidazole", "nitrofurantoin", "tazobactam",
- "rifampin", "sulfadiazine", "timentin", "trimethoprim", "(amika",
- "gentami", "vanco)cin", "(amoxi", "ampi", "dicloxa", "naf", "oxa",
- "peni", "pipera)cillin", "(azithro", "clarithro", "erythro",
- "clinda", "strepto", "tobra", "vanco)mycin", "cef(azolin",
- "tazidime", "adroxil", "epime", "otetan", "otaxime", "podoxime",
- "uroxime)", "(doxy", "mino", "tetra)cycline", "(levofl", "moxifl",
- "ofl)oxacin", "macro(bid", "dantin)", "(una", "zo)syn", sep = "|"),
- table = "prescriptions", sub_var = "drug", interval = "00:01:00",
- callback = "mimic_abx_presc", class = "rgx_itm"
- ),
- list(ids = c(
- 225798L, 225837L, 225838L, 225840L, 225842L, 225843L, 225844L,
- 225845L, 225847L, 225848L, 225850L, 225851L, 225853L, 225855L,
- 225857L, 225859L, 225860L, 225862L, 225863L, 225865L, 225866L,
- 225868L, 225869L, 225871L, 225873L, 225875L, 225876L, 225877L,
- 225879L, 225881L, 225882L, 225883L, 225884L, 225885L, 225886L,
- 225888L, 225889L, 225890L, 225892L, 225893L, 225895L, 225896L,
- 225897L, 225898L, 225899L, 225900L, 225902L, 225903L, 225905L,
- 227691L, 228003L), table = "inputevents_mv", sub_var = "itemid",
- callback = "transform_fun(set_val(TRUE))"
- )
- ),
- eicu = list(
- list(regex = paste(
- "bactrim", "cipro", "flagyl", "metronidazole", "zithromax", "zosyn",
- "(((amika", "cleo", "ofloxa)", "(azithro", "clinda", "tobra",
- "vanco)my)c", "(ampi", "oxa", "peni", "pipera)cill", "cefazol",
- "levaqu", "rifamp)in", sep = "|"), table = "infusiondrug",
- sub_var = "drugname", callback = "transform_fun(set_val(TRUE))",
- class = "rgx_itm"
- ),
- list(regex = paste(
- "cipro", "flagyl", "maxipime", "metronidazole", "tazobactam",
- "zosyn", "cef(azolin", "epime)", "(((azithro", "clinda", "vanco)my",
- "ofloxa", "vanco)c", "levaqu", "piperacill", "roceph)in", sep = "|"),
- table = "medication", sub_var = "drugname",
- callback = "transform_fun(set_val(TRUE))", class = "rgx_itm"
- )
- ),
- hirid = list(
- list(ids = c(
- 163L, 176L, 181L, 186L, 189L, 300L, 326L,
- 331L, 351L, 405L, 1000234L, 1000272L, 1000273L, 1000274L,
- 1000284L, 1000299L, 1000300L, 1000302L, 1000304L, 1000305L, 1000306L,
- 1000315L, 1000317L, 1000318L, 1000320L, 1000321L, 1000322L, 1000335L,
- 1000348L, 1000352L, 1000363L, 1000365L, 1000390L, 1000407L, 1000408L,
- 1000424L, 1000425L, 1000426L, 1000437L, 1000483L, 1000507L, 1000508L,
- 1000518L, 1000519L, 1000549L, 1000601L, 1000648L, 1000666L, 1000670L,
- 1000671L, 1000760L, 1000781L, 1000791L, 1000797L, 1000812L, 1000825L,
- 1000829L, 1000830L, 1000837L, 1000838L, 1000854L, 1000855L, 1000893L,
- 1000894L, 1001005L, 1001068L, 1001075L, 1001079L, 1001084L, 1001086L,
- 1001095L, 1001096L, 1001097L, 1001098L, 1001168L, 1001169L, 1001170L,
- 1001171L, 1001173L, 1001193L, 1001198L), table = "pharma",
- sub_var = "pharmaid", callback = "transform_fun(set_val(TRUE))")
- ),
- aumc = list(
- list(ids = c(
- 2L, 13L, 19L, 24L, 28L, 29L, 57L, 59L,
- 82L, 103L, 240L, 247L, 333L, 1133L, 1199L, 1300L,
- 1371L, 1795L, 2284L, 2834L, 3237L, 3741L, 5576L, 6834L,
- 6847L, 6871L, 6919L, 6948L, 6953L, 6958L, 7044L, 7064L,
- 7185L, 7187L, 7208L, 7227L, 7235L, 8064L, 8394L, 8942L,
- 9029L, 9030L, 9052L, 9070L, 9117L, 9128L, 9133L, 9142L,
- 9151L, 9152L, 12262L, 12389L, 12398L, 12956L, 12997L, 13057L,
- 13094L, 13102L, 15591L, 18860L, 19137L, 19773L, 20563L, 23166L,
- 24241L, 25776L, 27617L, 29321L), table = "drugitems",
- sub_var = "itemid", callback = "transform_fun(set_val(TRUE))")
- ),
- miiv = list(
- list(regex = paste(
- "aztreonam", "bactrim", "cephalexin", "chloramphenicol", "cipro",
- "flagyl", "metronidazole", "nitrofurantoin", "tazobactam",
- "rifampin", "sulfadiazine", "timentin", "trimethoprim", "(amika",
- "gentami", "vanco)cin", "(amoxi", "ampi", "dicloxa", "naf", "oxa",
- "peni", "pipera)cillin", "(azithro", "clarithro", "erythro",
- "clinda", "strepto", "tobra", "vanco)mycin", "cef(azolin",
- "tazidime", "adroxil", "epime", "otetan", "otaxime", "podoxime",
- "uroxime)", "(doxy", "mino", "tetra)cycline", "(levofl", "moxifl",
- "ofl)oxacin", "macro(bid", "dantin)", "(una", "zo)syn", sep = "|"),
- table = "prescriptions", sub_var = "drug",
- callback = "transform_fun(set_val(TRUE))", class = "rgx_itm"
- ),
- list(ids = c(
- 225798L, 225837L, 225838L, 225840L, 225842L, 225843L, 225844L,
- 225845L, 225847L, 225848L, 225850L, 225851L, 225853L, 225855L,
- 225857L, 225859L, 225860L, 225862L, 225863L, 225865L, 225866L,
- 225868L, 225869L, 225871L, 225873L, 225875L, 225876L, 225877L,
- 225879L, 225881L, 225882L, 225883L, 225884L, 225885L, 225886L,
- 225888L, 225889L, 225890L, 225892L, 225893L, 225895L, 225896L,
- 225897L, 225898L, 225899L, 225900L, 225902L, 225903L, 225905L,
- 227691L, 228003L), table = "inputevents", sub_var = "itemid",
- callback = "transform_fun(set_val(TRUE))"
- )
- ),
- sic = list(
- list(ids = c(
- 1406L, 1408L, 1410L, 1418L, 1421L, 1422L,
- 1423L, 1428L, 1431L, 1433L, 1436L, 1449L, 1454L,
- 1457L, 1458L, 1459L, 1460L, 1461L, 1603L, 1795L,
- 1913L, 1927L), table = "medication", sub_var = "DrugID",
- callback = "transform_fun(set_val(TRUE))"
- )
- )
- )
- ),
- samp = list(
- class = "lgl_cncpt",
- category = "microbiology",
- description = "body fluid sampling",
- omopid = 4133843L,
- sources = list(
- mimic = list(
- list(table = "microbiologyevents", val_var = "org_itemid",
- callback = "mimic_sampling", aux_time = "charttime",
- class = "col_itm")
- ),
- eicu = list(
- list(table = "microlab", val_var = "organism",
- callback = "transform_fun(comp_na(`!=`, 'no growth'))",
- class = "col_itm")
- ),
- aumc = list(
- list(ids = c(
- 8097L, 8418L, 8588L, 9189L, 9190L, 9191L, 9192L, 9193L, 9194L,
- 9195L, 9197L, 9198L, 9200L, 9202L, 9203L, 9204L, 9205L, 13024L,
- 19663L, 19664L), table = "procedureorderitems", sub_var = "itemid",
- callback = "transform_fun(set_val(TRUE))")
- ),
- miiv = list(
- list(table = "microbiologyevents", val_var = "org_itemid",
- callback = "mimic_sampling", aux_time = "charttime",
- class = "col_itm")
- )
- )
- ),
- tri = list(
- unit = "ng/mL",
- min = 0,
- description = "troponin I",
- omopid = 4007805L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 51002L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "troponin - I", table = "lab", sub_var = "labname")
- ),
- miiv = list(
- list(ids = 51002L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 270L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- bili_dir = list(
- unit = "mg/dL",
- min = 0,
- max = 50,
- description = "bilirubin direct",
- omopid = 4216632L,
- category = "chemistry",
- sources = list(
- mimic = list(
- list(ids = 50883L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "direct bilirubin", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000560L, table = "observations", sub_var = "variableid",
- callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = 6812L, table = "numericitems", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')")
- ),
- miiv = list(
- list(ids = 50883L, table = "labevents", sub_var = "itemid")
- ),
- sic = list(
- list(ids = 332L, table = "laboratory", sub_var = "LaboratoryID")
- )
- )
- ),
- temp = list(
- unit = c("C", "°C"),
- min = 32,
- max = 42,
- description = "temperature",
- omopid = 4302666L,
- category = "vitals",
- sources = list(
- mimic = list(
- list(ids = c(676L, 677L, 223762L), table = "chartevents",
- sub_var = "itemid"),
- list(ids = c(678L, 679L, 223761L, 224027L), table = "chartevents",
- sub_var = "itemid",
- callback = "convert_unit(fahr_to_cels, 'C', 'f')")
- ),
- eicu = list(
- list(table = "vitalperiodic", val_var = "temperature",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = c(410L, 400L, 7100L), table = "observations",
- sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(8658L, 13952L, 16110L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 223762L, table = "chartevents", sub_var = "itemid"),
- list(ids = c(223761L, 224027L), table = "chartevents",
- sub_var = "itemid",
- callback = "convert_unit(fahr_to_cels, 'C', 'f')")
- ),
- sic = list(
- list(ids = 709L, table = "data_float_h", sub_var = "DataID")
- )
- )
- ),
- etco2 = list(
- unit = c("mmHg", "mm Hg"),
- min = 10,
- max = 60,
- description = "endtidal CO2",
- omopid = 4353940L,
- category = "vitals",
- sources = list(
- mimic = list(
- list(ids = c(1817L, 228640L), table = "chartevents",
- sub_var = "itemid")
- ),
- hirid = list(
- list(ids = c(2200L, 8290L, 30010009L), table = "observations",
- sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(
- ids = c(6707L, 8884L, 8885L, 9658L, 12805L, 12356L),
- table = "numericitems", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 7.6), 'mmHg', 'None|Geen')"
- )
- ),
- miiv = list(
- list(ids = 228640L, table = "chartevents", sub_var = "itemid")
- )
- )
- ),
- ins = list(
- unit = "units/hr",
- min = 0,
- description = "insulin",
- omopid = 42537007L,
- category = "medications",
- sources = list(
- mimic = list(
- list(ids = c(30045L, 30100L), table = "inputevents_cv",
- sub_var = "itemid"),
- list(ids = c(223258L, 223260L), table = "inputevents_mv",
- sub_var = "itemid", val_var = "amount", end_var = "endtime",
- callback = "distribute_amount")
- ),
- eicu = list(
- list(regex = "^insulin (250.+)?\\(((ml|units)/hr)?\\)$",
- table = "infusiondrug", sub_var = "drugname", class = "rgx_itm")
- ),
- hirid = list(
- list(ids = c(15L, 1000724L), table = "pharma", sub_var = "pharmaid",
- callback = "aggregate_fun('sum', 'units')")
- ),
- aumc = list(
- list(ids = c(7624L, 9014L, 19129L), sub_var = "itemid",
- table = "drugitems")
- ),
- miiv = list(
- list(ids = c(223258L, 223260L), table = "inputevents",
- sub_var = "itemid", val_var = "amount", end_var = "endtime",
- callback = "distribute_amount")
- )
- )
- ),
- sex = list(
- target = "id_tbl",
- levels = c("Female", "Male"),
- class = "fct_cncpt",
- description = "patient sex",
- omopid = 37116947L,
- category = "demographics",
- sources = list(
- mimic = list(
- list(table = "patients", val_var = "gender",
- callback = "apply_map(c(M = 'Male', F = 'Female'))",
- class = "col_itm")
- ),
- eicu = list(
- list(table = "patient", val_var = "gender", class = "col_itm")
- ),
- hirid = list(
- list(table = "general", val_var = "sex",
- callback = "apply_map(c(M = 'Male', F = 'Female'))",
- class = "col_itm")
- ),
- aumc = list(
- list(val_var = "gender", table = "admissions",
- callback = strip_ws("apply_map(c(Vrouw = 'Female',
- Man = 'Male'))"),
- class = "col_itm")
- ),
- miiv = list(
- list(table = "patients", val_var = "gender",
- callback = "apply_map(c(M = 'Male', F = 'Female'))",
- class = "col_itm")
- ),
- sic = list(
- list(table = "cases", val_var = "Sex",
- callback = "apply_map(c(`735` = 'Male', `736` = 'Female'))",
- class = "col_itm")
- )
- )
- ),
- age = list(
- unit = "years",
- min = 0,
- max = 100,
- target = "id_tbl",
- description = "patient age",
- omopid = 4314456L,
- category = "demographics",
- sources = list(
- mimic = list(
- list(table = "patients", val_var = "dob",
- callback = "transform_fun(mimic_age)", class = "col_itm")
- ),
- eicu = list(
- list(table = "patient", val_var = "age",
- callback = "transform_fun(eicu_age)", class = "col_itm")
- ),
- hirid = list(
- list(table = "general", val_var = "age", class = "col_itm")
- ),
- aumc = list(
- list(val_var = "agegroup", table = "admissions",
- callback = strip_ws("apply_map(c(`18-39` = 30,
- `40-49` = 45,
- `50-59` = 55,
- `60-69` = 65,
- `70-79` = 75,
- `80+` = 90))"),
- class = "col_itm")
- ),
- miiv = list(
- list(table = "patients", val_var = "anchor_age", class = "col_itm")
- ),
- sic = list(
- list(table = "cases", val_var = "AgeOnAdmission", class = "col_itm")
- )
- )
- ),
- weight = list(
- unit = "kg",
- min = 1,
- max = 500,
- target = "id_tbl",
- description = "patient weight",
- omopid = 4099154L,
- category = "demographics",
- sources = list(
- mimic = list(
- list(ids = c(762L, 4183L, 226512L), table = "chartevents",
- sub_var = "itemid")
- ),
- eicu = list(
- list(table = "patient", val_var = "admissionweight",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = 10000400L, table = "observations",
- sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(val_var = "weightgroup", table = "admissions",
- callback = strip_ws("apply_map(c(`59-` = 50,
- `60-69` = 65,
- `70-79` = 75,
- `80-89` = 85,
- `90-99` = 95,
- `100-109` = 105,
- `110+` = 120))"),
- class = "col_itm")
- ),
- miiv = list(
- list(ids = 226512L, table = "chartevents", sub_var = "itemid")
- ),
- sic = list(
- list(table = "cases", val_var = "WeightOnAdmission", class = "col_itm",
- callback = "transform_fun(binary_op(`/`, 1000))")
- )
- )
- ),
- height = list(
- unit = "cm",
- min = 10,
- max = 230,
- target = "id_tbl",
- description = "patient height",
- omopid = 607590L,
- category = "demographics",
- sources = list(
- mimic = list(
- list(ids = c(920L, 1394L, 3485L, 4187L, 4188L, 3486L, 226707L),
- table = "chartevents", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')")
- ),
- eicu = list(
- list(table = "patient", val_var = "admissionheight",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = 10000450L, table = "observations",
- sub_var = "variableid", class = "hrd_itm")
- ),
- aumc = list(
- list(val_var = "heightgroup", table = "admissions",
- callback = strip_ws("apply_map(c(`159-` = 150,
- `160-169` = 165,
- `170-179` = 175,
- `180-189` = 185,
- `190+` = 200))"),
- class = "col_itm")
- ),
- miiv = list(
- list(ids = 226707L, table = "chartevents", sub_var = "itemid",
- callback = "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')")
- ),
- sic = list(
- list(table = "cases", val_var = "HeightOnAdmission", class = "col_itm")
- )
- )
- ),
- death = list(
- class = "lgl_cncpt",
- description = "in hospital mortality",
- omopid = 4306655L,
- category = "outcome",
- sources = list(
- mimic = list(
- list(table = "admissions", index_var = "deathtime",
- val_var = "hospital_expire_flag",
- callback = "transform_fun(comp_na(`==`, 1L))", class = "col_itm")
- ),
- eicu = list(
- list(table = "patient", index_var = "unitdischargeoffset",
- val_var = "hospitaldischargestatus",
- callback = "transform_fun(comp_na(`==`, 'Expired'))",
- class = "col_itm")
- ),
- hirid = list(
- list(ids = c(110L, 200L), table = "observations",
- sub_var = "variableid", callback = "hirid_death",
- class = "hrd_itm")
- ),
- aumc = list(
- list(table = "admissions", index_var = "dateofdeath",
- val_var = "dischargedat", callback = "aumc_death",
- class = "col_itm")
- ),
- miiv = list(
- list(table = "admissions", index_var = "deathtime",
- val_var = "hospital_expire_flag",
- callback = "transform_fun(comp_na(`==`, 1L))", class = "col_itm")
- )
- )
- ),
- adm = list(
- target = "id_tbl",
- levels = c("med", "surg", "other"),
- class = "fct_cncpt",
- description = "patient admission type",
- category = "demographics",
- sources = list(
- mimic = list(
- list(table = "services", val_var = "curr_service",
- callback = "apply_map(
- c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',
- VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',
- ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',
- NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',
- OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')
- )",
- class = "col_itm"
- )
- ),
- eicu = list(
- list(table = "admissiondx", val_var = "admitdxpath",
- callback = "eicu_adx", class = "col_itm")
- ),
- aumc = list(
- list(val_var = "specialty", table = "admissions",
- callback = strip_ws("apply_map(
- c(Cardiochirurgie = 'surg',
- Cardiologie = 'med',
- ders = 'other',
- Gynaecologie = 'other',
- `Heelkunde Gastro-enterologie` = 'surg',
- `Heelkunde Longen/Oncologie` = 'surg',
- `Heelkunde Oncologie` = 'surg',
- Hematologie = 'med',
- `Intensive Care Volwassenen` = 'other',
- Inwendig = 'med',
- `Keel, Neus & Oorarts` = 'surg',
- Longziekte = 'med',
- `Maag-,Darm-,Leverziekten` = 'med',
- Mondheelkunde = 'surg',
- Nefrologie = 'med',
- Neurochirurgie = 'surg',
- Neurologie = 'med',
- Obstetrie = 'other',
- `Oncologie Inwendig` = 'med',
- Oogheelkunde = 'surg',
- Orthopedie = 'surg',
- `Plastische chirurgie` = 'surg',
- Reumatologie = 'med',
- Traumatologie = 'surg',
- Urologie = 'surg',
- Vaatchirurgie = 'surg',
- Verloskunde = 'other'))"),
- class = "col_itm")
- ),
- miiv = list(
- list(table = "services", val_var = "curr_service",
- callback = "apply_map(
- c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',
- VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',
- ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',
- NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',
- OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')
- )",
- class = "col_itm"
- )
- )
- )
- ),
- los_icu = list(
- unit = "days",
- min = 0,
- target = "id_tbl",
- description = "ICU length of stay",
- category = "outcome",
- sources = list(
- mimic = list(
- list(callback = "los_callback", win_type = "icustay",
- class = "fun_itm")
- ),
- eicu = list(
- list(callback = "los_callback", win_type = "icustay",
- class = "fun_itm")
- ),
- hirid = list(
- list(callback = "los_callback", win_type = "icustay",
- class = "fun_itm")
- ),
- aumc = list(
- list(callback = "los_callback", win_type = "icustay",
- class = "fun_itm")
- ),
- miiv = list(
- list(callback = "los_callback", win_type = "icustay",
- class = "fun_itm")
- )
- )
- ),
- los_hosp = list(
- unit = "days",
- min = 0,
- target = "id_tbl",
- description = "hospital length of stay",
- omopid = 462369952L,
- category = "outcome",
- sources = list(
- mimic = list(
- list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
- ),
- eicu = list(
- list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
- ),
- miiv = list(
- list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
- )
- )
- ),
- pafi = list(
- concepts = c("po2", "fio2"),
- description = "Horowitz index",
- omopid = 4233883L,
- category = "respiratory",
- aggregate = c("min", "max"),
- callback = "pafi",
- class = "rec_cncpt"
- ),
- safi = list(
- concepts = c("o2sat", "fio2"),
- description = "SaO2/FiO2",
- category = "respiratory",
- aggregate = c("min", "max"),
- callback = "safi",
- class = "rec_cncpt"
- ),
- vent_ind = list(
- concepts = c("vent_start", "vent_end", "mech_vent"),
- description = "ventilation durations",
- omopid = 4230167L,
- category = "respiratory",
- interval = "00:01:00",
- callback = "vent_ind",
- target = "win_tbl",
- class = "rec_cncpt"
- ),
- vaso_ind = list(
- concepts = c("dopa_dur", "norepi_dur", "dobu_dur", "epi_dur"),
- description = "vasopressor indicator",
- omopid = 3655896L,
- category = "medications",
- callback = "vaso_ind",
- class = "rec_cncpt"
- ),
- gcs = list(
- concepts = c("egcs", "mgcs", "vgcs", "tgcs", "ett_gcs"),
- description = "Glasgow coma scale (non-sedated)",
- omopid = 4093836L,
- category = "neurological",
- aggregate = c("min", "min", "min", "min", "any"),
- callback = "gcs",
- class = "rec_cncpt"
- ),
- urine24 = list(
- concepts = "urine",
- description = "urine output per 24h",
- omopid = 4191836L,
- category = "output",
- callback = "urine24",
- class = "rec_cncpt"
- ),
- sofa_resp = list(
- concepts = c("pafi", "vent_ind"),
- description = "SOFA respiratory component",
- omopid = 1616907L,
- category = "outcome",
- callback = "sofa_resp",
- class = "rec_cncpt"
- ),
- sofa_coag = list(
- concepts = "plt",
- description = "SOFA coagulation component",
- omopid = 1616896L,
- category = "outcome",
- aggregate = "min",
- callback = "sofa_coag",
- class = "rec_cncpt"
- ),
- sofa_liver = list(
- concepts = "bili",
- description = "SOFA liver component",
- omopid = 1617043L,
- category = "outcome",
- aggregate = "max",
- callback = "sofa_liver",
- class = "rec_cncpt"
- ),
- sofa_cardio = list(
- concepts = c("map", "dopa60", "norepi60", "dobu60", "epi60"),
- description = "SOFA cardiovascular component",
- omopid = 1617534L,
- category = "outcome",
- aggregate = c("min", "max", "max", "max", "max"),
- callback = "sofa_cardio",
- class = "rec_cncpt"
- ),
- sofa_cns = list(
- concepts = "gcs",
- description = "SOFA central nervous system component",
- omopid = 1616439L,
- category = "outcome",
- callback = "sofa_cns",
- class = "rec_cncpt"
- ),
- sofa_renal = list(
- concepts = c("crea", "urine24"),
- description = "SOFA renal component",
- omopid = 1616355L,
- category = "outcome",
- aggregate = c("max", NA),
- callback = "sofa_renal",
- class = "rec_cncpt"
- ),
- sofa = list(
- concepts = c("sofa_resp", "sofa_coag", "sofa_liver", "sofa_cardio",
- "sofa_cns", "sofa_renal"),
- description = "sequential organ failure assessment score",
- omopid = 1616852L,
- category = "outcome",
- callback = "sofa_score",
- class = "rec_cncpt"
- ),
- qsofa = list(
- concepts = c("gcs", "sbp", "resp"),
- description = "quick SOFA score",
- omopid = 1616732L,
- category = "outcome",
- callback = "qsofa_score",
- class = "rec_cncpt"
- ),
- susp_inf = list(
- concepts = c("abx", "samp"),
- description = "suspected infection",
- omopid = 43021378L,
- category = "outcome",
- aggregate = lapply(list("sum", FALSE), list),
- callback = "susp_inf",
- class = "rec_cncpt"
- ),
- sep3 = list(
- concepts = c("sofa", "susp_inf"),
- description = "sepsis-3 criterion",
- omopid = 132797L,
- category = "outcome",
- callback = "sep3",
- keep_components = c(FALSE, TRUE),
- class = "rec_cncpt"
- ),
- bnd = list(
- unit = "%",
- description = "band form neutrophils",
- omopid = 4100147L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 51144L, table = "labevents", sub_var = "itemid")
- ),
- eicu = list(
- list(ids = "-bands", table = "lab", sub_var = "labname")
- ),
- hirid = list(
- list(ids = 24000557L, table = "observations", sub_var = "variableid",
- class = "hrd_itm")
- ),
- aumc = list(
- list(ids = c(6796L, 11586L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 51144L, table = "labevents", sub_var = "itemid")
- )
- )
- ),
- sirs = list(
- concepts = c("temp", "hr", "resp", "pco2", "wbc", "bnd"),
- description = "systemic inflammatory response syndrome score",
- omopid = 4140444L,
- category = "outcome",
- callback = "sirs_score",
- class = "rec_cncpt"
- ),
- supp_o2 = list(
- concepts = c("vent_ind", "fio2"),
- description = "supplemental oxygen",
- omopid = 36304401L,
- category = "respiratory",
- callback = "supp_o2",
- class = "rec_cncpt"
- ),
- avpu = list(
- concepts = "gcs",
- description = "AVPU scale",
- omopid = 40493498L,
- category = "neurological",
- callback = "avpu",
- class = "rec_cncpt"
- ),
- news = list(
- concepts = c("resp", "o2sat", "supp_o2", "temp", "sbp", "hr", "avpu"),
- description = "national early warning score",
- omopid = 44808550,
- category = "outcome",
- callback = "news_score",
- class = "rec_cncpt"
- ),
- mews = list(
- concepts = c("sbp", "hr", "resp", "temp","avpu"),
- description = "modified early warning score",
- omopid = 40484211L,
- category = "outcome",
- callback = "mews_score",
- class = "rec_cncpt"
- ),
- hba1c = list(
- unit = "%",
- description = "Hemoglobin A1C",
- omopid = 4184637L,
- category = "hematology",
- sources = list(
- mimic = list(
- list(ids = 50852L, table = "labevents", sub_var = "itemid")
- ),
- aumc = list(
- list(ids = c(11812L, 16166L), table = "numericitems",
- sub_var = "itemid")
- ),
- miiv = list(
- list(ids = 50852L, table = "labevents", sub_var = "itemid")
- )
- )
- ),
- bmi = list(
- concepts = c("weight", "height"),
- description = "patient body mass index",
- omopid = 4245997L,
- category = "demographics",
- callback = "bmi",
- target = "id_tbl",
- class = "rec_cncpt"
- ),
- adh_rate = list(
- unit = c("units/min", "U/min"),
- description = "vasopressin rate",
- omopid = 1507835L,
- category = "medications",
- sources = list(
- mimic = list(
- list(ids = 30051L, table = "inputevents_cv", sub_var = "itemid",
- grp_var = "linkorderid", callback = "combine_callbacks(
- convert_unit(binary_op(`/`, 60), 'units/min', 'Uhr'),
- mimic_rate_cv
- )"),
- list(ids = 222315L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", callback = "combine_callbacks(
- convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),
- mimic_rate_mv
- )")
- ),
- eicu = list(
- list(regex = "^vasopressin.*\\(.+/.+\\)$",
- table = "infusiondrug", sub_var = "drugname",
- callback = "eicu_rate_units(2.65, 0.53)",
- class = "rgx_itm")
- ),
- hirid = list(
- list(ids = c(112L, 113L), table = "pharma", sub_var = "pharmaid",
- grp_var = "infusionid", callback = "hirid_rate")
- ),
- aumc = list(
- list(ids = 12467L, table = "drugitems", sub_var = "itemid",
- rate_uom = "doserateunit", stop_var = "stop",
- callback = "aumc_rate_units(0.53)")
- ),
- miiv = list(
- list(ids = 222315L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", callback = "combine_callbacks(
- convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),
- mimic_rate_mv
- )")
- )
- )
- ),
- phn_rate = list(
- unit = "mcg/kg/min",
- description = "phenylephrine rate",
- omopid = 1135766L,
- category = "medications",
- sources = list(
- mimic = list(
- list(ids = 30127L, table = "inputevents_cv", sub_var = "itemid",
- grp_var = "linkorderid", callback = "combine_callbacks(
- mimic_kg_rate, mimic_rate_cv)
- "),
- list(ids = 30128L, table = "inputevents_cv", sub_var = "itemid",
- grp_var = "linkorderid", callback = "mimic_rate_cv"),
- list(ids = 221749L, table = "inputevents_mv", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- ),
- eicu = list(
- list(regex = "^phenylephrine.*\\(.+\\)$", table = "infusiondrug",
- sub_var = "drugname", weight_var = "patientweight",
- callback = "eicu_rate_kg(ml_to_mcg = 200)", class = "rgx_itm")
- ),
- miiv = list(
- list(ids = 221749L, table = "inputevents", sub_var = "itemid",
- stop_var = "endtime", callback = "mimic_rate_mv")
- )
- )
- ),
- norepi_equiv = list(
- description = "norepinephrine equivalents",
- category = "medications",
- concepts = c("epi_rate", "norepi_rate", "dopa_rate", "adh_rate",
- "phn_rate"),
- callback = "norepi_equiv",
- class = "rec_cncpt"
- ),
- cort = list(
- class = "lgl_cncpt",
- description = "corticosteroids",
- omopid = 304275008L,
- category = "medications",
- sources = list(
- hirid = list(
- list(ids = c( 146L, 151L, 1000325L, 1000383L, 1000431L,
- 1000432L, 1000433L, 1000434L, 1000435L, 1000486L,
- 1000487L, 1000488L, 1000769L, 1000770L, 1000929L),
- table = "pharma", sub_var = "pharmaid",
- callback = "transform_fun(set_val(TRUE))")
- ),
- aumc = list(
- list(ids = c(6922L, 6995L, 7106L, 8132L, 9042L, 9130L, 10628L),
- table = "drugitems", sub_var = "itemid",
- callback = "transform_fun(set_val(TRUE))")
- )
- )
- ),
- dex = list(
- min = 0,
- unit = "ml/hr",
- description = "dextrose (as D10)",
- omopid = 4197597L,
- category = "medications",
- target = "win_tbl",
- sources = list(
- mimic = list(
- list(ids = c(220950L, 228140L, 220952L), table = "inputevents_mv",
- sub_var = "itemid", dur_var = "endtime", amount_var = "amount",
- auom_var = "amountuom", callback = "combine_callbacks(
- mimv_rate,
- dex_to_10(c(228140L, 220952L), c(2, 5))
- )"),
- list(ids = c(30016L, 30017L), table = "inputevents_cv",
- sub_var = "itemid", grp_var = "linkorderid", val_var = "amount",
- unit_var = "amountuom", target = "ts_tbl", interval = "00:01:00",
- callback = "combine_callbacks(
- grp_mount_to_rate(mins(1L), hours(1L)),
- dex_to_10(30017L, 2)
- )")
- ),
- eicu = list(
- list(regex = "(d50|dextrose.+50 ?%)", table = "medication",
- sub_var = "drugname", dur_var = "drugstopoffset",
- callback = "eicu_dex_med", class = "rgx_itm"),
- list(regex = "(d10|dextrose.+10 ?%).+ml/hr", table = "infusiondrug",
- sub_var = "drugname", callback = "eicu_dex_inf", target = "ts_tbl",
- class = "rgx_itm")
- ),
- hirid = list(
- list(ids = c(1000022L, 1000690L, 1000689L, 1000544L, 1000746L,
- 1000835L, 1000060L, 1000545L, 1000567L),
- table = "pharma", sub_var = "pharmaid", grp_var = "infusionid",
- target = "ts_tbl", interval = "00:01:00",
- callback = "combine_callbacks(
- grp_mount_to_rate(mins(1L), hours(1L)),
- dex_to_10(list(c(1000689L, 1000544L, 1000746L, 1000835L),
- 1000060L, 1000545L, 1000567L), c(2, 3, 4, 5))
- )")
- ),
- aumc = list(
- list(ids = c(7254L, 7255L, 7256L, 8940L, 9571L), table = "drugitems",
- sub_var = "itemid", dur_var = "stop", rate_var = "doserateunit",
- callback = "combine_callbacks(
- aumc_rate,
- dex_to_10(list(7255L, 7256L, c(8940L, 9571L)),
- c(2, 3, 4))
- )"
- )
- ),
- miiv = list(
- list(ids = c(220950L, 228140L, 220952L), table = "inputevents",
- sub_var = "itemid", dur_var = "endtime", amount_var = "amount",
- auom_var = "amountuom", callback = "combine_callbacks(
- mimv_rate,
- dex_to_10(c(228140L, 220952L), c(2, 5))
- )")
- )
- ),
- class = c("unt_cncpt", "num_cncpt")
- )
-)
-
-cfg <- lapply(cfg, function(x) {
-
- if ("sources" %in% names(x)) {
-
- if ("mimic" %in% names(x[["sources"]]))
- x[["sources"]] <- c(x[["sources"]],
- mimic_demo = list(x[["sources"]][["mimic"]]))
-
- if ("eicu" %in% names(x[["sources"]]))
- x[["sources"]] <- c(x[["sources"]],
- eicu_demo = list(x[["sources"]][["eicu"]]))
-
- x[["sources"]] <- x[["sources"]][order(names(x[["sources"]]))]
- }
-
- x
-})
-
-
-pkg_dir <- rprojroot::find_root(rprojroot::is_r_package)
-cfg_dir <- file.path(pkg_dir, "inst", "extdata", "config")
-
-ricu::set_config(cfg[order(names(cfg))], "concept-dict", cfg_dir)
-
-devtools::install(pkg_dir)
diff --git a/inst/extdata/config/concept-dict.json b/inst/extdata/config/concept-dict.json
deleted file mode 100644
index 09084942..00000000
--- a/inst/extdata/config/concept-dict.json
+++ /dev/null
@@ -1,6591 +0,0 @@
-{
- "abx": {
- "class": "lgl_cncpt",
- "description": "antibiotics",
- "omopid": 4085730,
- "category": "medications",
- "sources": {
- "aumc": [
- {
- "ids": [2, 13, 19, 24, 28, 29, 57, 59, 82, 103, 240, 247, 333, 1133, 1199, 1300, 1371, 1795, 2284, 2834, 3237, 3741, 5576, 6834, 6847, 6871, 6919, 6948, 6953, 6958, 7044, 7064, 7185, 7187, 7208, 7227, 7235, 8064, 8394, 8942, 9029, 9030, 9052, 9070, 9117, 9128, 9133, 9142, 9151, 9152, 12262, 12389, 12398, 12956, 12997, 13057, 13094, 13102, 15591, 18860, 19137, 19773, 20563, 23166, 24241, 25776, 27617, 29321],
- "table": "drugitems",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "eicu": [
- {
- "regex": "bactrim|cipro|flagyl|metronidazole|zithromax|zosyn|(((amika|cleo|ofloxa)|(azithro|clinda|tobra|vanco)my)c|(ampi|oxa|peni|pipera)cill|cefazol|levaqu|rifamp)in",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "transform_fun(set_val(TRUE))",
- "class": "rgx_itm"
- },
- {
- "regex": "cipro|flagyl|maxipime|metronidazole|tazobactam|zosyn|cef(azolin|epime)|(((azithro|clinda|vanco)my|ofloxa|vanco)c|levaqu|piperacill|roceph)in",
- "table": "medication",
- "sub_var": "drugname",
- "callback": "transform_fun(set_val(TRUE))",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "bactrim|cipro|flagyl|metronidazole|zithromax|zosyn|(((amika|cleo|ofloxa)|(azithro|clinda|tobra|vanco)my)c|(ampi|oxa|peni|pipera)cill|cefazol|levaqu|rifamp)in",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "transform_fun(set_val(TRUE))",
- "class": "rgx_itm"
- },
- {
- "regex": "cipro|flagyl|maxipime|metronidazole|tazobactam|zosyn|cef(azolin|epime)|(((azithro|clinda|vanco)my|ofloxa|vanco)c|levaqu|piperacill|roceph)in",
- "table": "medication",
- "sub_var": "drugname",
- "callback": "transform_fun(set_val(TRUE))",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": [163, 176, 181, 186, 189, 300, 326, 331, 351, 405, 1000234, 1000272, 1000273, 1000274, 1000284, 1000299, 1000300, 1000302, 1000304, 1000305, 1000306, 1000315, 1000317, 1000318, 1000320, 1000321, 1000322, 1000335, 1000348, 1000352, 1000363, 1000365, 1000390, 1000407, 1000408, 1000424, 1000425, 1000426, 1000437, 1000483, 1000507, 1000508, 1000518, 1000519, 1000549, 1000601, 1000648, 1000666, 1000670, 1000671, 1000760, 1000781, 1000791, 1000797, 1000812, 1000825, 1000829, 1000830, 1000837, 1000838, 1000854, 1000855, 1000893, 1000894, 1001005, 1001068, 1001075, 1001079, 1001084, 1001086, 1001095, 1001096, 1001097, 1001098, 1001168, 1001169, 1001170, 1001171, 1001173, 1001193, 1001198],
- "table": "pharma",
- "sub_var": "pharmaid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "miiv": [
- {
- "regex": "aztreonam|bactrim|cephalexin|chloramphenicol|cipro|flagyl|metronidazole|nitrofurantoin|tazobactam|rifampin|sulfadiazine|timentin|trimethoprim|(amika|gentami|vanco)cin|(amoxi|ampi|dicloxa|naf|oxa|peni|pipera)cillin|(azithro|clarithro|erythro|clinda|strepto|tobra|vanco)mycin|cef(azolin|tazidime|adroxil|epime|otetan|otaxime|podoxime|uroxime)|(doxy|mino|tetra)cycline|(levofl|moxifl|ofl)oxacin|macro(bid|dantin)|(una|zo)syn",
- "table": "prescriptions",
- "sub_var": "drug",
- "callback": "transform_fun(set_val(TRUE))",
- "class": "rgx_itm"
- },
- {
- "ids": [225798, 225837, 225838, 225840, 225842, 225843, 225844, 225845, 225847, 225848, 225850, 225851, 225853, 225855, 225857, 225859, 225860, 225862, 225863, 225865, 225866, 225868, 225869, 225871, 225873, 225875, 225876, 225877, 225879, 225881, 225882, 225883, 225884, 225885, 225886, 225888, 225889, 225890, 225892, 225893, 225895, 225896, 225897, 225898, 225899, 225900, 225902, 225903, 225905, 227691, 228003],
- "table": "inputevents",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "mimic": [
- {
- "regex": "aztreonam|bactrim|cephalexin|chloramphenicol|cipro|flagyl|metronidazole|nitrofurantoin|tazobactam|rifampin|sulfadiazine|timentin|trimethoprim|(amika|gentami|vanco)cin|(amoxi|ampi|dicloxa|naf|oxa|peni|pipera)cillin|(azithro|clarithro|erythro|clinda|strepto|tobra|vanco)mycin|cef(azolin|tazidime|adroxil|epime|otetan|otaxime|podoxime|uroxime)|(doxy|mino|tetra)cycline|(levofl|moxifl|ofl)oxacin|macro(bid|dantin)|(una|zo)syn",
- "table": "prescriptions",
- "sub_var": "drug",
- "interval": "00:01:00",
- "callback": "mimic_abx_presc",
- "class": "rgx_itm"
- },
- {
- "ids": [225798, 225837, 225838, 225840, 225842, 225843, 225844, 225845, 225847, 225848, 225850, 225851, 225853, 225855, 225857, 225859, 225860, 225862, 225863, 225865, 225866, 225868, 225869, 225871, 225873, 225875, 225876, 225877, 225879, 225881, 225882, 225883, 225884, 225885, 225886, 225888, 225889, 225890, 225892, 225893, 225895, 225896, 225897, 225898, 225899, 225900, 225902, 225903, 225905, 227691, 228003],
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "mimic_demo": [
- {
- "regex": "aztreonam|bactrim|cephalexin|chloramphenicol|cipro|flagyl|metronidazole|nitrofurantoin|tazobactam|rifampin|sulfadiazine|timentin|trimethoprim|(amika|gentami|vanco)cin|(amoxi|ampi|dicloxa|naf|oxa|peni|pipera)cillin|(azithro|clarithro|erythro|clinda|strepto|tobra|vanco)mycin|cef(azolin|tazidime|adroxil|epime|otetan|otaxime|podoxime|uroxime)|(doxy|mino|tetra)cycline|(levofl|moxifl|ofl)oxacin|macro(bid|dantin)|(una|zo)syn",
- "table": "prescriptions",
- "sub_var": "drug",
- "interval": "00:01:00",
- "callback": "mimic_abx_presc",
- "class": "rgx_itm"
- },
- {
- "ids": [225798, 225837, 225838, 225840, 225842, 225843, 225844, 225845, 225847, 225848, 225850, 225851, 225853, 225855, 225857, 225859, 225860, 225862, 225863, 225865, 225866, 225868, 225869, 225871, 225873, 225875, 225876, 225877, 225879, 225881, 225882, 225883, 225884, 225885, 225886, 225888, 225889, 225890, 225892, 225893, 225895, 225896, 225897, 225898, 225899, 225900, 225902, 225903, 225905, 227691, 228003],
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "sic": [
- {
- "ids": [1406, 1408, 1410, 1418, 1421, 1422, 1423, 1428, 1431, 1433, 1436, 1449, 1454, 1457, 1458, 1459, 1460, 1461, 1603, 1795, 1913, 1927],
- "table": "medication",
- "sub_var": "DrugID",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ]
- }
- },
- "adh_rate": {
- "unit": ["units/min", "U/min"],
- "description": "vasopressin rate",
- "omopid": 1507835,
- "category": "medications",
- "sources": {
- "aumc": [
- {
- "ids": 12467,
- "table": "drugitems",
- "sub_var": "itemid",
- "rate_uom": "doserateunit",
- "stop_var": "stop",
- "callback": "aumc_rate_units(0.53)"
- }
- ],
- "eicu": [
- {
- "regex": "^vasopressin.*\\(.+/.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_rate_units(2.65, 0.53)",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^vasopressin.*\\(.+/.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_rate_units(2.65, 0.53)",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": [112, 113],
- "table": "pharma",
- "sub_var": "pharmaid",
- "grp_var": "infusionid",
- "callback": "hirid_rate"
- }
- ],
- "miiv": [
- {
- "ids": 222315,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),\n mimic_rate_mv\n )"
- }
- ],
- "mimic": [
- {
- "ids": 30051,
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'Uhr'),\n mimic_rate_cv\n )"
- },
- {
- "ids": 222315,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),\n mimic_rate_mv\n )"
- }
- ],
- "mimic_demo": [
- {
- "ids": 30051,
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'Uhr'),\n mimic_rate_cv\n )"
- },
- {
- "ids": 222315,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),\n mimic_rate_mv\n )"
- }
- ]
- }
- },
- "adm": {
- "target": "id_tbl",
- "levels": ["med", "surg", "other"],
- "class": "fct_cncpt",
- "description": "patient admission type",
- "category": "demographics",
- "sources": {
- "aumc": [
- {
- "val_var": "specialty",
- "table": "admissions",
- "callback": "apply_map( c(Cardiochirurgie = 'surg', Cardiologie = 'med', ders = 'other', Gynaecologie = 'other', `Heelkunde Gastro-enterologie` = 'surg', `Heelkunde Longen/Oncologie` = 'surg', `Heelkunde Oncologie` = 'surg', Hematologie = 'med', `Intensive Care Volwassenen` = 'other', Inwendig = 'med', `Keel, Neus & Oorarts` = 'surg', Longziekte = 'med', `Maag-,Darm-,Leverziekten` = 'med', Mondheelkunde = 'surg', Nefrologie = 'med', Neurochirurgie = 'surg', Neurologie = 'med', Obstetrie = 'other', `Oncologie Inwendig` = 'med', Oogheelkunde = 'surg', Orthopedie = 'surg', `Plastische chirurgie` = 'surg', Reumatologie = 'med', Traumatologie = 'surg', Urologie = 'surg', Vaatchirurgie = 'surg', Verloskunde = 'other'))",
- "class": "col_itm"
- }
- ],
- "eicu": [
- {
- "table": "admissiondx",
- "val_var": "admitdxpath",
- "callback": "eicu_adx",
- "class": "col_itm"
- }
- ],
- "eicu_demo": [
- {
- "table": "admissiondx",
- "val_var": "admitdxpath",
- "callback": "eicu_adx",
- "class": "col_itm"
- }
- ],
- "miiv": [
- {
- "table": "services",
- "val_var": "curr_service",
- "callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
- "class": "col_itm"
- }
- ],
- "mimic": [
- {
- "table": "services",
- "val_var": "curr_service",
- "callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
- "class": "col_itm"
- }
- ],
- "mimic_demo": [
- {
- "table": "services",
- "val_var": "curr_service",
- "callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
- "class": "col_itm"
- }
- ]
- }
- },
- "age": {
- "unit": "years",
- "min": 0,
- "max": 100,
- "target": "id_tbl",
- "description": "patient age",
- "omopid": 4314456,
- "category": "demographics",
- "sources": {
- "aumc": [
- {
- "val_var": "agegroup",
- "table": "admissions",
- "callback": "apply_map(c(`18-39` = 30, `40-49` = 45, `50-59` = 55, `60-69` = 65, `70-79` = 75, `80+` = 90))",
- "class": "col_itm"
- }
- ],
- "eicu": [
- {
- "table": "patient",
- "val_var": "age",
- "callback": "transform_fun(eicu_age)",
- "class": "col_itm"
- }
- ],
- "eicu_demo": [
- {
- "table": "patient",
- "val_var": "age",
- "callback": "transform_fun(eicu_age)",
- "class": "col_itm"
- }
- ],
- "hirid": [
- {
- "table": "general",
- "val_var": "age",
- "class": "col_itm"
- }
- ],
- "miiv": [
- {
- "table": "patients",
- "val_var": "anchor_age",
- "class": "col_itm"
- }
- ],
- "mimic": [
- {
- "table": "patients",
- "val_var": "dob",
- "callback": "transform_fun(mimic_age)",
- "class": "col_itm"
- }
- ],
- "mimic_demo": [
- {
- "table": "patients",
- "val_var": "dob",
- "callback": "transform_fun(mimic_age)",
- "class": "col_itm"
- }
- ],
- "sic": [
- {
- "table": "cases",
- "val_var": "AgeOnAdmission",
- "class": "col_itm"
- }
- ]
- }
- },
- "alb": {
- "unit": "g/dL",
- "min": 0,
- "max": 6,
- "description": "albumin",
- "omopid": 4017497,
- "category": "chemistry",
- "sources": {
- "aumc": [
- {
- "ids": [6801, 9937],
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 0.1), 'g/dL')"
- }
- ],
- "eicu": [
- {
- "ids": "albumin",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "albumin",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000605,
- "table": "observations",
- "sub_var": "variableid",
- "callback": "convert_unit(binary_op(`*`, 0.1), 'g/dL')",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50862,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50862,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50862,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 287,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "alp": {
- "unit": ["IU/L", "U/l"],
- "min": 0,
- "description": "alkaline phosphatase",
- "omopid": 4275206,
- "category": "chemistry",
- "sources": {
- "aumc": [
- {
- "ids": [6803, 11984],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "alkaline phos.",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "alkaline phos.",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 20002700,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50863,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50863,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50863,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 609,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "alt": {
- "unit": ["IU/L", "U/l"],
- "min": 0,
- "description": "alanine aminotransferase",
- "omopid": 4146380,
- "category": "chemistry",
- "sources": {
- "aumc": [
- {
- "ids": [6800, 11978],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "ALT (SGPT)",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "ALT (SGPT)",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 20002600,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50861,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50861,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50861,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 617,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "ast": {
- "unit": ["IU/L", "U/l"],
- "min": 0,
- "description": "aspartate aminotransferase",
- "omopid": 4263457,
- "category": "chemistry",
- "sources": {
- "aumc": [
- {
- "ids": [6806, 11990],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "AST (SGOT)",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "AST (SGOT)",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000330,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50878,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50878,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50878,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 616,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "avpu": {
- "concepts": "gcs",
- "description": "AVPU scale",
- "omopid": 40493498,
- "category": "neurological",
- "callback": "avpu",
- "class": "rec_cncpt"
- },
- "basos": {
- "unit": "%",
- "min": 0,
- "max": 50,
- "description": "basophils",
- "omopid": 4172647,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": 11710,
- "table": "numericitems",
- "sub_var": "itemid"
- },
- {
- "ids": 14256,
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "blood_cell_ratio"
- }
- ],
- "eicu": [
- {
- "ids": "-basos",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "-basos",
- "table": "lab",
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- "ids": [8368, 8441, 8555, 220051, 220180],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [8368, 8441, 8555, 220051, 220180],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": [702, 705],
- "table": "data_float_h",
- "sub_var": "DataID"
- }
- ]
- }
- },
- "death": {
- "class": "lgl_cncpt",
- "description": "in hospital mortality",
- "omopid": 4306655,
- "category": "outcome",
- "sources": {
- "aumc": [
- {
- "table": "admissions",
- "index_var": "dateofdeath",
- "val_var": "dischargedat",
- "callback": "aumc_death",
- "class": "col_itm"
- }
- ],
- "eicu": [
- {
- "table": "patient",
- "index_var": "unitdischargeoffset",
- "val_var": "hospitaldischargestatus",
- "callback": "transform_fun(comp_na(`==`, 'Expired'))",
- "class": "col_itm"
- }
- ],
- "eicu_demo": [
- {
- "table": "patient",
- "index_var": "unitdischargeoffset",
- "val_var": "hospitaldischargestatus",
- "callback": "transform_fun(comp_na(`==`, 'Expired'))",
- "class": "col_itm"
- }
- ],
- "hirid": [
- {
- "ids": [110, 200],
- "table": "observations",
- "sub_var": "variableid",
- "callback": "hirid_death",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "table": "admissions",
- "index_var": "deathtime",
- "val_var": "hospital_expire_flag",
- "callback": "transform_fun(comp_na(`==`, 1L))",
- "class": "col_itm"
- }
- ],
- "mimic": [
- {
- "table": "admissions",
- "index_var": "deathtime",
- "val_var": "hospital_expire_flag",
- "callback": "transform_fun(comp_na(`==`, 1L))",
- "class": "col_itm"
- }
- ],
- "mimic_demo": [
- {
- "table": "admissions",
- "index_var": "deathtime",
- "val_var": "hospital_expire_flag",
- "callback": "transform_fun(comp_na(`==`, 1L))",
- "class": "col_itm"
- }
- ]
- }
- },
- "dex": {
- "min": 0,
- "unit": "ml/hr",
- "description": "dextrose (as D10)",
- "omopid": 4197597,
- "category": "medications",
- "target": "win_tbl",
- "sources": {
- "aumc": [
- {
- "ids": [7254, 7255, 7256, 8940, 9571],
- "table": "drugitems",
- "sub_var": "itemid",
- "dur_var": "stop",
- "rate_var": "doserateunit",
- "callback": "combine_callbacks(\n aumc_rate,\n dex_to_10(list(7255L, 7256L, c(8940L, 9571L)),\n c(2, 3, 4))\n )"
- }
- ],
- "eicu": [
- {
- "regex": "(d50|dextrose.+50 ?%)",
- "table": "medication",
- "sub_var": "drugname",
- "dur_var": "drugstopoffset",
- "callback": "eicu_dex_med",
- "class": "rgx_itm"
- },
- {
- "regex": "(d10|dextrose.+10 ?%).+ml/hr",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_dex_inf",
- "target": "ts_tbl",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "(d50|dextrose.+50 ?%)",
- "table": "medication",
- "sub_var": "drugname",
- "dur_var": "drugstopoffset",
- "callback": "eicu_dex_med",
- "class": "rgx_itm"
- },
- {
- "regex": "(d10|dextrose.+10 ?%).+ml/hr",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_dex_inf",
- "target": "ts_tbl",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": [1000022, 1000690, 1000689, 1000544, 1000746, 1000835, 1000060, 1000545, 1000567],
- "table": "pharma",
- "sub_var": "pharmaid",
- "grp_var": "infusionid",
- "target": "ts_tbl",
- "interval": "00:01:00",
- "callback": "combine_callbacks(\n grp_mount_to_rate(mins(1L), hours(1L)),\n dex_to_10(list(c(1000689L, 1000544L, 1000746L, 1000835L),\n 1000060L, 1000545L, 1000567L), c(2, 3, 4, 5))\n )"
- }
- ],
- "miiv": [
- {
- "ids": [220950, 228140, 220952],
- "table": "inputevents",
- "sub_var": "itemid",
- "dur_var": "endtime",
- "amount_var": "amount",
- "auom_var": "amountuom",
- "callback": "combine_callbacks(\n mimv_rate,\n dex_to_10(c(228140L, 220952L), c(2, 5))\n )"
- }
- ],
- "mimic": [
- {
- "ids": [220950, 228140, 220952],
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "dur_var": "endtime",
- "amount_var": "amount",
- "auom_var": "amountuom",
- "callback": "combine_callbacks(\n mimv_rate,\n dex_to_10(c(228140L, 220952L), c(2, 5))\n )"
- },
- {
- "ids": [30016, 30017],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "val_var": "amount",
- "unit_var": "amountuom",
- "target": "ts_tbl",
- "interval": "00:01:00",
- "callback": "combine_callbacks(\n grp_mount_to_rate(mins(1L), hours(1L)),\n dex_to_10(30017L, 2)\n )"
- }
- ],
- "mimic_demo": [
- {
- "ids": [220950, 228140, 220952],
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "dur_var": "endtime",
- "amount_var": "amount",
- "auom_var": "amountuom",
- "callback": "combine_callbacks(\n mimv_rate,\n dex_to_10(c(228140L, 220952L), c(2, 5))\n )"
- },
- {
- "ids": [30016, 30017],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "val_var": "amount",
- "unit_var": "amountuom",
- "target": "ts_tbl",
- "interval": "00:01:00",
- "callback": "combine_callbacks(\n grp_mount_to_rate(mins(1L), hours(1L)),\n dex_to_10(30017L, 2)\n )"
- }
- ]
- },
- "class": ["unt_cncpt", "num_cncpt"]
- },
- "dobu_dur": {
- "description": "dobutamine duration",
- "category": "medications",
- "aggregate": "max",
- "sources": {
- "aumc": [
- {
- "ids": 7178,
- "table": "drugitems",
- "sub_var": "itemid",
- "stop_var": "stop",
- "grp_var": "orderid",
- "callback": "aumc_dur"
- }
- ],
- "eicu": [
- {
- "regex": "^dobu",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_duration(gap_length = hours(5L))",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^dobu",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_duration(gap_length = hours(5L))",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": 426,
- "table": "pharma",
- "sub_var": "pharmaid",
- "grp_var": "infusionid",
- "callback": "hirid_duration"
- }
- ],
- "miiv": [
- {
- "ids": 221653,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "mimic": [
- {
- "ids": [30042, 30306],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_incv"
- },
- {
- "ids": 221653,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "mimic_demo": [
- {
- "ids": [30042, 30306],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_incv"
- },
- {
- "ids": 221653,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "sic": [
- {
- "ids": [
- 1559
- ],
- "table": "medication",
- "sub_var": "DrugID",
- "stop_var": "OffsetDrugEnd",
- "callback": "sic_dur"
- }
- ]
- }
- },
- "dobu_rate": {
- "unit": ["mcg/kg/min", "mcgkgmin"],
- "min": 0,
- "max": 50,
- "description": "dobutamine rate",
- "omopid": 1337720,
- "category": "medications",
- "sources": {
- "aumc": [
- {
- "ids": 7178,
- "table": "drugitems",
- "sub_var": "itemid",
- "rel_weight": "doserateperkg",
- "rate_uom": "doserateunit",
- "stop_var": "stop",
- "callback": "aumc_rate_kg"
- }
- ],
- "eicu": [
- {
- "regex": "^dobu.*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 2000)",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^dobu.*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 2000)",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": 426,
- "table": "pharma",
- "sub_var": "pharmaid",
- "grp_var": "infusionid",
- "callback": "hirid_rate_kg"
- }
- ],
- "miiv": [
- {
- "ids": 221653,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic": [
- {
- "ids": [30042, 30306],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221653,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic_demo": [
- {
- "ids": [30042, 30306],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221653,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "sic": [
- {
- "ids": 1559,
- "table": "medication",
- "sub_var": "DrugID",
- "val_var": "AmountPerMinute",
- "stop_var": "OffsetDrugEnd",
- "callback": "sic_rate_kg"
- }
- ]
- }
- },
- "dobu60": {
- "concepts": ["dobu_rate", "dobu_dur"],
- "description": "dobutamine administration for min 1h",
- "category": "medications",
- "interval": "00:01:00",
- "callback": "vaso60",
- "class": "rec_cncpt"
- },
- "dopa_dur": {
- "description": "dopamine duration",
- "category": "medications",
- "aggregate": "max",
- "sources": {
- "aumc": [
- {
- "ids": 7179,
- "table": "drugitems",
- "sub_var": "itemid",
- "stop_var": "stop",
- "grp_var": "orderid",
- "callback": "aumc_dur"
- }
- ],
- "eicu": [
- {
- "regex": "^dopa",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_duration(gap_length = hours(5L))",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^dopa",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_duration(gap_length = hours(5L))",
- "class": "rgx_itm"
- }
- ],
- "miiv": [
- {
- "ids": 221662,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "mimic": [
- {
- "ids": [30043, 30125, 30307],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_incv"
- },
- {
- "ids": 221662,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "mimic_demo": [
- {
- "ids": [30043, 30125, 30307],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_incv"
- },
- {
- "ids": 221662,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "sic": [
- {
- "ids": 1618,
- "table": "medication",
- "sub_var": "DrugID",
- "stop_var": "OffsetDrugEnd",
- "callback": "sic_dur"
- }
- ]
- }
- },
- "dopa_rate": {
- "unit": ["mcg/kg/min", "mcgkgmin"],
- "min": 0,
- "max": 50,
- "description": "dopamine rate",
- "omopid": 1337860,
- "category": "medications",
- "sources": {
- "aumc": [
- {
- "ids": 7179,
- "table": "drugitems",
- "sub_var": "itemid",
- "rel_weight": "doserateperkg",
- "rate_uom": "doserateunit",
- "stop_var": "stop",
- "callback": "aumc_rate_kg"
- }
- ],
- "eicu": [
- {
- "regex": "^dopa.*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 1600)",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^dopa.*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 1600)",
- "class": "rgx_itm"
- }
- ],
- "miiv": [
- {
- "ids": 221662,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic": [
- {
- "ids": [30043, 30125, 30307],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221662,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic_demo": [
- {
- "ids": [30043, 30125, 30307],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221662,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "sic": [
- {
- "ids": 1618,
- "table": "medication",
- "sub_var": "DrugID",
- "val_var": "AmountPerMinute",
- "stop_var": "OffsetDrugEnd",
- "callback": "sic_rate_kg"
- }
- ]
- }
- },
- "dopa60": {
- "concepts": ["dopa_rate", "dopa_dur"],
- "description": "dopamine administration for min 1h",
- "category": "outcome",
- "interval": "00:01:00",
- "callback": "vaso60",
- "class": "rec_cncpt"
- },
- "egcs": {
- "min": 1,
- "max": 4,
- "description": "GCS eye",
- "omopid": 4084277,
- "category": "neurological",
- "sources": {
- "aumc": [
- {
- "ids": 6732,
- "table": "listitems",
- "sub_var": "itemid",
- "callback": "apply_map( c(`Geen reactie` = 1, `Reactie op pijnprikkel` = 2, `Reactie op verbale prikkel` = 3, `Spontane reactie` = 4) )"
- },
- {
- "ids": 13077,
- "table": "listitems",
- "sub_var": "itemid",
- "callback": "apply_map( c(`Niet` = 1, `Op pijn` = 2, `Op aanspreken` = 3, `Spontaan` = 4) )"
- }
- ],
- "eicu": [
- {
- "ids": "Eyes",
- "table": "nursecharting",
- "sub_var": "nursingchartcelltypevalname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "Eyes",
- "table": "nursecharting",
- "sub_var": "nursingchartcelltypevalname"
- }
- ],
- "hirid": [
- {
- "ids": 10000300,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 220739,
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [184, 220739],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [184, 220739],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ]
- }
- },
- "eos": {
- "unit": "%",
- "min": 0,
- "max": 50,
- "description": "eosinophils",
- "omopid": 4216098,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": 6773,
- "table": "numericitems",
- "sub_var": "itemid"
- },
- {
- "ids": 9967,
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "blood_cell_ratio"
- }
- ],
- "eicu": [
- {
- "ids": "-eos",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "-eos",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "miiv": [
- {
- "ids": 51200,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51200,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51200,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 197,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "epi_dur": {
- "description": "epinephrine duration",
- "category": "medications",
- "aggregate": "max",
- "sources": {
- "aumc": [
- {
- "ids": 6818,
- "table": "drugitems",
- "sub_var": "itemid",
- "stop_var": "stop",
- "grp_var": "orderid",
- "callback": "aumc_dur"
- }
- ],
- "eicu": [
- {
- "regex": "^epi( |n)",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_duration(gap_length = hours(5L))",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^epi( |n)",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_duration(gap_length = hours(5L))",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": [71, 1000649, 1000650, 1000655, 1000750],
- "table": "pharma",
- "sub_var": "pharmaid",
- "grp_var": "infusionid",
- "callback": "hirid_duration"
- }
- ],
- "miiv": [
- {
- "ids": 221289,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "mimic": [
- {
- "ids": [30044, 30119, 30309],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_incv"
- },
- {
- "ids": 221289,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "mimic_demo": [
- {
- "ids": [30044, 30119, 30309],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_incv"
- },
- {
- "ids": 221289,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "sic": [
- {
- "ids": [
- 1502
- ],
- "table": "medication",
- "sub_var": "DrugID",
- "stop_var": "OffsetDrugEnd",
- "callback": "sic_dur"
- }
- ]
- }
- },
- "epi_rate": {
- "unit": ["mcg/kg/min", "mcgkgmin"],
- "min": 0,
- "max": 1.5,
- "description": "epinephrine rate",
- "omopid": 1343916,
- "category": "medications",
- "sources": {
- "aumc": [
- {
- "ids": 6818,
- "table": "drugitems",
- "sub_var": "itemid",
- "rel_weight": "doserateperkg",
- "rate_uom": "doserateunit",
- "stop_var": "stop",
- "callback": "aumc_rate_kg"
- }
- ],
- "eicu": [
- {
- "regex": "^epi( |n).*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 40)",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^epi( |n).*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 40)",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": [71, 1000649, 1000650, 1000655, 1000750],
- "table": "pharma",
- "sub_var": "pharmaid",
- "grp_var": "infusionid",
- "callback": "hirid_rate_kg"
- }
- ],
- "miiv": [
- {
- "ids": 221289,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic": [
- {
- "ids": [30044, 30119, 30309],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221289,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic_demo": [
- {
- "ids": [30044, 30119, 30309],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221289,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "sic": [
- {
- "ids": 1502,
- "table": "medication",
- "sub_var": "DrugID",
- "val_var": "AmountPerMinute",
- "stop_var": "OffsetDrugEnd",
- "callback": "sic_rate_kg"
- }
- ]
- }
- },
- "epi60": {
- "concepts": ["epi_rate", "epi_dur"],
- "description": "epinephrine administration for min 1h",
- "category": "outcome",
- "interval": "00:01:00",
- "callback": "vaso60",
- "class": "rec_cncpt"
- },
- "esr": {
- "unit": ["mm/hr", "mm/1h"],
- "min": 0,
- "max": 200,
- "description": "erythrocyte sedimentation rate",
- "omopid": 4212065,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": [6808, 11902],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "hirid": [
- {
- "ids": 24000668,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51288,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51288,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51288,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ]
- }
- },
- "etco2": {
- "unit": ["mmHg", "mm Hg"],
- "min": 10,
- "max": 60,
- "description": "endtidal CO2",
- "omopid": 4353940,
- "category": "vitals",
- "sources": {
- "aumc": [
- {
- "ids": [6707, 8884, 8885, 9658, 12805, 12356],
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 7.6), 'mmHg', 'None|Geen')"
- }
- ],
- "hirid": [
- {
- "ids": [2200, 8290, 30010009],
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 228640,
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [1817, 228640],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [1817, 228640],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ]
- }
- },
- "ett_gcs": {
- "class": "lgl_cncpt",
- "description": "tracheostomy",
- "omopid": 4097216,
- "category": "respiratory",
- "target": "win_tbl",
- "sources": {
- "aumc": [
- {
- "ids": 6735,
- "table": "listitems",
- "sub_var": "itemid",
- "target": "ts_tbl",
- "callback": "combine_callbacks(\n transform_fun(comp_na(`==`, 'Geïntubeerd')),\n ts_to_win_tbl(mins(1L))\n )"
- }
- ],
- "eicu": [
- {
- "class": "fun_itm",
- "callback": "combine_callbacks(\n fwd_concept('rass'),\n transform_fun(comp_na(`<=`, -3)),\n ts_to_win_tbl(mins(360L))\n )"
- }
- ],
- "eicu_demo": [
- {
- "class": "fun_itm",
- "callback": "combine_callbacks(\n fwd_concept('rass'),\n transform_fun(comp_na(`<=`, -3)),\n ts_to_win_tbl(mins(360L))\n )"
- }
- ],
- "hirid": [
- {
- "class": "fun_itm",
- "callback": "combine_callbacks(\n fwd_concept('mech_vent'),\n transform_fun(comp_na(`==`, 'invasive'))\n )"
- }
- ],
- "miiv": [
- {
- "ids": "No Response-ETT",
- "table": "chartevents",
- "sub_var": "value",
- "target": "ts_tbl",
- "callback": "combine_callbacks(\n transform_fun(set_val(TRUE)),\n ts_to_win_tbl(mins(1L))\n )"
- }
- ],
- "mimic": [
- {
- "ids": ["1.0 ET/Trach", "No Response-ETT"],
- "table": "chartevents",
- "sub_var": "value",
- "target": "ts_tbl",
- "callback": "combine_callbacks(\n transform_fun(set_val(TRUE)),\n ts_to_win_tbl(mins(1L))\n )"
- }
- ],
- "mimic_demo": [
- {
- "ids": ["1.0 ET/Trach", "No Response-ETT"],
- "table": "chartevents",
- "sub_var": "value",
- "target": "ts_tbl",
- "callback": "combine_callbacks(\n transform_fun(set_val(TRUE)),\n ts_to_win_tbl(mins(1L))\n )"
- }
- ]
- }
- },
- "fgn": {
- "unit": "mg/dL",
- "min": 0,
- "max": 1500,
- "description": "fibrinogen",
- "omopid": 4094436,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": [6776, 9989, 10175],
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 100), 'mg/dL')"
- }
- ],
- "eicu": [
- {
- "ids": "fibrinogen",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "fibrinogen",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000536,
- "table": "observations",
- "sub_var": "variableid",
- "callback": "convert_unit(binary_op(`*`, 100), 'mg/dL')",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51214,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51214,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51214,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 344,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "fio2": {
- "unit": "%",
- "min": 21,
- "max": 100,
- "description": "fraction of inspired oxygen",
- "omopid": 4353936,
- "category": "blood gas",
- "sources": {
- "aumc": [
- {
- "ids": 12279,
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "FiO2",
- "table": "respiratorycharting",
- "sub_var": "respchartvaluelabel",
- "callback": "transform_fun(percent_as_numeric)"
- },
- {
- "ids": "FiO2",
- "table": "lab",
- "sub_var": "labname",
- "callback": "convert_unit(set_val(NA), '%', 'mm\\\\(hg\\\\)')"
- }
- ],
- "eicu_demo": [
- {
- "ids": "FiO2",
- "table": "respiratorycharting",
- "sub_var": "respchartvaluelabel",
- "callback": "transform_fun(percent_as_numeric)"
- },
- {
- "ids": "FiO2",
- "table": "lab",
- "sub_var": "labname",
- "callback": "convert_unit(set_val(NA), '%', 'mm\\\\(hg\\\\)')"
- }
- ],
- "hirid": [
- {
- "ids": 2010,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 223835,
- "table": "chartevents",
- "sub_var": "itemid"
- },
- {
- "ids": 50816,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [3420, 223835],
- "table": "chartevents",
- "sub_var": "itemid"
- },
- {
- "ids": 50816,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [3420, 223835],
- "table": "chartevents",
- "sub_var": "itemid"
- },
- {
- "ids": 50816,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 2283,
- "table": "data_float_h",
- "sub_var": "DataID"
- }
- ]
- }
- },
- "gcs": {
- "concepts": ["egcs", "mgcs", "vgcs", "tgcs", "ett_gcs"],
- "description": "Glasgow coma scale (non-sedated)",
- "omopid": 4093836,
- "category": "neurological",
- "aggregate": ["min", "min", "min", "min", "any"],
- "callback": "gcs",
- "class": "rec_cncpt"
- },
- "glu": {
- "unit": "mg/dL",
- "min": 0,
- "max": 1000,
- "description": "glucose",
- "omopid": 4144235,
- "category": "chemistry",
- "sources": {
- "aumc": [
- {
- "ids": [6833, 9557, 9947],
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 18.016), 'mg/dL')"
- }
- ],
- "eicu": [
- {
- "ids": "glucose",
- "table": "lab",
- "sub_var": "labname"
- },
- {
- "ids": "bedside glucose",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "glucose",
- "table": "lab",
- "sub_var": "labname"
- },
- {
- "ids": "bedside glucose",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": [20005110, 24000523, 24000585],
- "table": "observations",
- "sub_var": "variableid",
- "callback": "convert_unit(binary_op(`*`, 18.016), 'mg/dL')",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": [50809, 50931],
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [50809, 50931],
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [50809, 50931],
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": [348, 656],
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "hba1c": {
- "unit": "%",
- "description": "Hemoglobin A1C",
- "omopid": 4184637,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": [11812, 16166],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "miiv": [
- {
- "ids": 50852,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50852,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50852,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ]
- }
- },
- "hbco": {
- "description": "carboxyhemoglobin",
- "omopid": 4056787,
- "category": "blood gas",
- "sources": {
- "aumc": [
- {
- "ids": 11690,
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "Carboxyhemoglobin",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "Carboxyhemoglobin",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000526,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ]
- }
- },
- "hct": {
- "unit": "%",
- "min": 15,
- "max": 60,
- "description": "hematocrit",
- "omopid": 4151358,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": [6777, 11423, 11545],
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "transform_fun(binary_op(`*`, 100))"
- }
- ],
- "eicu": [
- {
- "ids": "Hct",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "Hct",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "miiv": [
- {
- "ids": 51221,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51221,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51221,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": [217, 682],
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "height": {
- "unit": "cm",
- "min": 10,
- "max": 230,
- "target": "id_tbl",
- "description": "patient height",
- "omopid": 607590,
- "category": "demographics",
- "sources": {
- "aumc": [
- {
- "val_var": "heightgroup",
- "table": "admissions",
- "callback": "apply_map(c(`159-` = 150, `160-169` = 165, `170-179` = 175, `180-189` = 185, `190+` = 200))",
- "class": "col_itm"
- }
- ],
- "eicu": [
- {
- "table": "patient",
- "val_var": "admissionheight",
- "class": "col_itm"
- }
- ],
- "eicu_demo": [
- {
- "table": "patient",
- "val_var": "admissionheight",
- "class": "col_itm"
- }
- ],
- "hirid": [
- {
- "ids": 10000450,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 226707,
- "table": "chartevents",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
- }
- ],
- "mimic": [
- {
- "ids": [920, 1394, 3485, 4187, 4188, 3486, 226707],
- "table": "chartevents",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
- }
- ],
- "mimic_demo": [
- {
- "ids": [920, 1394, 3485, 4187, 4188, 3486, 226707],
- "table": "chartevents",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
- }
- ],
- "sic": [
- {
- "table": "cases",
- "val_var": "HeightOnAdmission",
- "class": "col_itm"
- }
- ]
- }
- },
- "hgb": {
- "unit": "g/dL",
- "min": 4,
- "max": 18,
- "description": "hemoglobin",
- "omopid": 4118981,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": [6778, 9553, 9960, 10286, 19703],
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 1.611344), 'g/dL')"
- }
- ],
- "eicu": [
- {
- "ids": "Hgb",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "Hgb",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": [24000548, 24000836, 20000900],
- "table": "observations",
- "sub_var": "variableid",
- "callback": "convert_unit(binary_op(`*`, 0.1), 'g/dL', 'g/l')",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51222,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51222,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51222,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": [658, 289],
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "hr": {
- "unit": ["bpm", "/min"],
- "min": 0,
- "max": 300,
- "description": "heart rate",
- "omopid": 4239408,
- "category": "vitals",
- "sources": {
- "aumc": [
- {
- "ids": 6640,
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "table": "vitalperiodic",
- "val_var": "heartrate",
- "class": "col_itm"
- }
- ],
- "eicu_demo": [
- {
- "table": "vitalperiodic",
- "val_var": "heartrate",
- "class": "col_itm"
- }
- ],
- "hirid": [
- {
- "ids": 200,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 220045,
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [211, 220045],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [211, 220045],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 708,
- "table": "data_float_h",
- "sub_var": "DataID"
- }
- ]
- }
- },
- "inr_pt": {
- "description": "prothrombin time/international normalized ratio",
- "omopid": 4306239,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": 11893,
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- ],
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- }
- },
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- ],
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- {
- "regex": "^insulin (250.+)?\\(((ml|units)/hr)?\\)$",
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- ],
- "hirid": [
- {
- "ids": [15, 1000724],
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- "mimic": [
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- {
- "ids": [223258, 223260],
- "table": "inputevents_mv",
- "sub_var": "itemid",
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- "callback": "distribute_amount"
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- {
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- "table": "inputevents_mv",
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- ]
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- "omopid": 4207483,
- "category": "chemistry",
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- ],
- "hirid": [
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- "ids": [20000500, 24000520, 24000833, 24000867],
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- "table": "labevents",
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- "table": "laboratory",
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- ]
- }
- },
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- "unit": "mmol/L",
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- "max": 50,
- "description": "lactate",
- "omopid": 4191725,
- "category": "blood gas",
- "sources": {
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- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "lactate",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
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- {
- "ids": "lactate",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000524,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
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- "ids": 50813,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50813,
- "table": "labevents",
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- }
- ],
- "mimic_demo": [
- {
- "ids": 50813,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": [657, 454],
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "los_hosp": {
- "unit": "days",
- "min": 0,
- "target": "id_tbl",
- "description": "hospital length of stay",
- "omopid": 462369952,
- "category": "outcome",
- "sources": {
- "eicu": [
- {
- "callback": "los_callback",
- "win_type": "hadm",
- "class": "fun_itm"
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- ],
- "eicu_demo": [
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- ],
- "miiv": [
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- "callback": "los_callback",
- "win_type": "hadm",
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- ],
- "mimic": [
- {
- "callback": "los_callback",
- "win_type": "hadm",
- "class": "fun_itm"
- }
- ],
- "mimic_demo": [
- {
- "callback": "los_callback",
- "win_type": "hadm",
- "class": "fun_itm"
- }
- ]
- }
- },
- "los_icu": {
- "unit": "days",
- "min": 0,
- "target": "id_tbl",
- "description": "ICU length of stay",
- "category": "outcome",
- "sources": {
- "aumc": [
- {
- "callback": "los_callback",
- "win_type": "icustay",
- "class": "fun_itm"
- }
- ],
- "eicu": [
- {
- "callback": "los_callback",
- "win_type": "icustay",
- "class": "fun_itm"
- }
- ],
- "eicu_demo": [
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- "callback": "los_callback",
- "win_type": "icustay",
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- }
- ],
- "hirid": [
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- "callback": "los_callback",
- "win_type": "icustay",
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- }
- ],
- "miiv": [
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- "win_type": "icustay",
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- ],
- "mimic": [
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- "callback": "los_callback",
- "win_type": "icustay",
- "class": "fun_itm"
- }
- ],
- "mimic_demo": [
- {
- "callback": "los_callback",
- "win_type": "icustay",
- "class": "fun_itm"
- }
- ]
- }
- },
- "lymph": {
- "unit": "%",
- "min": 0,
- "max": 100,
- "description": "lymphocytes",
- "omopid": 4254663,
- "category": "hematology",
- "sources": {
- "aumc": [
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- "ids": 11846,
- "table": "numericitems",
- "sub_var": "itemid"
- },
- {
- "ids": 14258,
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "blood_cell_ratio"
- }
- ],
- "eicu": [
- {
- "ids": "-lymphs",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "-lymphs",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000480,
- "table": "observations",
- "sub_var": "variableid",
- "callback": "blood_cell_ratio",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
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- "ids": 51244,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51244,
- "table": "labevents",
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- ],
- "mimic_demo": [
- {
- "ids": 51244,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 223,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
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- ]
- }
- },
- "map": {
- "unit": ["mmHg", "mm Hg"],
- "min": 0,
- "max": 250,
- "description": "mean arterial pressure",
- "omopid": 4239021,
- "category": "vitals",
- "sources": {
- "aumc": [
- {
- "ids": 6642,
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "table": "vitalperiodic",
- "val_var": "systemicmean",
- "class": "col_itm"
- },
- {
- "table": "vitalaperiodic",
- "val_var": "noninvasivemean",
- "class": "col_itm"
- }
- ],
- "eicu_demo": [
- {
- "table": "vitalperiodic",
- "val_var": "systemicmean",
- "class": "col_itm"
- },
- {
- "table": "vitalaperiodic",
- "val_var": "noninvasivemean",
- "class": "col_itm"
- }
- ],
- "hirid": [
- {
- "ids": [110, 610],
- "table": "observations",
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- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": [220052, 220181, 225312],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [52, 443, 456, 6072, 220052, 220181, 225312],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [52, 443, 456, 6072, 220052, 220181, 225312],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": [703, 706],
- "table": "data_float_h",
- "sub_var": "DataID"
- }
- ]
- }
- },
- "mch": {
- "unit": "pg",
- "min": 0,
- "description": "mean corpuscular hemoglobin",
- "omopid": 4182871,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": 11679,
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 0.016113), 'pg')"
- }
- ],
- "eicu": [
- {
- "ids": "MCH",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "MCH",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000160,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51248,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51248,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51248,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 566,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "mchc": {
- "unit": "%",
- "min": 20,
- "max": 50,
- "description": "mean corpuscular hemoglobin concentration",
- "omopid": 4290193,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": 18666,
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 1.611), '%')"
- }
- ],
- "eicu": [
- {
- "ids": "MCHC",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "MCHC",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000170,
- "table": "observations",
- "sub_var": "variableid",
- "callback": "convert_unit(binary_op(`*`, 0.16114), '%')",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51249,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51249,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51249,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 290,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "mcv": {
- "unit": "fL",
- "min": 50,
- "max": 150,
- "description": "mean corpuscular volume",
- "omopid": 4016239,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": 9968,
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "MCV",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "MCV",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000150,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51250,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51250,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51250,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 286,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "mech_vent": {
- "class": "fct_cncpt",
- "target": "win_tbl",
- "levels": ["invasive", "noninvasive"],
- "description": "mechanical ventilation windows",
- "omopid": 4230167,
- "category": "respiratory",
- "sources": {
- "aumc": [
- {
- "ids": [9328, 10740, 12635],
- "table": "processitems",
- "sub_var": "itemid",
- "dur_var": "stop",
- "callback": "apply_map(c(`Beademen` = 'invasive',\n `Beademen non-invasief` = 'noninvasive',\n `Tracheostoma` = 'invasive'))"
- }
- ],
- "hirid": [
- {
- "ids": 15001552,
- "table": "observations",
- "sub_var": "variableid",
- "target": "ts_tbl",
- "interval": "00:01:00",
- "class": "hrd_itm",
- "callback": "combine_callbacks(hirid_vent,\n apply_map(c(`1` = 'invasive',\n `2` = 'invasive',\n `3` = 'noninvasive',\n `4` = 'noninvasive',\n `5` = 'noninvasive',\n `6` = 'noninvasive')))"
- }
- ],
- "miiv": [
- {
- "ids": [225792, 225794],
- "table": "procedureevents",
- "sub_var": "itemid",
- "dur_var": "endtime",
- "callback": "apply_map(c(`225792` = 'invasive',\n `225794` = 'noninvasive'),\n var = 'sub_var')"
- }
- ]
- }
- },
- "methb": {
- "unit": "%",
- "min": 0,
- "max": 100,
- "description": "methemoglobin",
- "omopid": 4204561,
- "category": "blood gas",
- "sources": {
- "aumc": [
- {
- "ids": 11692,
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "Methemoglobin",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "Methemoglobin",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000549,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50814,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50814,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50814,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ]
- }
- },
- "mews": {
- "concepts": ["sbp", "hr", "resp", "temp", "avpu"],
- "description": "modified early warning score",
- "omopid": 40484211,
- "category": "outcome",
- "callback": "mews_score",
- "class": "rec_cncpt"
- },
- "mg": {
- "unit": "mg/dL",
- "min": 0.5,
- "max": 5,
- "description": "magnesium",
- "omopid": 4243005,
- "category": "chemistry",
- "sources": {
- "aumc": [
- {
- "ids": [6839, 9952],
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 2.431), 'mg/dL')"
- }
- ],
- "eicu": [
- {
- "ids": "magnesium",
- "table": "lab",
- "sub_var": "labname",
- "callback": "convert_unit(binary_op(`/`, 1.215), 'mg/dL', 'mEq/L')"
- }
- ],
- "eicu_demo": [
- {
- "ids": "magnesium",
- "table": "lab",
- "sub_var": "labname",
- "callback": "convert_unit(binary_op(`/`, 1.215), 'mg/dL', 'mEq/L')"
- }
- ],
- "hirid": [
- {
- "ids": 24000230,
- "table": "observations",
- "sub_var": "variableid",
- "callback": "convert_unit(binary_op(`*`, 2.431), 'mg/dL')",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50960,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50960,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50960,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 468,
- "table": "laboratory",
- "sub_var": "LaboratoryID",
- "callback": "transform_fun(binary_op(`*`, 2.431))"
- }
- ]
- }
- },
- "mgcs": {
- "min": 1,
- "max": 6,
- "description": "GCS motor",
- "omopid": 4083352,
- "category": "neurological",
- "sources": {
- "aumc": [
- {
- "ids": 6734,
- "table": "listitems",
- "sub_var": "itemid",
- "callback": "apply_map( c(`Geen reactie` = 1, `Strekken` = 2, `Decortatie reflex (abnormaal buigen)` = 3, `Spastische reactie (terugtrekken)` = 4, `Localiseert pijn` = 5, `Volgt verbale commando's op` = 6) )"
- },
- {
- "ids": 13072,
- "table": "listitems",
- "sub_var": "itemid",
- "callback": "apply_map( c(`Geen reactie` = 1, `Strekken op pijn` = 2, `Abnormaal buigen bij pijn` = 3, `Terugtrekken bij pijn` = 4, `Localiseren pijn` = 5, `Voert opdrachten uit` = 6) )"
- }
- ],
- "eicu": [
- {
- "ids": "Motor",
- "table": "nursecharting",
- "sub_var": "nursingchartcelltypevalname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "Motor",
- "table": "nursecharting",
- "sub_var": "nursingchartcelltypevalname"
- }
- ],
- "hirid": [
- {
- "ids": 10000200,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 223901,
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [454, 223901],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [454, 223901],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ]
- }
- },
- "na": {
- "unit": ["mEq/L", "mmol/l"],
- "min": 110,
- "max": 165,
- "description": "sodium",
- "omopid": 4208938,
- "category": "chemistry",
- "sources": {
- "aumc": [
- {
- "ids": [6840, 9555, 9924, 10284],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "sodium",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "sodium",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": [20000400, 24000519, 24000658, 24000835, 24000866],
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
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- ],
- "miiv": [
- {
- "ids": 50983,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50983,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50983,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": [469, 686],
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "neut": {
- "unit": "%",
- "min": 0,
- "max": 100,
- "description": "neutrophils",
- "omopid": 4148615,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": [6786, 11856],
- "table": "numericitems",
- "sub_var": "itemid"
- },
- {
- "ids": 14254,
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "blood_cell_ratio"
- }
- ],
- "eicu": [
- {
- "ids": "-polys",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "-polys",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 24000550,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51256,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51256,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51256,
- "table": "labevents",
- "sub_var": "itemid"
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- ],
- "sic": [
- {
- "ids": 230,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "news": {
- "concepts": ["resp", "o2sat", "supp_o2", "temp", "sbp", "hr", "avpu"],
- "description": "national early warning score",
- "omopid": 44808550,
- "category": "outcome",
- "callback": "news_score",
- "class": "rec_cncpt"
- },
- "norepi_dur": {
- "description": "norepinephrine duration",
- "category": "medications",
- "aggregate": "max",
- "sources": {
- "aumc": [
- {
- "ids": 7229,
- "table": "drugitems",
- "sub_var": "itemid",
- "stop_var": "stop",
- "grp_var": "orderid",
- "callback": "aumc_dur"
- }
- ],
- "eicu": [
- {
- "regex": "^norepi",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_duration(gap_length = hours(5L))",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^norepi",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "callback": "eicu_duration(gap_length = hours(5L))",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": [1000462, 1000656, 1000657, 1000658],
- "table": "pharma",
- "sub_var": "pharmaid",
- "grp_var": "infusionid",
- "callback": "hirid_duration"
- }
- ],
- "miiv": [
- {
- "ids": 221906,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "mimic": [
- {
- "ids": [30047, 30120],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_incv"
- },
- {
- "ids": 221906,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "mimic_demo": [
- {
- "ids": [30047, 30120],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_incv"
- },
- {
- "ids": 221906,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "grp_var": "linkorderid",
- "callback": "mimic_dur_inmv"
- }
- ],
- "sic": [
- {
- "ids": [
- 1562
- ],
- "table": "medication",
- "sub_var": "DrugID",
- "stop_var": "OffsetDrugEnd",
- "callback": "sic_dur"
- }
- ]
- }
- },
- "norepi_equiv": {
- "description": "norepinephrine equivalents",
- "category": "medications",
- "concepts": ["epi_rate", "norepi_rate", "dopa_rate", "adh_rate", "phn_rate"],
- "callback": "norepi_equiv",
- "class": "rec_cncpt"
- },
- "norepi_rate": {
- "unit": ["mcg/kg/min", "mcgkgmin"],
- "min": 0,
- "max": 3,
- "description": "norepinephrine rate",
- "omopid": 1321341,
- "category": "medications",
- "sources": {
- "aumc": [
- {
- "ids": 7229,
- "table": "drugitems",
- "sub_var": "itemid",
- "rel_weight": "doserateperkg",
- "rate_uom": "doserateunit",
- "stop_var": "stop",
- "callback": "aumc_rate_kg"
- }
- ],
- "eicu": [
- {
- "regex": "^norepi.*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 32)",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^norepi.*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 32)",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": [1000462, 1000656, 1000657, 1000658],
- "table": "pharma",
- "sub_var": "pharmaid",
- "grp_var": "infusionid",
- "callback": "hirid_rate_kg"
- }
- ],
- "miiv": [
- {
- "ids": 221906,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic": [
- {
- "ids": [30047, 30120],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221906,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic_demo": [
- {
- "ids": [30047, 30120],
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221906,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "sic": [
- {
- "ids": 1562,
- "table": "medication",
- "sub_var": "DrugID",
- "val_var": "AmountPerMinute",
- "stop_var": "OffsetDrugEnd",
- "callback": "sic_rate_kg"
- }
- ]
- }
- },
- "norepi60": {
- "concepts": ["norepi_rate", "norepi_dur"],
- "description": "norepinephrine administration for min 1h",
- "category": "outcome",
- "interval": "00:01:00",
- "callback": "vaso60",
- "class": "rec_cncpt"
- },
- "o2sat": {
- "unit": ["%", "% Sat."],
- "min": 50,
- "max": 100,
- "description": "oxygen saturation",
- "omopid": 40483579,
- "category": "respiratory",
- "sources": {
- "aumc": [
- {
- "ids": [6709, 8903],
- "table": "numericitems",
- "sub_var": "itemid"
- },
- {
- "ids": 12311,
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "transform_fun(binary_op(`*`, 100))"
- }
- ],
- "eicu": [
- {
- "table": "vitalperiodic",
- "val_var": "sao2",
- "unit_val": "%",
- "class": "col_itm"
- },
- {
- "ids": "O2 Sat (%)",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "table": "vitalperiodic",
- "val_var": "sao2",
- "unit_val": "%",
- "class": "col_itm"
- },
- {
- "ids": "O2 Sat (%)",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": [4000, 8280, 20000800],
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": [220277, 226253, 50817],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [646, 220277, 226253, 50817],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [646, 220277, 226253, 50817],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 710,
- "table": "data_float_h",
- "sub_var": "DataID"
- }
- ]
- }
- },
- "pafi": {
- "concepts": ["po2", "fio2"],
- "description": "Horowitz index",
- "omopid": 4233883,
- "category": "respiratory",
- "aggregate": ["min", "max"],
- "callback": "pafi",
- "class": "rec_cncpt"
- },
- "pco2": {
- "unit": ["mmHg", "mm Hg"],
- "min": 10,
- "max": 150,
- "description": "CO2 partial pressure",
- "omopid": 4097882,
- "category": "blood gas",
- "sources": {
- "aumc": [
- {
- "ids": [6846, 9990, 21213],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "paCO2",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "paCO2",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 20001200,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50818,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50818,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50818,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 687,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "ph": {
- "min": 6.8,
- "max": 8,
- "description": "pH of blood",
- "omopid": 4097822,
- "category": "blood gas",
- "sources": {
- "aumc": [
- {
- "ids": [6848, 12310],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "pH",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "pH",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 20000300,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50820,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50820,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50820,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 688,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "phn_rate": {
- "unit": "mcg/kg/min",
- "description": "phenylephrine rate",
- "omopid": 1135766,
- "category": "medications",
- "sources": {
- "eicu": [
- {
- "regex": "^phenylephrine.*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 200)",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "regex": "^phenylephrine.*\\(.+\\)$",
- "table": "infusiondrug",
- "sub_var": "drugname",
- "weight_var": "patientweight",
- "callback": "eicu_rate_kg(ml_to_mcg = 200)",
- "class": "rgx_itm"
- }
- ],
- "miiv": [
- {
- "ids": 221749,
- "table": "inputevents",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic": [
- {
- "ids": 30127,
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "combine_callbacks(\n mimic_kg_rate, mimic_rate_cv)\n "
- },
- {
- "ids": 30128,
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221749,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ],
- "mimic_demo": [
- {
- "ids": 30127,
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "combine_callbacks(\n mimic_kg_rate, mimic_rate_cv)\n "
- },
- {
- "ids": 30128,
- "table": "inputevents_cv",
- "sub_var": "itemid",
- "grp_var": "linkorderid",
- "callback": "mimic_rate_cv"
- },
- {
- "ids": 221749,
- "table": "inputevents_mv",
- "sub_var": "itemid",
- "stop_var": "endtime",
- "callback": "mimic_rate_mv"
- }
- ]
- }
- },
- "phos": {
- "unit": "mg/dL",
- "min": 0,
- "max": 40,
- "description": "phosphate",
- "omopid": 4017907,
- "category": "chemistry",
- "sources": {
- "aumc": [
- {
- "ids": [6828, 9935],
- "table": "numericitems",
- "sub_var": "itemid",
- "callback": "convert_unit(binary_op(`*`, 3.097521), 'mg/dL')"
- }
- ],
- "eicu": [
- {
- "ids": "phosphate",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "phosphate",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 20002500,
- "table": "observations",
- "sub_var": "variableid",
- "callback": "convert_unit(binary_op(`*`, 3.097521), 'mg/dL')",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50970,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50970,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50970,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 471,
- "table": "laboratory",
- "sub_var": "LaboratoryID",
- "callback": "transform_fun(binary_op(`*`, 3.097521))"
- }
- ]
- }
- },
- "plt": {
- "unit": ["K/uL", "G/l"],
- "min": 5,
- "max": 1200,
- "description": "platelet count",
- "omopid": 4267147,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": [6797, 9964, 10409, 14252],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "platelets x 1000",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "platelets x 1000",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 20000110,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51265,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51265,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51265,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 314,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "po2": {
- "unit": ["mmHg", "mm Hg"],
- "min": 40,
- "max": 600,
- "description": "O2 partial pressure",
- "omopid": 4094581,
- "category": "blood gas",
- "sources": {
- "aumc": [
- {
- "ids": [7433, 9996, 21214],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "paO2",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "paO2",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 20000200,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 50821,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 50821,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 50821,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": [664, 689],
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "pt": {
- "unit": "sec",
- "min": 0,
- "description": "prothrombine time",
- "omopid": 4245261,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": 6789,
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "PT",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "PT",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "miiv": [
- {
- "ids": 51274,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51274,
- "table": "labevents",
- "sub_var": "itemid"
- }
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- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "urine": {
- "unit": "mL",
- "min": 0,
- "max": 2000,
- "aggregate": "sum",
- "description": "urine output",
- "omopid": 4264378,
- "category": "output",
- "sources": {
- "aumc": [
- {
- "ids": 8794,
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": ["Urine", "URINE CATHETER"],
- "table": "intakeoutput",
- "sub_var": "celllabel"
- },
- {
- "regex": "catheter.+output|output.+catheter",
- "table": "intakeoutput",
- "sub_var": "celllabel",
- "class": "rgx_itm"
- }
- ],
- "eicu_demo": [
- {
- "ids": ["Urine", "URINE CATHETER"],
- "table": "intakeoutput",
- "sub_var": "celllabel"
- },
- {
- "regex": "catheter.+output|output.+catheter",
- "table": "intakeoutput",
- "sub_var": "celllabel",
- "class": "rgx_itm"
- }
- ],
- "hirid": [
- {
- "ids": 30005110,
- "table": "observations",
- "sub_var": "variableid",
- "callback": "hirid_urine",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": [226557, 226558, 226559, 226560, 226561, 226563, 226564, 226565, 226566, 226567, 226584, 227510],
- "table": "outputevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [40055, 40056, 40057, 40065, 40069, 40085, 40086, 40094, 40096, 40405, 40428, 40473, 40715, 43175, 226557, 226558, 226559, 226560, 226561, 226563, 226564, 226565, 226566, 226567, 226584, 227510],
- "table": "outputevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [40055, 40056, 40057, 40065, 40069, 40085, 40086, 40094, 40096, 40405, 40428, 40473, 40715, 43175, 226557, 226558, 226559, 226560, 226561, 226563, 226564, 226565, 226566, 226567, 226584, 227510],
- "table": "outputevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 725,
- "table": "data_float_h",
- "sub_var": "DataID"
- }
- ]
- }
- },
- "urine24": {
- "concepts": "urine",
- "description": "urine output per 24h",
- "omopid": 4191836,
- "category": "output",
- "callback": "urine24",
- "class": "rec_cncpt"
- },
- "vaso_ind": {
- "concepts": ["dopa_dur", "norepi_dur", "dobu_dur", "epi_dur"],
- "description": "vasopressor indicator",
- "omopid": 3655896,
- "category": "medications",
- "callback": "vaso_ind",
- "class": "rec_cncpt"
- },
- "vent_end": {
- "class": "lgl_cncpt",
- "description": "ventilation end",
- "category": "respiratory",
- "sources": {
- "eicu": [
- {
- "table": "respiratorycare",
- "val_var": "ventendoffset",
- "callback": "vent_flag",
- "class": "col_itm"
- },
- {
- "table": "respiratorycare",
- "val_var": "priorventendoffset",
- "callback": "vent_flag",
- "class": "col_itm"
- },
- {
- "ids": ["off", "Off", "Suspended"],
- "table": "respiratorycharting",
- "sub_var": "respchartvalue",
- "val_var": "respchartvaluelabel",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "eicu_demo": [
- {
- "table": "respiratorycare",
- "val_var": "ventendoffset",
- "callback": "vent_flag",
- "class": "col_itm"
- },
- {
- "table": "respiratorycare",
- "val_var": "priorventendoffset",
- "callback": "vent_flag",
- "class": "col_itm"
- },
- {
- "ids": ["off", "Off", "Suspended"],
- "table": "respiratorycharting",
- "sub_var": "respchartvalue",
- "val_var": "respchartvaluelabel",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "mimic": [
- {
- "ids": [225468, 225477, 227194],
- "table": "procedureevents_mv",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- },
- {
- "ids": [467, 469, 226732],
- "table": "chartevents",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "mimic_demo": [
- {
- "ids": [225468, 225477, 227194],
- "table": "procedureevents_mv",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- },
- {
- "ids": [467, 469, 226732],
- "table": "chartevents",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ]
- }
- },
- "vent_ind": {
- "concepts": ["vent_start", "vent_end", "mech_vent"],
- "description": "ventilation durations",
- "omopid": 4230167,
- "category": "respiratory",
- "interval": "00:01:00",
- "callback": "vent_ind",
- "target": "win_tbl",
- "class": "rec_cncpt"
- },
- "vent_start": {
- "class": "lgl_cncpt",
- "description": "ventilation start",
- "category": "respiratory",
- "sources": {
- "eicu": [
- {
- "table": "respiratorycare",
- "val_var": "ventstartoffset",
- "callback": "vent_flag",
- "class": "col_itm"
- },
- {
- "table": "respiratorycare",
- "val_var": "priorventstartoffset",
- "callback": "vent_flag",
- "class": "col_itm"
- },
- {
- "ids": ["Start", "Continued", "respFlowPtVentData"],
- "table": "respiratorycharting",
- "sub_var": "respcharttypecat",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "eicu_demo": [
- {
- "table": "respiratorycare",
- "val_var": "ventstartoffset",
- "callback": "vent_flag",
- "class": "col_itm"
- },
- {
- "table": "respiratorycare",
- "val_var": "priorventstartoffset",
- "callback": "vent_flag",
- "class": "col_itm"
- },
- {
- "ids": ["Start", "Continued", "respFlowPtVentData"],
- "table": "respiratorycharting",
- "sub_var": "respcharttypecat",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "mimic": [
- {
- "ids": [1, 60, 218, 221, 223, 436, 437, 444, 445, 448, 449, 450, 459, 501, 502, 503, 505, 506, 535, 543, 639, 654, 667, 668, 669, 670, 671, 672, 681, 682, 683, 684, 686, 1211, 1340, 1486, 1600, 1655, 2000, 3459, 5865, 5866, 220339, 223848, 223849, 224419, 224684, 224685, 224686, 224687, 224695, 224696, 224697, 224700, 224701, 224702, 224703, 224704, 224705, 224706, 224707, 224709, 224738, 224746, 224747, 224750, 226873, 227187],
- "table": "chartevents",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ],
- "mimic_demo": [
- {
- "ids": [1, 60, 218, 221, 223, 436, 437, 444, 445, 448, 449, 450, 459, 501, 502, 503, 505, 506, 535, 543, 639, 654, 667, 668, 669, 670, 671, 672, 681, 682, 683, 684, 686, 1211, 1340, 1486, 1600, 1655, 2000, 3459, 5865, 5866, 220339, 223848, 223849, 224419, 224684, 224685, 224686, 224687, 224695, 224696, 224697, 224700, 224701, 224702, 224703, 224704, 224705, 224706, 224707, 224709, 224738, 224746, 224747, 224750, 226873, 227187],
- "table": "chartevents",
- "sub_var": "itemid",
- "callback": "transform_fun(set_val(TRUE))"
- }
- ]
- }
- },
- "vgcs": {
- "min": 1,
- "max": 5,
- "description": "GCS verbal",
- "omopid": 4084912,
- "category": "neurological",
- "sources": {
- "aumc": [
- {
- "ids": 6735,
- "table": "listitems",
- "sub_var": "itemid",
- "callback": "apply_map( c(`Geen reactie (geen zichtbare poging tot praten)` = 1, `Onbegrijpelijke geluiden` = 2, `Onduidelijke woorden (pogingen tot communicatie, maar onduidelijk)` = 3, `Verwarde conversatie` = 4, `Helder en adequaat (communicatie mogelijk)` = 5) )"
- },
- {
- "ids": 13066,
- "table": "listitems",
- "sub_var": "itemid",
- "callback": "apply_map( c(`Geen geluid` = 1, `Onverstaanbare woorden` = 2, `Onjuiste woorden` = 3, `Verwarde taal` = 4, `Georiënteerd` = 5) )"
- }
- ],
- "eicu": [
- {
- "ids": "Verbal",
- "table": "nursecharting",
- "sub_var": "nursingchartcelltypevalname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "Verbal",
- "table": "nursecharting",
- "sub_var": "nursingchartcelltypevalname"
- }
- ],
- "hirid": [
- {
- "ids": 10000100,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 223900,
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [723, 223900],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [723, 223900],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ]
- }
- },
- "wbc": {
- "unit": ["K/uL", "G/l"],
- "min": 0,
- "description": "white blood cell count",
- "omopid": 4298431,
- "category": "hematology",
- "sources": {
- "aumc": [
- {
- "ids": [6779, 9965],
- "table": "numericitems",
- "sub_var": "itemid"
- }
- ],
- "eicu": [
- {
- "ids": "WBC x 1000",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "eicu_demo": [
- {
- "ids": "WBC x 1000",
- "table": "lab",
- "sub_var": "labname"
- }
- ],
- "hirid": [
- {
- "ids": 20000700,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 51301,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": 51301,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": 51301,
- "table": "labevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "ids": 301,
- "table": "laboratory",
- "sub_var": "LaboratoryID"
- }
- ]
- }
- },
- "weight": {
- "unit": "kg",
- "min": 1,
- "max": 500,
- "target": "id_tbl",
- "description": "patient weight",
- "omopid": 4099154,
- "category": "demographics",
- "sources": {
- "aumc": [
- {
- "val_var": "weightgroup",
- "table": "admissions",
- "callback": "apply_map(c(`59-` = 50, `60-69` = 65, `70-79` = 75, `80-89` = 85, `90-99` = 95, `100-109` = 105, `110+` = 120))",
- "class": "col_itm"
- }
- ],
- "eicu": [
- {
- "table": "patient",
- "val_var": "admissionweight",
- "class": "col_itm"
- }
- ],
- "eicu_demo": [
- {
- "table": "patient",
- "val_var": "admissionweight",
- "class": "col_itm"
- }
- ],
- "hirid": [
- {
- "ids": 10000400,
- "table": "observations",
- "sub_var": "variableid",
- "class": "hrd_itm"
- }
- ],
- "miiv": [
- {
- "ids": 226512,
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic": [
- {
- "ids": [762, 4183, 226512],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "mimic_demo": [
- {
- "ids": [762, 4183, 226512],
- "table": "chartevents",
- "sub_var": "itemid"
- }
- ],
- "sic": [
- {
- "table": "cases",
- "val_var": "WeightOnAdmission",
- "class": "col_itm",
- "callback": "transform_fun(binary_op(`/`, 1000))"
- }
- ]
- }
- }
-}
diff --git a/inst/extdata/config/concept-dict/blood_gas.json b/inst/extdata/config/concept-dict/blood_gas.json
new file mode 100644
index 00000000..2b536a4c
--- /dev/null
+++ b/inst/extdata/config/concept-dict/blood_gas.json
@@ -0,0 +1,810 @@
+{
+ "be": {
+ "unit": [
+ "mEq/L",
+ "mmol/l"
+ ],
+ "min": -25,
+ "max": 25,
+ "description": "base excess",
+ "omopid": 4284393,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6807,
+ 9994
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "dir_var": "tag",
+ "callback": "aumc_bxs"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "Base Excess",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "Base Excess",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20001300,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50802,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50802,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50802,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [668, 449],
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5211,
+ 5249
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "cai": {
+ "unit": "mmol/L",
+ "min": 0.5,
+ "max": 2,
+ "description": "calcium ionized",
+ "omopid": 46272910,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6815,
+ 8915,
+ 9560,
+ 9561,
+ 10267
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "ionized calcium",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "ionized calcium",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000522,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50808,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50808,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50808,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [655, 452],
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "ids": 5215,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "fio2": {
+ "unit": "%",
+ "min": 21,
+ "max": 100,
+ "description": "fraction of inspired oxygen",
+ "omopid": 4353936,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 12279,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "FiO2",
+ "table": "respiratorycharting",
+ "sub_var": "respchartvaluelabel",
+ "callback": "transform_fun(percent_as_numeric)"
+ },
+ {
+ "ids": "FiO2",
+ "table": "lab",
+ "sub_var": "labname",
+ "callback": "convert_unit(set_val(NA), '%', 'mm\\\\(hg\\\\)')"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "FiO2",
+ "table": "respiratorycharting",
+ "sub_var": "respchartvaluelabel",
+ "callback": "transform_fun(percent_as_numeric)"
+ },
+ {
+ "ids": "FiO2",
+ "table": "lab",
+ "sub_var": "labname",
+ "callback": "convert_unit(set_val(NA), '%', 'mm\\\\(hg\\\\)')"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 2010,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 223835,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": 50816,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 3420,
+ 223835
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": 50816,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 3420,
+ 223835
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": 50816,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 2283,
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ },
+ {
+ "ids": 684,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "ids": 5222,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+
+ ]
+ }
+ },
+ "hbco": {
+ "description": "carboxyhemoglobin",
+ "omopid": 4056787,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 11690,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "Carboxyhemoglobin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "Carboxyhemoglobin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000526,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [196, 660],
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5219
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "lact": {
+ "unit": "mmol/L",
+ "min": 0,
+ "max": 50,
+ "description": "lactate",
+ "omopid": 4191725,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6837,
+ 9580,
+ 10053
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "lactate",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "lactate",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000524,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50813,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50813,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50813,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [
+ 657,
+ 465,
+ 454
+ ],
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5227
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "methb": {
+ "unit": "%",
+ "min": 0,
+ "max": 100,
+ "description": "methemoglobin",
+ "omopid": 4204561,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 11692,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "Methemoglobin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "Methemoglobin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000549,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50814,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50814,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50814,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 661,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5228
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "pco2": {
+ "unit": [
+ "mmHg",
+ "mm Hg"
+ ],
+ "min": 10,
+ "max": 150,
+ "description": "CO2 partial pressure",
+ "omopid": 4097882,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6846,
+ 9990,
+ 21213
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "paCO2",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "paCO2",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20001200,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50818,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50818,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50818,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 687,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5235,
+ 5236
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "ph": {
+ "min": 6.8,
+ "max": 8,
+ "description": "pH of blood",
+ "omopid": 4097822,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6848,
+ 12310
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "pH",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "pH",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20000300,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50820,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50820,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50820,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 688,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5237,
+ 5238
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "po2": {
+ "unit": [
+ "mmHg",
+ "mm Hg"
+ ],
+ "min": 40,
+ "max": 600,
+ "description": "O2 partial pressure",
+ "omopid": 4094581,
+ "category": "blood gas",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 7433,
+ 9996,
+ 21214
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "paO2",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "paO2",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20000200,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50821,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50821,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50821,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [
+ 664,
+ 689
+ ],
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5239,
+ 5244,
+ 5242
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "tco2": {
+ "unit": "mEq/L",
+ "min": 5,
+ "max": 60,
+ "description": "totcal CO2",
+ "omopid": 4193415,
+ "category": "blood gas",
+ "sources": {
+ "eicu": [
+ {
+ "ids": "Total CO2",
+ "table": "lab",
+ "sub_var": "labname",
+ "callback": "convert_unit(set_val(NA), 'mEq/L', 'lpm')"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "Total CO2",
+ "table": "lab",
+ "sub_var": "labname",
+ "callback": "convert_unit(set_val(NA), 'mEq/L', 'lpm')"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50804,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50804,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50804,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": [
+ {
+ "ids": 5256,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/chemistry.json b/inst/extdata/config/concept-dict/chemistry.json
new file mode 100644
index 00000000..12e92d91
--- /dev/null
+++ b/inst/extdata/config/concept-dict/chemistry.json
@@ -0,0 +1,1767 @@
+{
+ "alb": {
+ "unit": "g/dL",
+ "min": 0,
+ "max": 6,
+ "description": "albumin",
+ "omopid": 4017497,
+ "category": "chemistry",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6801,
+ 9937
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 0.1), 'g/dL')"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "albumin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "albumin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000605,
+ "table": "observations",
+ "sub_var": "variableid",
+ "callback": "convert_unit(binary_op(`*`, 0.1), 'g/dL')",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50862,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50862,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50862,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 287,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5024,
+ 6465
+ ],
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 0.1), 'g/dL')"
+ }
+ ]
+ }
+ },
+ "alp": {
+ "unit": [
+ "IU/L",
+ "U/l"
+ ],
+ "min": 0,
+ "description": "alkaline phosphatase",
+ "omopid": 4275206,
+ "category": "chemistry",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6803,
+ 11984
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "alkaline phos.",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "alkaline phos.",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20002700,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50863,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50863,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50863,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 609,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5025
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "alt": {
+ "unit": [
+ "IU/L",
+ "U/l"
+ ],
+ "min": 0,
+ "description": "alanine aminotransferase",
+ "omopid": 4146380,
+ "category": "chemistry",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6800,
+ 11978
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "ALT (SGPT)",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "ALT (SGPT)",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20002600,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50861,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50861,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50861,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 617,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "ids": [5026, 5195],
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "ast": {
+ "unit": [
+ "IU/L",
+ "U/l"
+ ],
+ "min": 0,
+ "description": "aspartate aminotransferase",
+ "omopid": 4263457,
+ "category": "chemistry",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6806,
+ 11990
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "AST (SGOT)",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "AST (SGOT)",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000330,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50878,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50878,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50878,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 616,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5031
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "bicar": {
+ "unit": [
+ "mEq/L",
+ "mmol/l"
+ ],
+ "min": 5,
+ "max": 50,
+ "description": "bicarbonate",
+ "omopid": 4194291,
+ "category": "chemistry",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6810,
+ 9992
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "bicarbonate",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "bicarbonate",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20004200,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50882,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50882,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50882,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 456,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5248
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "bili": {
+ "unit": "mg/dL",
+ "min": 0,
+ "max": 100,
+ "description": "total bilirubin",
+ "omopid": 4118986,
+ "category": "chemistry",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6813,
+ 9945
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "total bilirubin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "total bilirubin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20004300,
+ "table": "observations",
+ "sub_var": "variableid",
+ "callback": "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50885,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50885,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50885,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 333,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5075
+ ],
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')"
+ }
+ ]
+ }
+ },
+ "bili_dir": {
+ "unit": "mg/dL",
+ "min": 0,
+ "max": 50,
+ "description": "bilirubin direct",
+ "omopid": 4216632,
+ "category": "chemistry",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6812,
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "direct bilirubin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "direct bilirubin",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000560,
+ "table": "observations",
+ "sub_var": "variableid",
+ "callback": "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 50883,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 50883,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 50883,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 332,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5042
+ ],
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')"
+ }
+ ]
+ }
+ },
+ "bun": {
+ "unit": "mg/dL",
+ "min": 0,
+ "max": 200,
+ "description": "blood urea nitrogen",
+ "omopid": 4017361,
+ "category": "chemistry",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6850,
+ 9943
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 2.8), 'mg/dL')"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "BUN",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "BUN",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20004100,
+ "table": "observations",
+ "sub_var": "variableid",
+ "callback": "convert_unit(binary_op(`*`, 2.8), 'mg/dL')",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 51006,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 51006,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 51006,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5224
+ ],
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 2.8), 'mg/dL')"
+ }
+ ]
+ }
+ },
+ "ca": {
+ "unit": "mg/dL",
+ "min": 4,
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+ ],
+ "mimic_demo": [
+ {
+ "ids": 51003,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 481,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "callback": "convert_unit(binary_op(`/`, 1000), 'ng/mL', 'ng/L')",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 6525
+ ],
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`/`, 1000), 'ng/mL', 'pg/m')"
+ },
+ {
+ "table": "labevents",
+ "ids": [
+ 6525
+ ],
+ "sub_var": "itemid",
+ "val_var": "value",
+ "callback": "apply_map(c(`<0.003` = 0.003))"
+ }
+ ]
+ }
+ },
+ "tri": {
+ "unit": "ng/mL",
+ "min": 0,
+ "description": "troponin I",
+ "omopid": 4007805,
+ "category": "chemistry",
+ "sources": {
+ "eicu": [
+ {
+ "ids": "troponin - I",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "troponin - I",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 51002,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 51002,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 51002,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 270,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 6192
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/demographics.json b/inst/extdata/config/concept-dict/demographics.json
new file mode 100644
index 00000000..f4723d6d
--- /dev/null
+++ b/inst/extdata/config/concept-dict/demographics.json
@@ -0,0 +1,423 @@
+{
+ "adm": {
+ "target": "id_tbl",
+ "levels": [
+ "med",
+ "surg",
+ "other"
+ ],
+ "class": "fct_cncpt",
+ "description": "patient admission type",
+ "category": "demographics",
+ "sources": {
+ "aumc": [
+ {
+ "val_var": "specialty",
+ "table": "admissions",
+ "callback": "apply_map( c(Cardiochirurgie = 'surg', Cardiologie = 'med', ders = 'other', Gynaecologie = 'other', `Heelkunde Gastro-enterologie` = 'surg', `Heelkunde Longen/Oncologie` = 'surg', `Heelkunde Oncologie` = 'surg', Hematologie = 'med', `Intensive Care Volwassenen` = 'other', Inwendig = 'med', `Keel, Neus & Oorarts` = 'surg', Longziekte = 'med', `Maag-,Darm-,Leverziekten` = 'med', Mondheelkunde = 'surg', Nefrologie = 'med', Neurochirurgie = 'surg', Neurologie = 'med', Obstetrie = 'other', `Oncologie Inwendig` = 'med', Oogheelkunde = 'surg', Orthopedie = 'surg', `Plastische chirurgie` = 'surg', Reumatologie = 'med', Traumatologie = 'surg', Urologie = 'surg', Vaatchirurgie = 'surg', Verloskunde = 'other'))",
+ "class": "col_itm"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "admissiondx",
+ "val_var": "admitdxpath",
+ "callback": "eicu_adx",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "admissiondx",
+ "val_var": "admitdxpath",
+ "callback": "eicu_adx",
+ "class": "col_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "table": "services",
+ "val_var": "curr_service",
+ "callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
+ "class": "col_itm"
+ }
+ ],
+ "mimic": [
+ {
+ "table": "services",
+ "val_var": "curr_service",
+ "callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
+ "class": "col_itm"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "table": "services",
+ "val_var": "curr_service",
+ "callback": "apply_map(\n c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',\n VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',\n ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',\n NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',\n OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')\n )",
+ "class": "col_itm"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "age": {
+ "unit": "years",
+ "min": 0,
+ "max": 100,
+ "target": "id_tbl",
+ "description": "patient age",
+ "omopid": 4314456,
+ "category": "demographics",
+ "sources": {
+ "aumc": [
+ {
+ "val_var": "agegroup",
+ "table": "admissions",
+ "callback": "apply_map(c(`18-39` = 30, `40-49` = 45, `50-59` = 55, `60-69` = 65, `70-79` = 75, `80+` = 90))",
+ "class": "col_itm"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "patient",
+ "val_var": "age",
+ "callback": "transform_fun(eicu_age)",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "patient",
+ "val_var": "age",
+ "callback": "transform_fun(eicu_age)",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "table": "general",
+ "val_var": "age",
+ "class": "col_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "table": "patients",
+ "val_var": "anchor_age",
+ "class": "col_itm"
+ }
+ ],
+ "mimic": [
+ {
+ "table": "patients",
+ "val_var": "dob",
+ "callback": "transform_fun(mimic_age)",
+ "class": "col_itm"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "table": "patients",
+ "val_var": "dob",
+ "callback": "transform_fun(mimic_age)",
+ "class": "col_itm"
+ }
+ ],
+ "sic": [
+ {
+ "table": "cases",
+ "val_var": "ageonadmission",
+ "class": "col_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "patients",
+ "val_var": "dob",
+ "callback": "transform_fun(mimic_age)",
+ "class": "col_itm"
+ }
+ ]
+ }
+ },
+ "bmi": {
+ "concepts": [
+ "weight",
+ "height"
+ ],
+ "description": "patient body mass index",
+ "omopid": 4245997,
+ "category": "demographics",
+ "callback": "bmi",
+ "target": "id_tbl",
+ "class": "rec_cncpt"
+ },
+ "height": {
+ "unit": "cm",
+ "min": 10,
+ "max": 230,
+ "target": "id_tbl",
+ "description": "patient height",
+ "omopid": 607590,
+ "category": "demographics",
+ "sources": {
+ "aumc": [
+ {
+ "val_var": "heightgroup",
+ "table": "admissions",
+ "callback": "apply_map(c(`159-` = 150, `160-169` = 165, `170-179` = 175, `180-189` = 185, `190+` = 200))",
+ "class": "col_itm"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "patient",
+ "val_var": "admissionheight",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "patient",
+ "val_var": "admissionheight",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 10000450,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 226707,
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 920,
+ 1394,
+ 3485,
+ 4187,
+ 4188,
+ 3486,
+ 226707
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 920,
+ 1394,
+ 3485,
+ 4187,
+ 4188,
+ 3486,
+ 226707
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')"
+ }
+ ],
+ "sic": [
+ {
+ "table": "cases",
+ "val_var": "heightonadmission",
+ "class": "col_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ 1013
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "sex": {
+ "target": "id_tbl",
+ "levels": [
+ "Female",
+ "Male"
+ ],
+ "class": "fct_cncpt",
+ "description": "patient sex",
+ "omopid": 37116947,
+ "category": "demographics",
+ "sources": {
+ "aumc": [
+ {
+ "val_var": "gender",
+ "table": "admissions",
+ "callback": "apply_map(c(Vrouw = 'Female', Man = 'Male'))",
+ "class": "col_itm"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "patient",
+ "val_var": "gender",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "patient",
+ "val_var": "gender",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "table": "general",
+ "val_var": "sex",
+ "callback": "apply_map(c(M = 'Male', F = 'Female'))",
+ "class": "col_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "table": "patients",
+ "val_var": "gender",
+ "callback": "apply_map(c(M = 'Male', F = 'Female'))",
+ "class": "col_itm"
+ }
+ ],
+ "mimic": [
+ {
+ "table": "patients",
+ "val_var": "gender",
+ "callback": "apply_map(c(M = 'Male', F = 'Female'))",
+ "class": "col_itm"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "table": "patients",
+ "val_var": "gender",
+ "callback": "apply_map(c(M = 'Male', F = 'Female'))",
+ "class": "col_itm"
+ }
+ ],
+ "sic": [
+ {
+ "table": "cases",
+ "val_var": "sex",
+ "class": "col_itm",
+ "callback": "apply_map(c(`735` = 'Male', `736` = 'Female'))"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "patients",
+ "val_var": "gender",
+ "class": "col_itm",
+ "callback": "apply_map(c(M = 'Male', F = 'Female'))"
+ }
+ ]
+ }
+ },
+ "weight": {
+ "unit": "kg",
+ "min": 1,
+ "max": 500,
+ "target": "id_tbl",
+ "description": "patient weight",
+ "omopid": 4099154,
+ "category": "demographics",
+ "sources": {
+ "aumc": [
+ {
+ "val_var": "weightgroup",
+ "table": "admissions",
+ "callback": "apply_map(c(`59-` = 50, `60-69` = 65, `70-79` = 75, `80-89` = 85, `90-99` = 95, `100-109` = 105, `110+` = 120))",
+ "class": "col_itm"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "patient",
+ "val_var": "admissionweight",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "patient",
+ "val_var": "admissionweight",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 10000400,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 226512,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 762,
+ 4183,
+ 226512
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 762,
+ 4183,
+ 226512
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "table": "cases",
+ "val_var": "weightonadmission",
+ "class": "col_itm",
+ "callback": "transform_fun(binary_op(`/`, 1000))"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ 1014
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/hematology.json b/inst/extdata/config/concept-dict/hematology.json
new file mode 100644
index 00000000..735e071b
--- /dev/null
+++ b/inst/extdata/config/concept-dict/hematology.json
@@ -0,0 +1,1491 @@
+{
+ "basos": {
+ "unit": "%",
+ "min": 0,
+ "max": 50,
+ "description": "basophils",
+ "omopid": 4172647,
+ "category": "hematology",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 11710,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": 14256,
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "blood_cell_ratio"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "-basos",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "-basos",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 51146,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 51146,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 51146,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 174,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ },
+ {
+ "ids": 295,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "callback": "blood_cell_ratio",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5492
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "bnd": {
+ "unit": "%",
+ "description": "band form neutrophils",
+ "omopid": 4100147,
+ "category": "hematology",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6796,
+ 11586
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "-bands",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "-bands",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000557,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 51144,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 51144,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 51144,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "eos": {
+ "unit": "%",
+ "min": 0,
+ "max": 50,
+ "description": "eosinophils",
+ "omopid": 4216098,
+ "category": "hematology",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6773,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": 9967,
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "blood_cell_ratio"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "-eos",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "-eos",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 51200,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 51200,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 51200,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 197,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ },
+ {
+ "ids": 299,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "callback": "blood_cell_ratio",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 5002
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "esr": {
+ "unit": [
+ "mm/hr",
+ "mm/1h"
+ ],
+ "min": 0,
+ "max": 200,
+ "description": "erythrocyte sedimentation rate",
+ "omopid": 4212065,
+ "category": "hematology",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6808,
+ 11902
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000668,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 51288,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 51288,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 51288,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "fgn": {
+ "unit": "mg/dL",
+ "min": 0,
+ "max": 1500,
+ "description": "fibrinogen",
+ "omopid": 4094436,
+ "category": "hematology",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6776,
+ 9989,
+ 10175
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 100), 'mg/dL')"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "fibrinogen",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "fibrinogen",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 24000536,
+ "table": "observations",
+ "sub_var": "variableid",
+ "callback": "convert_unit(binary_op(`*`, 100), 'mg/dL')",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 51214,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 51214,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 51214,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 344,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "hba1c": {
+ "unit": "%",
+ "description": "Hemoglobin A1C",
+ "omopid": 4184637,
+ "category": "hematology",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 11812,
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+ "ids": "WBC x 1000",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "WBC x 1000",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 20000700,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 51301,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 51301,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 51301,
+ "table": "labevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 301,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "labevents",
+ "ids": [
+ 6516
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/medications.json b/inst/extdata/config/concept-dict/medications.json
new file mode 100644
index 00000000..770deb8f
--- /dev/null
+++ b/inst/extdata/config/concept-dict/medications.json
@@ -0,0 +1,1845 @@
+{
+ "abx": {
+ "class": "lgl_cncpt",
+ "description": "antibiotics",
+ "omopid": 4085730,
+ "category": "medications",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 2,
+ 13,
+ 19,
+ 24,
+ 28,
+ 29,
+ 57,
+ 59,
+ 82,
+ 103,
+ 240,
+ 247,
+ 333,
+ 1133,
+ 1199,
+ 1300,
+ 1371,
+ 1795,
+ 2284,
+ 2834,
+ 3237,
+ 3741,
+ 5576,
+ 6834,
+ 6847,
+ 6871,
+ 6919,
+ 6948,
+ 6953,
+ 6958,
+ 7044,
+ 7064,
+ 7185,
+ 7187,
+ 7208,
+ 7227,
+ 7235,
+ 8064,
+ 8394,
+ 8942,
+ 9029,
+ 9030,
+ 9052,
+ 9070,
+ 9117,
+ 9128,
+ 9133,
+ 9142,
+ 9151,
+ 9152,
+ 12262,
+ 12389,
+ 12398,
+ 12956,
+ 12997,
+ 13057,
+ 13094,
+ 13102,
+ 15591,
+ 18860,
+ 19137,
+ 19773,
+ 20563,
+ 23166,
+ 24241,
+ 25776,
+ 27617,
+ 29321
+ ],
+ "table": "drugitems",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "eicu": [
+ {
+ "regex": "bactrim|cipro|flagyl|metronidazole|zithromax|zosyn|(((amika|cleo|ofloxa)|(azithro|clinda|tobra|vanco)my)c|(ampi|oxa|peni|pipera)cill|cefazol|levaqu|rifamp)in",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "callback": "transform_fun(set_val(TRUE))",
+ "class": "rgx_itm"
+ },
+ {
+ "regex": "cipro|flagyl|maxipime|metronidazole|tazobactam|zosyn|cef(azolin|epime)|(((azithro|clinda|vanco)my|ofloxa|vanco)c|levaqu|piperacill|roceph)in",
+ "table": "medication",
+ "sub_var": "drugname",
+ "callback": "transform_fun(set_val(TRUE))",
+ "class": "rgx_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "regex": "bactrim|cipro|flagyl|metronidazole|zithromax|zosyn|(((amika|cleo|ofloxa)|(azithro|clinda|tobra|vanco)my)c|(ampi|oxa|peni|pipera)cill|cefazol|levaqu|rifamp)in",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "callback": "transform_fun(set_val(TRUE))",
+ "class": "rgx_itm"
+ },
+ {
+ "regex": "cipro|flagyl|maxipime|metronidazole|tazobactam|zosyn|cef(azolin|epime)|(((azithro|clinda|vanco)my|ofloxa|vanco)c|levaqu|piperacill|roceph)in",
+ "table": "medication",
+ "sub_var": "drugname",
+ "callback": "transform_fun(set_val(TRUE))",
+ "class": "rgx_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 163,
+ 176,
+ 181,
+ 186,
+ 189,
+ 300,
+ 326,
+ 331,
+ 351,
+ 405,
+ 1000234,
+ 1000272,
+ 1000273,
+ 1000274,
+ 1000284,
+ 1000299,
+ 1000300,
+ 1000302,
+ 1000304,
+ 1000305,
+ 1000306,
+ 1000315,
+ 1000317,
+ 1000318,
+ 1000320,
+ 1000321,
+ 1000322,
+ 1000335,
+ 1000348,
+ 1000352,
+ 1000363,
+ 1000365,
+ 1000390,
+ 1000407,
+ 1000408,
+ 1000424,
+ 1000425,
+ 1000426,
+ 1000437,
+ 1000483,
+ 1000507,
+ 1000508,
+ 1000518,
+ 1000519,
+ 1000549,
+ 1000601,
+ 1000648,
+ 1000666,
+ 1000670,
+ 1000671,
+ 1000760,
+ 1000781,
+ 1000791,
+ 1000797,
+ 1000812,
+ 1000825,
+ 1000829,
+ 1000830,
+ 1000837,
+ 1000838,
+ 1000854,
+ 1000855,
+ 1000893,
+ 1000894,
+ 1001005,
+ 1001068,
+ 1001075,
+ 1001079,
+ 1001084,
+ 1001086,
+ 1001095,
+ 1001096,
+ 1001097,
+ 1001098,
+ 1001168,
+ 1001169,
+ 1001170,
+ 1001171,
+ 1001173,
+ 1001193,
+ 1001198
+ ],
+ "table": "pharma",
+ "sub_var": "pharmaid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "miiv": [
+ {
+ "regex": "aztreonam|bactrim|cephalexin|chloramphenicol|cipro|flagyl|metronidazole|nitrofurantoin|tazobactam|rifampin|sulfadiazine|timentin|trimethoprim|(amika|gentami|vanco)cin|(amoxi|ampi|dicloxa|naf|oxa|peni|pipera)cillin|(azithro|clarithro|erythro|clinda|strepto|tobra|vanco)mycin|cef(azolin|tazidime|adroxil|epime|otetan|otaxime|podoxime|uroxime)|(doxy|mino|tetra)cycline|(levofl|moxifl|ofl)oxacin|macro(bid|dantin)|(una|zo)syn",
+ "table": "prescriptions",
+ "sub_var": "drug",
+ "callback": "transform_fun(set_val(TRUE))",
+ "class": "rgx_itm"
+ },
+ {
+ "ids": [
+ 225798,
+ 225837,
+ 225838,
+ 225840,
+ 225842,
+ 225843,
+ 225844,
+ 225845,
+ 225847,
+ 225848,
+ 225850,
+ 225851,
+ 225853,
+ 225855,
+ 225857,
+ 225859,
+ 225860,
+ 225862,
+ 225863,
+ 225865,
+ 225866,
+ 225868,
+ 225869,
+ 225871,
+ 225873,
+ 225875,
+ 225876,
+ 225877,
+ 225879,
+ 225881,
+ 225882,
+ 225883,
+ 225884,
+ 225885,
+ 225886,
+ 225888,
+ 225889,
+ 225890,
+ 225892,
+ 225893,
+ 225895,
+ 225896,
+ 225897,
+ 225898,
+ 225899,
+ 225900,
+ 225902,
+ 225903,
+ 225905,
+ 227691,
+ 228003
+ ],
+ "table": "inputevents",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "mimic": [
+ {
+ "regex": "aztreonam|bactrim|cephalexin|chloramphenicol|cipro|flagyl|metronidazole|nitrofurantoin|tazobactam|rifampin|sulfadiazine|timentin|trimethoprim|(amika|gentami|vanco)cin|(amoxi|ampi|dicloxa|naf|oxa|peni|pipera)cillin|(azithro|clarithro|erythro|clinda|strepto|tobra|vanco)mycin|cef(azolin|tazidime|adroxil|epime|otetan|otaxime|podoxime|uroxime)|(doxy|mino|tetra)cycline|(levofl|moxifl|ofl)oxacin|macro(bid|dantin)|(una|zo)syn",
+ "table": "prescriptions",
+ "sub_var": "drug",
+ "interval": "00:01:00",
+ "callback": "mimic_abx_presc",
+ "class": "rgx_itm"
+ },
+ {
+ "ids": [
+ 225798,
+ 225837,
+ 225838,
+ 225840,
+ 225842,
+ 225843,
+ 225844,
+ 225845,
+ 225847,
+ 225848,
+ 225850,
+ 225851,
+ 225853,
+ 225855,
+ 225857,
+ 225859,
+ 225860,
+ 225862,
+ 225863,
+ 225865,
+ 225866,
+ 225868,
+ 225869,
+ 225871,
+ 225873,
+ 225875,
+ 225876,
+ 225877,
+ 225879,
+ 225881,
+ 225882,
+ 225883,
+ 225884,
+ 225885,
+ 225886,
+ 225888,
+ 225889,
+ 225890,
+ 225892,
+ 225893,
+ 225895,
+ 225896,
+ 225897,
+ 225898,
+ 225899,
+ 225900,
+ 225902,
+ 225903,
+ 225905,
+ 227691,
+ 228003
+ ],
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "regex": "aztreonam|bactrim|cephalexin|chloramphenicol|cipro|flagyl|metronidazole|nitrofurantoin|tazobactam|rifampin|sulfadiazine|timentin|trimethoprim|(amika|gentami|vanco)cin|(amoxi|ampi|dicloxa|naf|oxa|peni|pipera)cillin|(azithro|clarithro|erythro|clinda|strepto|tobra|vanco)mycin|cef(azolin|tazidime|adroxil|epime|otetan|otaxime|podoxime|uroxime)|(doxy|mino|tetra)cycline|(levofl|moxifl|ofl)oxacin|macro(bid|dantin)|(una|zo)syn",
+ "table": "prescriptions",
+ "sub_var": "drug",
+ "interval": "00:01:00",
+ "callback": "mimic_abx_presc",
+ "class": "rgx_itm"
+ },
+ {
+ "ids": [
+ 225798,
+ 225837,
+ 225838,
+ 225840,
+ 225842,
+ 225843,
+ 225844,
+ 225845,
+ 225847,
+ 225848,
+ 225850,
+ 225851,
+ 225853,
+ 225855,
+ 225857,
+ 225859,
+ 225860,
+ 225862,
+ 225863,
+ 225865,
+ 225866,
+ 225868,
+ 225869,
+ 225871,
+ 225873,
+ 225875,
+ 225876,
+ 225877,
+ 225879,
+ 225881,
+ 225882,
+ 225883,
+ 225884,
+ 225885,
+ 225886,
+ 225888,
+ 225889,
+ 225890,
+ 225892,
+ 225893,
+ 225895,
+ 225896,
+ 225897,
+ 225898,
+ 225899,
+ 225900,
+ 225902,
+ 225903,
+ 225905,
+ 227691,
+ 228003
+ ],
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [1401, 1406, 1408, 1410, 1418, 1421, 1422, 1423, 1428, 1431, 1433, 1436, 1439, 1446, 1449, 1451, 1454, 1455, 1456, 1457, 1458, 1459, 1460, 1461, 1462, 1577, 1603, 1628, 1605, 1997, 1693, 1606, 1813, 1913, 1927, 1819],
+ "table": "medication",
+ "sub_var": "drugid"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "adh_rate": {
+ "unit": [
+ "units/min",
+ "U/min"
+ ],
+ "description": "vasopressin rate",
+ "omopid": 1507835,
+ "category": "medications",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 12467,
+ "table": "drugitems",
+ "sub_var": "itemid",
+ "rate_uom": "doserateunit",
+ "stop_var": "stop",
+ "callback": "aumc_rate_units(0.53)"
+ }
+ ],
+ "eicu": [
+ {
+ "regex": "^vasopressin.*\\(.+/.+\\)$",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "callback": "eicu_rate_units(2.65, 0.53)",
+ "class": "rgx_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "regex": "^vasopressin.*\\(.+/.+\\)$",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "callback": "eicu_rate_units(2.65, 0.53)",
+ "class": "rgx_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 112,
+ 113
+ ],
+ "table": "pharma",
+ "sub_var": "pharmaid",
+ "grp_var": "infusionid",
+ "callback": "hirid_rate"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 222315,
+ "table": "inputevents",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),\n mimic_rate_mv\n )"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 30051,
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'Uhr'),\n mimic_rate_cv\n )"
+ },
+ {
+ "ids": 222315,
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),\n mimic_rate_mv\n )"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 30051,
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'Uhr'),\n mimic_rate_cv\n )"
+ },
+ {
+ "ids": 222315,
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "callback": "combine_callbacks(\n convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),\n mimic_rate_mv\n )"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "cort": {
+ "class": "lgl_cncpt",
+ "description": "corticosteroids",
+ "omopid": 304275008,
+ "category": "medications",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6922,
+ 6995,
+ 7106,
+ 8132,
+ 9042,
+ 9130,
+ 10628
+ ],
+ "table": "drugitems",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 146,
+ 151,
+ 1000325,
+ 1000383,
+ 1000431,
+ 1000432,
+ 1000433,
+ 1000434,
+ 1000435,
+ 1000486,
+ 1000487,
+ 1000488,
+ 1000769,
+ 1000770,
+ 1000929
+ ],
+ "table": "pharma",
+ "sub_var": "pharmaid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [1397, 1506, 1524, 1525, 1751, 1977],
+ "table": "medication",
+ "sub_var": "drugid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "dex": {
+ "min": 0,
+ "unit": "ml/hr",
+ "description": "dextrose (as D10)",
+ "omopid": 4197597,
+ "category": "medications",
+ "target": "win_tbl",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 7254,
+ 7255,
+ 7256,
+ 8940,
+ 9571
+ ],
+ "table": "drugitems",
+ "sub_var": "itemid",
+ "dur_var": "stop",
+ "rate_var": "doserateunit",
+ "callback": "combine_callbacks(\n aumc_rate,\n dex_to_10(list(7255L, 7256L, c(8940L, 9571L)),\n c(2, 3, 4))\n )"
+ }
+ ],
+ "eicu": [
+ {
+ "regex": "(d50|dextrose.+50 ?%)",
+ "table": "medication",
+ "sub_var": "drugname",
+ "dur_var": "drugstopoffset",
+ "callback": "eicu_dex_med",
+ "class": "rgx_itm"
+ },
+ {
+ "regex": "(d10|dextrose.+10 ?%).+ml/hr",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "callback": "eicu_dex_inf",
+ "target": "ts_tbl",
+ "class": "rgx_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "regex": "(d50|dextrose.+50 ?%)",
+ "table": "medication",
+ "sub_var": "drugname",
+ "dur_var": "drugstopoffset",
+ "callback": "eicu_dex_med",
+ "class": "rgx_itm"
+ },
+ {
+ "regex": "(d10|dextrose.+10 ?%).+ml/hr",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "callback": "eicu_dex_inf",
+ "target": "ts_tbl",
+ "class": "rgx_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 1000022,
+ 1000690,
+ 1000689,
+ 1000544,
+ 1000746,
+ 1000835,
+ 1000060,
+ 1000545,
+ 1000567
+ ],
+ "table": "pharma",
+ "sub_var": "pharmaid",
+ "grp_var": "infusionid",
+ "target": "ts_tbl",
+ "interval": "00:01:00",
+ "callback": "combine_callbacks(\n grp_mount_to_rate(mins(1L), hours(1L)),\n dex_to_10(list(c(1000689L, 1000544L, 1000746L, 1000835L),\n 1000060L, 1000545L, 1000567L), c(2, 3, 4, 5))\n )"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": [
+ 220950,
+ 228140,
+ 220952
+ ],
+ "table": "inputevents",
+ "sub_var": "itemid",
+ "dur_var": "endtime",
+ "amount_var": "amount",
+ "auom_var": "amountuom",
+ "callback": "combine_callbacks(\n mimv_rate,\n dex_to_10(c(228140L, 220952L), c(2, 5))\n )"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 220950,
+ 228140,
+ 220952
+ ],
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "dur_var": "endtime",
+ "amount_var": "amount",
+ "auom_var": "amountuom",
+ "callback": "combine_callbacks(\n mimv_rate,\n dex_to_10(c(228140L, 220952L), c(2, 5))\n )"
+ },
+ {
+ "ids": [
+ 30016,
+ 30017
+ ],
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "val_var": "amount",
+ "unit_var": "amountuom",
+ "target": "ts_tbl",
+ "interval": "00:01:00",
+ "callback": "combine_callbacks(\n grp_mount_to_rate(mins(1L), hours(1L)),\n dex_to_10(30017L, 2)\n )"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 220950,
+ 228140,
+ 220952
+ ],
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "dur_var": "endtime",
+ "amount_var": "amount",
+ "auom_var": "amountuom",
+ "callback": "combine_callbacks(\n mimv_rate,\n dex_to_10(c(228140L, 220952L), c(2, 5))\n )"
+ },
+ {
+ "ids": [
+ 30016,
+ 30017
+ ],
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "val_var": "amount",
+ "unit_var": "amountuom",
+ "target": "ts_tbl",
+ "interval": "00:01:00",
+ "callback": "combine_callbacks(\n grp_mount_to_rate(mins(1L), hours(1L)),\n dex_to_10(30017L, 2)\n )"
+ }
+ ],
+ "picdb": []
+ },
+ "class": [
+ "unt_cncpt",
+ "num_cncpt"
+ ]
+ },
+ "dobu_dur": {
+ "description": "dobutamine duration",
+ "category": "medications",
+ "aggregate": "max",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 7178,
+ "table": "drugitems",
+ "sub_var": "itemid",
+ "stop_var": "stop",
+ "grp_var": "orderid",
+ "callback": "aumc_dur"
+ }
+ ],
+ "eicu": [
+ {
+ "regex": "^dobu",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "callback": "eicu_duration(gap_length = hours(5L))",
+ "class": "rgx_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "regex": "^dobu",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "callback": "eicu_duration(gap_length = hours(5L))",
+ "class": "rgx_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 426,
+ "table": "pharma",
+ "sub_var": "pharmaid",
+ "grp_var": "infusionid",
+ "callback": "hirid_duration"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 221653,
+ "table": "inputevents",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "grp_var": "linkorderid",
+ "callback": "mimic_dur_inmv"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 30042,
+ 30306
+ ],
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
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+ "category": "medications",
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+ "dopa_rate",
+ "adh_rate",
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+ "callback": "eicu_rate_kg(ml_to_mcg = 32)",
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+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "callback": "mimic_rate_cv"
+ },
+ {
+ "ids": 221906,
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "callback": "mimic_rate_mv"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 30047,
+ 30120
+ ],
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "callback": "mimic_rate_cv"
+ },
+ {
+ "ids": 221906,
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "callback": "mimic_rate_mv"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 1562,
+ "table": "medication",
+ "sub_var": "drugid",
+ "val_var": "amountperminute",
+ "stop_var": "offsetdrugend",
+ "class": "sic_itm",
+ "callback": "sic_rate_kg"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "phn_rate": {
+ "unit": "mcg/kg/min",
+ "description": "phenylephrine rate",
+ "omopid": 1135766,
+ "category": "medications",
+ "sources": {
+ "eicu": [
+ {
+ "regex": "^phenylephrine.*\\(.+\\)$",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "weight_var": "patientweight",
+ "callback": "eicu_rate_kg(ml_to_mcg = 200)",
+ "class": "rgx_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "regex": "^phenylephrine.*\\(.+\\)$",
+ "table": "infusiondrug",
+ "sub_var": "drugname",
+ "weight_var": "patientweight",
+ "callback": "eicu_rate_kg(ml_to_mcg = 200)",
+ "class": "rgx_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 221749,
+ "table": "inputevents",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "callback": "mimic_rate_mv"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 30127,
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "callback": "combine_callbacks(\n mimic_kg_rate, mimic_rate_cv)\n "
+ },
+ {
+ "ids": 30128,
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "callback": "mimic_rate_cv"
+ },
+ {
+ "ids": 221749,
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "callback": "mimic_rate_mv"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 30127,
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "callback": "combine_callbacks(\n mimic_kg_rate, mimic_rate_cv)\n "
+ },
+ {
+ "ids": 30128,
+ "table": "inputevents_cv",
+ "sub_var": "itemid",
+ "grp_var": "linkorderid",
+ "callback": "mimic_rate_cv"
+ },
+ {
+ "ids": 221749,
+ "table": "inputevents_mv",
+ "sub_var": "itemid",
+ "stop_var": "endtime",
+ "callback": "mimic_rate_mv"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "vaso_ind": {
+ "concepts": [
+ "dopa_dur",
+ "norepi_dur",
+ "dobu_dur",
+ "epi_dur"
+ ],
+ "description": "vasopressor indicator",
+ "omopid": 3655896,
+ "category": "medications",
+ "callback": "vaso_ind",
+ "class": "rec_cncpt"
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/microbiology.json b/inst/extdata/config/concept-dict/microbiology.json
new file mode 100644
index 00000000..7a380e64
--- /dev/null
+++ b/inst/extdata/config/concept-dict/microbiology.json
@@ -0,0 +1,91 @@
+{
+ "samp": {
+ "class": "lgl_cncpt",
+ "category": "microbiology",
+ "description": "body fluid sampling",
+ "omopid": 4133843,
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 8097,
+ 8418,
+ 8588,
+ 9189,
+ 9190,
+ 9191,
+ 9192,
+ 9193,
+ 9194,
+ 9195,
+ 9197,
+ 9198,
+ 9200,
+ 9202,
+ 9203,
+ 9204,
+ 9205,
+ 13024,
+ 19663,
+ 19664
+ ],
+ "table": "procedureorderitems",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "microlab",
+ "val_var": "organism",
+ "callback": "transform_fun(comp_na(`!=`, 'no growth'))",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "microlab",
+ "val_var": "organism",
+ "callback": "transform_fun(comp_na(`!=`, 'no growth'))",
+ "class": "col_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "table": "microbiologyevents",
+ "val_var": "org_itemid",
+ "callback": "mimic_sampling",
+ "aux_time": "charttime",
+ "class": "col_itm"
+ }
+ ],
+ "mimic": [
+ {
+ "table": "microbiologyevents",
+ "val_var": "org_itemid",
+ "callback": "mimic_sampling",
+ "aux_time": "charttime",
+ "class": "col_itm"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "table": "microbiologyevents",
+ "val_var": "org_itemid",
+ "callback": "mimic_sampling",
+ "aux_time": "charttime",
+ "class": "col_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "microbiologyevents",
+ "val_var": "org_itemid",
+ "callback": "picdb_sampling",
+ "aux_time": "charttime",
+ "class": "col_itm"
+ }
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/neurological.json b/inst/extdata/config/concept-dict/neurological.json
new file mode 100644
index 00000000..22a714b6
--- /dev/null
+++ b/inst/extdata/config/concept-dict/neurological.json
@@ -0,0 +1,350 @@
+{
+ "avpu": {
+ "concepts": "gcs",
+ "description": "AVPU scale",
+ "omopid": 40493498,
+ "category": "neurological",
+ "callback": "avpu",
+ "class": "rec_cncpt"
+ },
+ "egcs": {
+ "min": 1,
+ "max": 4,
+ "description": "GCS eye",
+ "omopid": 4084277,
+ "category": "neurological",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6732,
+ "table": "listitems",
+ "sub_var": "itemid",
+ "callback": "apply_map( c(`Geen reactie` = 1, `Reactie op pijnprikkel` = 2, `Reactie op verbale prikkel` = 3, `Spontane reactie` = 4) )"
+ },
+ {
+ "ids": 13077,
+ "table": "listitems",
+ "sub_var": "itemid",
+ "callback": "apply_map( c(`Niet` = 1, `Op pijn` = 2, `Op aanspreken` = 3, `Spontaan` = 4) )"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "Eyes",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "Eyes",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 10000300,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 220739,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 184,
+ 220739
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 184,
+ 220739
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "gcs": {
+ "concepts": [
+ "egcs",
+ "mgcs",
+ "vgcs",
+ "tgcs",
+ "ett_gcs"
+ ],
+ "description": "Glasgow coma scale (non-sedated)",
+ "omopid": 4093836,
+ "category": "neurological",
+ "aggregate": [
+ "min",
+ "min",
+ "min",
+ "min",
+ "any"
+ ],
+ "callback": "gcs",
+ "class": "rec_cncpt"
+ },
+ "mgcs": {
+ "min": 1,
+ "max": 6,
+ "description": "GCS motor",
+ "omopid": 4083352,
+ "category": "neurological",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6734,
+ "table": "listitems",
+ "sub_var": "itemid",
+ "callback": "apply_map( c(`Geen reactie` = 1, `Strekken` = 2, `Decortatie reflex (abnormaal buigen)` = 3, `Spastische reactie (terugtrekken)` = 4, `Localiseert pijn` = 5, `Volgt verbale commando's op` = 6) )"
+ },
+ {
+ "ids": 13072,
+ "table": "listitems",
+ "sub_var": "itemid",
+ "callback": "apply_map( c(`Geen reactie` = 1, `Strekken op pijn` = 2, `Abnormaal buigen bij pijn` = 3, `Terugtrekken bij pijn` = 4, `Localiseren pijn` = 5, `Voert opdrachten uit` = 6) )"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "Motor",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "Motor",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 10000200,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 223901,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 454,
+ 223901
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 454,
+ 223901
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "rass": {
+ "min": -5,
+ "max": 4,
+ "description": "Richmond agitation sedation scale",
+ "omopid": 36684829,
+ "category": "neurological",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 14444,
+ "sub_var": "itemid",
+ "table": "listitems",
+ "callback": "transform_fun(aumc_rass)"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "Sedation Score",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "Sedation Score",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 15001565,
+ "table": "observations",
+ "sub_var": "variableid",
+ "callback": "transform_fun(floor)",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 228096,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 228096,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 228096,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "tgcs": {
+ "min": 3,
+ "max": 15,
+ "description": "GCS total",
+ "omopid": 4093836,
+ "category": "neurological",
+ "sources": {
+ "eicu": [
+ {
+ "ids": "GCS Total",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "GCS Total",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": 198,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": 198,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "vgcs": {
+ "min": 1,
+ "max": 5,
+ "description": "GCS verbal",
+ "omopid": 4084912,
+ "category": "neurological",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6735,
+ "table": "listitems",
+ "sub_var": "itemid",
+ "callback": "apply_map( c(`Geen reactie (geen zichtbare poging tot praten)` = 1, `Onbegrijpelijke geluiden` = 2, `Onduidelijke woorden (pogingen tot communicatie, maar onduidelijk)` = 3, `Verwarde conversatie` = 4, `Helder en adequaat (communicatie mogelijk)` = 5) )"
+ },
+ {
+ "ids": 13066,
+ "table": "listitems",
+ "sub_var": "itemid",
+ "callback": "apply_map( c(`Geen geluid` = 1, `Onverstaanbare woorden` = 2, `Onjuiste woorden` = 3, `Verwarde taal` = 4, `Geori\u00ebnteerd` = 5) )"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": "Verbal",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": "Verbal",
+ "table": "nursecharting",
+ "sub_var": "nursingchartcelltypevalname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 10000100,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 223900,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 723,
+ 223900
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 723,
+ 223900
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "picdb": []
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/outcome.json b/inst/extdata/config/concept-dict/outcome.json
new file mode 100644
index 00000000..95009c78
--- /dev/null
+++ b/inst/extdata/config/concept-dict/outcome.json
@@ -0,0 +1,420 @@
+{
+ "death": {
+ "class": "lgl_cncpt",
+ "description": "in hospital mortality",
+ "omopid": 4306655,
+ "category": "outcome",
+ "sources": {
+ "aumc": [
+ {
+ "table": "admissions",
+ "index_var": "dateofdeath",
+ "val_var": "dischargedat",
+ "callback": "aumc_death",
+ "class": "col_itm"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "patient",
+ "index_var": "unitdischargeoffset",
+ "val_var": "hospitaldischargestatus",
+ "callback": "transform_fun(comp_na(`==`, 'Expired'))",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "patient",
+ "index_var": "unitdischargeoffset",
+ "val_var": "hospitaldischargestatus",
+ "callback": "transform_fun(comp_na(`==`, 'Expired'))",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 110,
+ 200
+ ],
+ "table": "observations",
+ "sub_var": "variableid",
+ "callback": "hirid_death",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "table": "admissions",
+ "index_var": "deathtime",
+ "val_var": "hospital_expire_flag",
+ "callback": "transform_fun(comp_na(`==`, 1L))",
+ "class": "col_itm"
+ }
+ ],
+ "mimic": [
+ {
+ "table": "admissions",
+ "index_var": "deathtime",
+ "val_var": "hospital_expire_flag",
+ "callback": "transform_fun(comp_na(`==`, 1L))",
+ "class": "col_itm"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "table": "admissions",
+ "index_var": "deathtime",
+ "val_var": "hospital_expire_flag",
+ "callback": "transform_fun(comp_na(`==`, 1L))",
+ "class": "col_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "admissions",
+ "index_var": "deathtime",
+ "val_var": "hospital_expire_flag",
+ "callback": "transform_fun(comp_na(`==`, 1L))",
+ "class": "col_itm"
+ }
+ ],
+ "sic": [
+ {
+ "table": "cases",
+ "index_var": "offsetofdeath",
+ "adm_time": "offsetafterfirstadmission",
+ "val_var": "timeofstay",
+ "callback": "sic_death",
+ "class": "col_itm"
+ }
+ ]
+ }
+ },
+ "dopa60": {
+ "concepts": [
+ "dopa_rate",
+ "dopa_dur"
+ ],
+ "description": "dopamine administration for min 1h",
+ "category": "outcome",
+ "interval": "00:01:00",
+ "callback": "vaso60",
+ "class": "rec_cncpt"
+ },
+ "epi60": {
+ "concepts": [
+ "epi_rate",
+ "epi_dur"
+ ],
+ "description": "epinephrine administration for min 1h",
+ "category": "outcome",
+ "interval": "00:01:00",
+ "callback": "vaso60",
+ "class": "rec_cncpt"
+ },
+ "los_hosp": {
+ "unit": "days",
+ "min": 0,
+ "target": "id_tbl",
+ "description": "hospital length of stay",
+ "omopid": 462369952,
+ "category": "outcome",
+ "sources": {
+ "eicu": [
+ {
+ "callback": "los_callback",
+ "win_type": "hadm",
+ "class": "fun_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "callback": "los_callback",
+ "win_type": "hadm",
+ "class": "fun_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "callback": "los_callback",
+ "win_type": "hadm",
+ "class": "fun_itm"
+ }
+ ],
+ "mimic": [
+ {
+ "callback": "los_callback",
+ "win_type": "hadm",
+ "class": "fun_itm"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "callback": "los_callback",
+ "win_type": "hadm",
+ "class": "fun_itm"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "los_icu": {
+ "unit": "days",
+ "min": 0,
+ "target": "id_tbl",
+ "description": "ICU length of stay",
+ "category": "outcome",
+ "sources": {
+ "aumc": [
+ {
+ "callback": "los_callback",
+ "win_type": "icustay",
+ "class": "fun_itm"
+ }
+ ],
+ "eicu": [
+ {
+ "callback": "los_callback",
+ "win_type": "icustay",
+ "class": "fun_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "callback": "los_callback",
+ "win_type": "icustay",
+ "class": "fun_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "callback": "los_callback",
+ "win_type": "icustay",
+ "class": "fun_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "callback": "los_callback",
+ "win_type": "icustay",
+ "class": "fun_itm"
+ }
+ ],
+ "mimic": [
+ {
+ "callback": "los_callback",
+ "win_type": "icustay",
+ "class": "fun_itm"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "callback": "los_callback",
+ "win_type": "icustay",
+ "class": "fun_itm"
+ }
+ ],
+ "sic": [
+ {
+ "table": "cases",
+ "val_var": "timeofstay",
+ "callback": "transform_fun(binary_op(`/`, 60 * 60 * 24))",
+ "class": "col_itm"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "mews": {
+ "concepts": [
+ "sbp",
+ "hr",
+ "resp",
+ "temp",
+ "avpu"
+ ],
+ "description": "modified early warning score",
+ "omopid": 40484211,
+ "category": "outcome",
+ "callback": "mews_score",
+ "class": "rec_cncpt"
+ },
+ "news": {
+ "concepts": [
+ "resp",
+ "o2sat",
+ "supp_o2",
+ "temp",
+ "sbp",
+ "hr",
+ "avpu"
+ ],
+ "description": "national early warning score",
+ "omopid": 44808550,
+ "category": "outcome",
+ "callback": "news_score",
+ "class": "rec_cncpt"
+ },
+ "norepi60": {
+ "concepts": [
+ "norepi_rate",
+ "norepi_dur"
+ ],
+ "description": "norepinephrine administration for min 1h",
+ "category": "outcome",
+ "interval": "00:01:00",
+ "callback": "vaso60",
+ "class": "rec_cncpt"
+ },
+ "qsofa": {
+ "concepts": [
+ "gcs",
+ "sbp",
+ "resp"
+ ],
+ "description": "quick SOFA score",
+ "omopid": 1616732,
+ "category": "outcome",
+ "callback": "qsofa_score",
+ "class": "rec_cncpt"
+ },
+ "sep3": {
+ "concepts": [
+ "sofa",
+ "susp_inf"
+ ],
+ "description": "sepsis-3 criterion",
+ "omopid": 132797,
+ "category": "outcome",
+ "callback": "sep3",
+ "keep_components": [
+ false,
+ true
+ ],
+ "class": "rec_cncpt"
+ },
+ "sirs": {
+ "concepts": [
+ "temp",
+ "hr",
+ "resp",
+ "pco2",
+ "wbc",
+ "bnd"
+ ],
+ "description": "systemic inflammatory response syndrome score",
+ "omopid": 4140444,
+ "category": "outcome",
+ "callback": "sirs_score",
+ "class": "rec_cncpt"
+ },
+ "sofa": {
+ "concepts": [
+ "sofa_resp",
+ "sofa_coag",
+ "sofa_liver",
+ "sofa_cardio",
+ "sofa_cns",
+ "sofa_renal"
+ ],
+ "description": "sequential organ failure assessment score",
+ "omopid": 1616852,
+ "category": "outcome",
+ "callback": "sofa_score",
+ "class": "rec_cncpt"
+ },
+ "sofa_cardio": {
+ "concepts": [
+ "map",
+ "dopa60",
+ "norepi60",
+ "dobu60",
+ "epi60"
+ ],
+ "description": "SOFA cardiovascular component",
+ "omopid": 1617534,
+ "category": "outcome",
+ "aggregate": [
+ "min",
+ "max",
+ "max",
+ "max",
+ "max"
+ ],
+ "callback": "sofa_cardio",
+ "class": "rec_cncpt"
+ },
+ "sofa_cns": {
+ "concepts": "gcs",
+ "description": "SOFA central nervous system component",
+ "omopid": 1616439,
+ "category": "outcome",
+ "callback": "sofa_cns",
+ "class": "rec_cncpt"
+ },
+ "sofa_coag": {
+ "concepts": "plt",
+ "description": "SOFA coagulation component",
+ "omopid": 1616896,
+ "category": "outcome",
+ "aggregate": "min",
+ "callback": "sofa_coag",
+ "class": "rec_cncpt"
+ },
+ "sofa_liver": {
+ "concepts": "bili",
+ "description": "SOFA liver component",
+ "omopid": 1617043,
+ "category": "outcome",
+ "aggregate": "max",
+ "callback": "sofa_liver",
+ "class": "rec_cncpt"
+ },
+ "sofa_renal": {
+ "concepts": [
+ "crea",
+ "urine24"
+ ],
+ "description": "SOFA renal component",
+ "omopid": 1616355,
+ "category": "outcome",
+ "aggregate": [
+ "max",
+ null
+ ],
+ "callback": "sofa_renal",
+ "class": "rec_cncpt"
+ },
+ "sofa_resp": {
+ "concepts": [
+ "pafi",
+ "vent_ind"
+ ],
+ "description": "SOFA respiratory component",
+ "omopid": 1616907,
+ "category": "outcome",
+ "callback": "sofa_resp",
+ "class": "rec_cncpt"
+ },
+ "susp_inf": {
+ "concepts": [
+ "abx",
+ "samp"
+ ],
+ "description": "suspected infection",
+ "omopid": 43021378,
+ "category": "outcome",
+ "aggregate": [
+ [
+ "sum"
+ ],
+ [
+ false
+ ]
+ ],
+ "callback": "susp_inf",
+ "class": "rec_cncpt"
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/output.json b/inst/extdata/config/concept-dict/output.json
new file mode 100644
index 00000000..73953d48
--- /dev/null
+++ b/inst/extdata/config/concept-dict/output.json
@@ -0,0 +1,175 @@
+{
+ "urine": {
+ "unit": "mL",
+ "min": 0,
+ "max": 2000,
+ "aggregate": "sum",
+ "description": "urine output",
+ "omopid": 4264378,
+ "category": "output",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 8794,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "ids": [
+ "Urine",
+ "URINE CATHETER"
+ ],
+ "table": "intakeoutput",
+ "sub_var": "celllabel"
+ },
+ {
+ "regex": "catheter.+output|output.+catheter",
+ "table": "intakeoutput",
+ "sub_var": "celllabel",
+ "class": "rgx_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "ids": [
+ "Urine",
+ "URINE CATHETER"
+ ],
+ "table": "intakeoutput",
+ "sub_var": "celllabel"
+ },
+ {
+ "regex": "catheter.+output|output.+catheter",
+ "table": "intakeoutput",
+ "sub_var": "celllabel",
+ "class": "rgx_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 30005110,
+ "table": "observations",
+ "sub_var": "variableid",
+ "callback": "hirid_urine",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": [
+ 226557,
+ 226558,
+ 226559,
+ 226560,
+ 226561,
+ 226563,
+ 226564,
+ 226565,
+ 226566,
+ 226567,
+ 226584,
+ 227510
+ ],
+ "table": "outputevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 40055,
+ 40056,
+ 40057,
+ 40065,
+ 40069,
+ 40085,
+ 40086,
+ 40094,
+ 40096,
+ 40405,
+ 40428,
+ 40473,
+ 40715,
+ 43175,
+ 226557,
+ 226558,
+ 226559,
+ 226560,
+ 226561,
+ 226563,
+ 226564,
+ 226565,
+ 226566,
+ 226567,
+ 226584,
+ 227510
+ ],
+ "table": "outputevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 40055,
+ 40056,
+ 40057,
+ 40065,
+ 40069,
+ 40085,
+ 40086,
+ 40094,
+ 40096,
+ 40405,
+ 40428,
+ 40473,
+ 40715,
+ 43175,
+ 226557,
+ 226558,
+ 226559,
+ 226560,
+ 226561,
+ 226563,
+ 226564,
+ 226565,
+ 226566,
+ 226567,
+ 226584,
+ 227510
+ ],
+ "table": "outputevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 725,
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ "1008"
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "urine24": {
+ "concepts": "urine",
+ "description": "urine output per 24h",
+ "omopid": 4191836,
+ "category": "output",
+ "callback": "urine24",
+ "class": "rec_cncpt"
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/respiratory.json b/inst/extdata/config/concept-dict/respiratory.json
new file mode 100644
index 00000000..5e64f8fe
--- /dev/null
+++ b/inst/extdata/config/concept-dict/respiratory.json
@@ -0,0 +1,721 @@
+{
+ "ett_gcs": {
+ "class": "lgl_cncpt",
+ "description": "tracheostomy",
+ "omopid": 4097216,
+ "category": "respiratory",
+ "target": "win_tbl",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6735,
+ "table": "listitems",
+ "sub_var": "itemid",
+ "target": "ts_tbl",
+ "callback": "combine_callbacks(\n transform_fun(comp_na(`==`, 'Ge\u00efntubeerd')),\n ts_to_win_tbl(mins(1L))\n )"
+ }
+ ],
+ "eicu": [
+ {
+ "class": "fun_itm",
+ "callback": "combine_callbacks(\n fwd_concept('rass'),\n transform_fun(comp_na(`<=`, -3)),\n ts_to_win_tbl(mins(360L))\n )"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "class": "fun_itm",
+ "callback": "combine_callbacks(\n fwd_concept('rass'),\n transform_fun(comp_na(`<=`, -3)),\n ts_to_win_tbl(mins(360L))\n )"
+ }
+ ],
+ "hirid": [
+ {
+ "class": "fun_itm",
+ "callback": "combine_callbacks(\n fwd_concept('mech_vent'),\n transform_fun(comp_na(`==`, 'invasive'))\n )"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": "No Response-ETT",
+ "table": "chartevents",
+ "sub_var": "value",
+ "target": "ts_tbl",
+ "callback": "combine_callbacks(\n transform_fun(set_val(TRUE)),\n ts_to_win_tbl(mins(1L))\n )"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ "1.0 ET/Trach",
+ "No Response-ETT"
+ ],
+ "table": "chartevents",
+ "sub_var": "value",
+ "target": "ts_tbl",
+ "callback": "combine_callbacks(\n transform_fun(set_val(TRUE)),\n ts_to_win_tbl(mins(1L))\n )"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ "1.0 ET/Trach",
+ "No Response-ETT"
+ ],
+ "table": "chartevents",
+ "sub_var": "value",
+ "target": "ts_tbl",
+ "callback": "combine_callbacks(\n transform_fun(set_val(TRUE)),\n ts_to_win_tbl(mins(1L))\n )"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "mech_vent": {
+ "class": "fct_cncpt",
+ "target": "win_tbl",
+ "levels": [
+ "invasive",
+ "noninvasive"
+ ],
+ "description": "mechanical ventilation windows",
+ "omopid": 4230167,
+ "category": "respiratory",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 9328,
+ 10740,
+ 12635
+ ],
+ "table": "processitems",
+ "sub_var": "itemid",
+ "dur_var": "stop",
+ "callback": "apply_map(c(`Beademen` = 'invasive',\n `Beademen non-invasief` = 'noninvasive',\n `Tracheostoma` = 'invasive'))"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 15001552,
+ "table": "observations",
+ "sub_var": "variableid",
+ "target": "ts_tbl",
+ "interval": "00:01:00",
+ "class": "hrd_itm",
+ "callback": "combine_callbacks(hirid_vent,\n apply_map(c(`1` = 'invasive',\n `2` = 'invasive',\n `3` = 'noninvasive',\n `4` = 'noninvasive',\n `5` = 'noninvasive',\n `6` = 'noninvasive')))"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": [
+ 225792,
+ 225794
+ ],
+ "table": "procedureevents",
+ "sub_var": "itemid",
+ "dur_var": "endtime",
+ "callback": "apply_map(c(`225792` = 'invasive',\n `225794` = 'noninvasive'),\n var = 'sub_var')"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "o2sat": {
+ "unit": [
+ "%",
+ "% Sat."
+ ],
+ "min": 50,
+ "max": 100,
+ "description": "oxygen saturation",
+ "omopid": 40483579,
+ "category": "respiratory",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6709,
+ 8903
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": 12311,
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "transform_fun(binary_op(`*`, 100))"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "sao2",
+ "unit_val": "%",
+ "class": "col_itm"
+ },
+ {
+ "ids": "O2 Sat (%)",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "sao2",
+ "unit_val": "%",
+ "class": "col_itm"
+ },
+ {
+ "ids": "O2 Sat (%)",
+ "table": "lab",
+ "sub_var": "labname"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 4000,
+ 8280,
+ 20000800
+ ],
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": [
+ 220277,
+ 226253,
+ 50817
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 646,
+ 220277,
+ 226253,
+ 50817
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 646,
+ 220277,
+ 226253,
+ 50817
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 710,
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ "1006"
+ ],
+ "sub_var": "itemid"
+ },
+ {
+ "table": "labevents",
+ "ids": [
+ 5252
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "pafi": {
+ "concepts": [
+ "po2",
+ "fio2"
+ ],
+ "description": "Horowitz index",
+ "omopid": 4233883,
+ "category": "respiratory",
+ "aggregate": [
+ "min",
+ "max"
+ ],
+ "callback": "pafi",
+ "class": "rec_cncpt"
+ },
+ "resp": {
+ "unit": [
+ "insp/min",
+ "/min"
+ ],
+ "min": 0,
+ "max": 120,
+ "description": "respiratory rate",
+ "omopid": 4313591,
+ "category": "respiratory",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 8874,
+ 12266
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "respiration",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "respiration",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 300,
+ 310
+ ],
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": [
+ 220210,
+ 224688,
+ 224689,
+ 224690
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 618,
+ 619,
+ 220210,
+ 224688,
+ 224689,
+ 224690
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 618,
+ 619,
+ 220210,
+ 224688,
+ 224689,
+ 224690
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 719,
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ "1004"
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "safi": {
+ "concepts": [
+ "o2sat",
+ "fio2"
+ ],
+ "description": "SaO2/FiO2",
+ "category": "respiratory",
+ "aggregate": [
+ "min",
+ "max"
+ ],
+ "callback": "safi",
+ "class": "rec_cncpt"
+ },
+ "supp_o2": {
+ "concepts": [
+ "vent_ind",
+ "fio2"
+ ],
+ "description": "supplemental oxygen",
+ "omopid": 36304401,
+ "category": "respiratory",
+ "callback": "supp_o2",
+ "class": "rec_cncpt"
+ },
+ "vent_end": {
+ "class": "lgl_cncpt",
+ "description": "ventilation end",
+ "category": "respiratory",
+ "sources": {
+ "eicu": [
+ {
+ "table": "respiratorycare",
+ "val_var": "ventendoffset",
+ "callback": "vent_flag",
+ "class": "col_itm"
+ },
+ {
+ "table": "respiratorycare",
+ "val_var": "priorventendoffset",
+ "callback": "vent_flag",
+ "class": "col_itm"
+ },
+ {
+ "ids": [
+ "off",
+ "Off",
+ "Suspended"
+ ],
+ "table": "respiratorycharting",
+ "sub_var": "respchartvalue",
+ "val_var": "respchartvaluelabel",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "respiratorycare",
+ "val_var": "ventendoffset",
+ "callback": "vent_flag",
+ "class": "col_itm"
+ },
+ {
+ "table": "respiratorycare",
+ "val_var": "priorventendoffset",
+ "callback": "vent_flag",
+ "class": "col_itm"
+ },
+ {
+ "ids": [
+ "off",
+ "Off",
+ "Suspended"
+ ],
+ "table": "respiratorycharting",
+ "sub_var": "respchartvalue",
+ "val_var": "respchartvaluelabel",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 225468,
+ 225477,
+ 227194
+ ],
+ "table": "procedureevents_mv",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ },
+ {
+ "ids": [
+ 467,
+ 469,
+ 226732
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 225468,
+ 225477,
+ 227194
+ ],
+ "table": "procedureevents_mv",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ },
+ {
+ "ids": [
+ 467,
+ 469,
+ 226732
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "picdb": []
+ }
+ },
+ "vent_ind": {
+ "concepts": [
+ "vent_start",
+ "vent_end",
+ "mech_vent"
+ ],
+ "description": "ventilation durations",
+ "omopid": 4230167,
+ "category": "respiratory",
+ "interval": "00:01:00",
+ "callback": "vent_ind",
+ "target": "win_tbl",
+ "class": "rec_cncpt"
+ },
+ "vent_start": {
+ "class": "lgl_cncpt",
+ "description": "ventilation start",
+ "category": "respiratory",
+ "sources": {
+ "eicu": [
+ {
+ "table": "respiratorycare",
+ "val_var": "ventstartoffset",
+ "callback": "vent_flag",
+ "class": "col_itm"
+ },
+ {
+ "table": "respiratorycare",
+ "val_var": "priorventstartoffset",
+ "callback": "vent_flag",
+ "class": "col_itm"
+ },
+ {
+ "ids": [
+ "Start",
+ "Continued",
+ "respFlowPtVentData"
+ ],
+ "table": "respiratorycharting",
+ "sub_var": "respcharttypecat",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "respiratorycare",
+ "val_var": "ventstartoffset",
+ "callback": "vent_flag",
+ "class": "col_itm"
+ },
+ {
+ "table": "respiratorycare",
+ "val_var": "priorventstartoffset",
+ "callback": "vent_flag",
+ "class": "col_itm"
+ },
+ {
+ "ids": [
+ "Start",
+ "Continued",
+ "respFlowPtVentData"
+ ],
+ "table": "respiratorycharting",
+ "sub_var": "respcharttypecat",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 1,
+ 60,
+ 218,
+ 221,
+ 223,
+ 436,
+ 437,
+ 444,
+ 445,
+ 448,
+ 449,
+ 450,
+ 459,
+ 501,
+ 502,
+ 503,
+ 505,
+ 506,
+ 535,
+ 543,
+ 639,
+ 654,
+ 667,
+ 668,
+ 669,
+ 670,
+ 671,
+ 672,
+ 681,
+ 682,
+ 683,
+ 684,
+ 686,
+ 1211,
+ 1340,
+ 1486,
+ 1600,
+ 1655,
+ 2000,
+ 3459,
+ 5865,
+ 5866,
+ 220339,
+ 223848,
+ 223849,
+ 224419,
+ 224684,
+ 224685,
+ 224686,
+ 224687,
+ 224695,
+ 224696,
+ 224697,
+ 224700,
+ 224701,
+ 224702,
+ 224703,
+ 224704,
+ 224705,
+ 224706,
+ 224707,
+ 224709,
+ 224738,
+ 224746,
+ 224747,
+ 224750,
+ 226873,
+ 227187
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 1,
+ 60,
+ 218,
+ 221,
+ 223,
+ 436,
+ 437,
+ 444,
+ 445,
+ 448,
+ 449,
+ 450,
+ 459,
+ 501,
+ 502,
+ 503,
+ 505,
+ 506,
+ 535,
+ 543,
+ 639,
+ 654,
+ 667,
+ 668,
+ 669,
+ 670,
+ 671,
+ 672,
+ 681,
+ 682,
+ 683,
+ 684,
+ 686,
+ 1211,
+ 1340,
+ 1486,
+ 1600,
+ 1655,
+ 2000,
+ 3459,
+ 5865,
+ 5866,
+ 220339,
+ 223848,
+ 223849,
+ 224419,
+ 224684,
+ 224685,
+ 224686,
+ 224687,
+ 224695,
+ 224696,
+ 224697,
+ 224700,
+ 224701,
+ 224702,
+ 224703,
+ 224704,
+ 224705,
+ 224706,
+ 224707,
+ 224709,
+ 224738,
+ 224746,
+ 224747,
+ 224750,
+ 226873,
+ 227187
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "transform_fun(set_val(TRUE))"
+ }
+ ],
+ "picdb": []
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/vitals.json b/inst/extdata/config/concept-dict/vitals.json
new file mode 100644
index 00000000..75967e5e
--- /dev/null
+++ b/inst/extdata/config/concept-dict/vitals.json
@@ -0,0 +1,609 @@
+{
+ "dbp": {
+ "unit": [
+ "mmHg",
+ "mm Hg"
+ ],
+ "min": 0,
+ "max": 200,
+ "description": "diastolic blood pressure",
+ "omopid": 4154790,
+ "category": "vitals",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6643,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "systemicdiastolic",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "systemicdiastolic",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 120,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": [
+ 220051,
+ 220180
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 8368,
+ 8441,
+ 8555,
+ 220051,
+ 220180
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 8368,
+ 8441,
+ 8555,
+ 220051,
+ 220180
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [
+ 702,
+ 705
+ ],
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ 1015
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "etco2": {
+ "unit": [
+ "mmHg",
+ "mm Hg"
+ ],
+ "min": 10,
+ "max": 60,
+ "description": "endtidal CO2",
+ "omopid": 4353940,
+ "category": "vitals",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 6707,
+ 8884,
+ 8885,
+ 9658,
+ 12805,
+ 12356
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid",
+ "callback": "convert_unit(binary_op(`*`, 7.6), 'mmHg', 'None|Geen')"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 2200,
+ 8290,
+ 30010009
+ ],
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 228640,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 1817,
+ 228640
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 1817,
+ 228640
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 716,
+ "table": "laboratory",
+ "sub_var": "laboratoryid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ ]
+ }
+ },
+ "hr": {
+ "unit": [
+ "bpm",
+ "/min"
+ ],
+ "min": 0,
+ "max": 300,
+ "description": "heart rate",
+ "omopid": 4239408,
+ "category": "vitals",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6640,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "heartrate",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "heartrate",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 200,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 220045,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 211,
+ 220045
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 211,
+ 220045
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [708, 724],
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ 1003, 1002
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "map": {
+ "unit": [
+ "mmHg",
+ "mm Hg"
+ ],
+ "min": 0,
+ "max": 250,
+ "description": "mean arterial pressure",
+ "omopid": 4239021,
+ "category": "vitals",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6642,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "systemicmean",
+ "class": "col_itm"
+ },
+ {
+ "table": "vitalaperiodic",
+ "val_var": "noninvasivemean",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "systemicmean",
+ "class": "col_itm"
+ },
+ {
+ "table": "vitalaperiodic",
+ "val_var": "noninvasivemean",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 110,
+ 610
+ ],
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": [
+ 220052,
+ 220181,
+ 225312
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 52,
+ 443,
+ 456,
+ 6072,
+ 220052,
+ 220181,
+ 225312
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 52,
+ 443,
+ 456,
+ 6072,
+ 220052,
+ 220181,
+ 225312
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [
+ 703,
+ 706
+ ],
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ ]
+ }
+ },
+ "sbp": {
+ "unit": [
+ "mmHg",
+ "mm Hg"
+ ],
+ "min": 0,
+ "max": 300,
+ "description": "systolic blood pressure",
+ "omopid": 4152194,
+ "category": "vitals",
+ "sources": {
+ "aumc": [
+ {
+ "ids": 6641,
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "systemicsystolic",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "systemicsystolic",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": 100,
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": [
+ 220050,
+ 220179
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 51,
+ 455,
+ 6701,
+ 220050,
+ 220179
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 51,
+ 455,
+ 6701,
+ 220050,
+ 220179
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ }
+ ],
+ "sic": [
+ {
+ "ids": [
+ 701,
+ 704
+ ],
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ 1016
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ },
+ "temp": {
+ "unit": [
+ "C",
+ "\u00b0C"
+ ],
+ "min": 30,
+ "max": 44,
+ "description": "temperature",
+ "omopid": 4302666,
+ "category": "vitals",
+ "sources": {
+ "aumc": [
+ {
+ "ids": [
+ 8658,
+ 13952,
+ 16110
+ ],
+ "table": "numericitems",
+ "sub_var": "itemid"
+ }
+ ],
+ "eicu": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "temperature",
+ "class": "col_itm"
+ }
+ ],
+ "eicu_demo": [
+ {
+ "table": "vitalperiodic",
+ "val_var": "temperature",
+ "class": "col_itm"
+ }
+ ],
+ "hirid": [
+ {
+ "ids": [
+ 410,
+ 400,
+ 7100
+ ],
+ "table": "observations",
+ "sub_var": "variableid",
+ "class": "hrd_itm"
+ }
+ ],
+ "miiv": [
+ {
+ "ids": 223762,
+ "table": "chartevents",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": [
+ 223761,
+ 224027
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "convert_unit(fahr_to_cels, 'C', 'f')"
+ }
+ ],
+ "mimic": [
+ {
+ "ids": [
+ 676,
+ 677,
+ 223762
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": [
+ 678,
+ 679,
+ 223761,
+ 224027
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "convert_unit(fahr_to_cels, 'C', 'f')"
+ }
+ ],
+ "mimic_demo": [
+ {
+ "ids": [
+ 676,
+ 677,
+ 223762
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid"
+ },
+ {
+ "ids": [
+ 678,
+ 679,
+ 223761,
+ 224027
+ ],
+ "table": "chartevents",
+ "sub_var": "itemid",
+ "callback": "convert_unit(fahr_to_cels, 'C', 'f')"
+ }
+ ],
+ "sic": [
+ {
+ "ids": 709,
+ "table": "data_float_h",
+ "val_var": "rawdata",
+ "sub_var": "dataid",
+ "class": "sic_itm"
+ }
+ ],
+ "picdb": [
+ {
+ "table": "chartevents",
+ "ids": [
+ 1001
+ ],
+ "sub_var": "itemid"
+ },
+ {
+ "table": "labevents",
+ "ids": [
+ 5253
+ ],
+ "sub_var": "itemid"
+ }
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/inst/extdata/config/data-sources.R b/inst/extdata/config/data-sources.R
deleted file mode 100644
index 1a578b1e..00000000
--- a/inst/extdata/config/data-sources.R
+++ /dev/null
@@ -1,1791 +0,0 @@
-
-download_pysionet_schema <- function(url) {
-
- dat <- ricu:::download_pysionet_file(
- url, dest = NULL, user = NULL, pass = NULL
- )
-
- message("downloading schema at ", url)
-
- xml2::as_list(xml2::read_xml(rawToChar(dat)))
-}
-
-get_table_info <- function(url) {
-
- res <- download_pysionet_schema(url)
- res <- res[["database"]][["tables"]]
-
- res <- lapply(res, function(x) {
- cols <- names(x) == "column"
- names <- vapply(x[cols], attr, character(1L), "name")
- types <- vapply(x[cols], attr, character(1L), "type")
- list(
- table_name = tolower(attr(x, "name")),
- num_rows = as.integer(attr(x, "numRows")),
- cols = as_col_spec(names, types)
- )
- })
-
- unname(res)
-}
-
-col_spec_map <- function(type) {
- switch(type,
- bool = list(spec = "col_logical"),
- int2 = ,
- int4 = list(spec = "col_integer"),
- int8 = ,
- numeric = ,
- float8 = list(spec = "col_double"),
- bpchar = ,
- text = ,
- varchar = list(spec = "col_character"),
- timestamp = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- stop("unknown type")
- )
-}
-
-as_col_spec <- function(names, types) {
- Map(c, Map(list, name = tolower(names), col = names),
- lapply(types, col_spec_map))
-}
-
-as_tbl_spec <- function(files, defaults, time_vars, tbl_info, partitioning) {
-
- mod_col <- function(x) {
- x[["name"]] <- x[["col"]]
- x[["col"]] <- NULL
- x
- }
-
- do_as <- function(file, default, time, tbl, part) {
-
- all_cols <- vapply(tbl[["cols"]], `[[`, character(1L), "name")
-
- stopifnot(all(vapply(default, `%in%`, logical(1L), all_cols)))
-
- if (length(time)) {
- default <- c(default, list(time_vars = unname(time)))
- }
-
- tbl <- c(list(files = file, defaults = default), tbl)
-
- tbl[["table_name"]] <- NULL
- tbl[["cols"]] <- setNames(lapply(tbl[["cols"]], mod_col), all_cols)
-
- if (!is.null(part)) {
- stopifnot(isTRUE(names(part) %in% all_cols))
- tbl <- c(tbl, list(partitioning = list(col = names(part),
- breaks = part[[1L]])))
- }
-
- tbl
- }
-
- tbls <- vapply(tbl_info, `[[`, character(1L), "table_name")
-
- res <- Map(do_as, files[tbls], defaults[tbls], time_vars[tbls], tbl_info,
- partitioning[tbls])
- names(res) <- tolower(tbls)
-
- res
-}
-
-as_minimal_tbl_spec <- function(x) {
- x[setdiff(names(x), c("files", "num_rows", "cols"))]
-}
-
-eicu_tbl_cfg <- function(info, is_demo = FALSE) {
-
- files <- c("admissionDrug.csv.gz",
- "admissionDx.csv.gz",
- "allergy.csv.gz",
- "apacheApsVar.csv.gz",
- "apachePatientResult.csv.gz",
- "apachePredVar.csv.gz",
- "carePlanCareProvider.csv.gz",
- "carePlanEOL.csv.gz",
- "carePlanGeneral.csv.gz",
- "carePlanGoal.csv.gz",
- "carePlanInfectiousDisease.csv.gz",
- "customLab.csv.gz",
- "diagnosis.csv.gz",
- "hospital.csv.gz",
- "infusionDrug.csv.gz",
- "intakeOutput.csv.gz",
- "lab.csv.gz",
- "medication.csv.gz",
- "microLab.csv.gz",
- "note.csv.gz",
- "nurseAssessment.csv.gz",
- "nurseCare.csv.gz",
- "nurseCharting.csv.gz",
- "pastHistory.csv.gz",
- "patient.csv.gz",
- "physicalExam.csv.gz",
- "respiratoryCare.csv.gz",
- "respiratoryCharting.csv.gz",
- "treatment.csv.gz",
- "vitalAperiodic.csv.gz",
- "vitalPeriodic.csv.gz")
- names(files) <- sub("\\.csv\\.gz", "", tolower(files))
-
- if (is_demo) {
- files <- sub("Drug\\.csv\\.gz", "drug.csv.gz", files)
- }
-
- defaults <- list(
- admissiondrug = list(
- index_var = "drugoffset",
- val_var = "drugdosage",
- unit_var = "drugunit"
- ),
- admissiondx = list(
- index_var = "admitdxenteredoffset",
- val_var = "admitdxtext"
- ),
- allergy = list(
- index_var = "allergyoffset",
- val_var = "allergyname"
- ),
- apacheapsvar = list(),
- apachepatientresult = list(
- val_var = "apachescore"
- ),
- apachepredvar = list(),
- careplancareprovider = list(
- index_var = "careprovidersaveoffset",
- val_var = "specialty"
- ),
- careplaneol = list(
- index_var = "cpleoldiscussionoffset"
- ),
- careplangeneral = list(
- index_var = "cplitemoffset",
- val_var = "cplitemvalue"
- ),
- careplangoal = list(
- index_var = "cplgoaloffset",
- val_var = "cplgoalvalue"
- ),
- careplaninfectiousdisease = list(
- index_var = "cplinfectdiseaseoffset",
- val_var = "infectdiseasesite"
- ),
- customlab = list(
- index_var = "labotheroffset",
- val_var = "labotherresult"
- ),
- diagnosis = list(
- index_var = "diagnosisoffset",
- val_var = "icd9code"
- ),
- hospital = list(
- id_var = "hospitalid",
- val_var = "numbedscategory"
- ),
- infusiondrug = list(
- index_var = "infusionoffset",
- val_var = "drugrate"
- ),
- intakeoutput = list(
- index_var = "intakeoutputoffset",
- val_var = "cellvaluenumeric"
- ),
- lab = list(
- index_var = "labresultoffset",
- val_var = "labresult",
- unit_var = "labmeasurenameinterface"
- ),
- medication = list(
- index_var = "drugstartoffset",
- val_var = "dosage"
- ),
- microlab = list(
- index_var = "culturetakenoffset",
- val_var = "organism"
- ),
- note = list(
- index_var = "noteoffset",
- val_var = "notetext"
- ),
- nurseassessment = list(
- index_var = "nurseassessoffset",
- val_var = "cellattributevalue"
- ),
- nursecare = list(
- index_var = "nursecareoffset",
- val_var = "cellattributevalue"
- ),
- nursecharting = list(
- index_var = "nursingchartoffset",
- val_var = "nursingchartvalue"
- ),
- pasthistory = list(
- index_var = "pasthistoryoffset",
- val_var = "pasthistoryvalue"
- ),
- patient = list(
- val_var = "unitdischargestatus"
- ),
- physicalexam = list(
- index_var = "physicalexamoffset",
- val_var = "physicalexamvalue"
- ),
- respiratorycare = list(
- index_var = "respcarestatusoffset"
- ),
- respiratorycharting = list(
- index_var = "respchartoffset",
- val_var = "respchartvalue"
- ),
- treatment = list(
- index_var = "treatmentoffset",
- val_var = "treatmentstring"
- ),
- vitalaperiodic = list(
- index_var = "observationoffset"
- ),
- vitalperiodic = list(
- index_var = "observationoffset"
- )
- )
-
- part <- list(
- nursecharting = list(
- patientunitstayid = `if`(is_demo,
- 1775421L,
- c(514528L, 1037072L, 1453997L, 1775421L, 2499831L, 2937948L, 3213286L)
- )
- ),
- vitalperiodic = list(
- patientunitstayid = `if`(is_demo,
- 1775421L,
- c(514528L, 1037072L, 1453997L, 1775421L, 2499831L, 2937948L, 3213286L)
- )
- )
- )
-
- if (is_demo) {
-
- info <- lapply(info, `[[<-`, "num_rows", NULL)
-
- } else {
-
- tbl <- vapply(info, `[[`, character(1L), "table_name") == "respiratorycare"
- new <- info[[which(tbl)]][["cols"]]
- col <- vapply(new, `[[`, character(1L), "col") == "apneaparams"
-
- new[[which(col)]][["col"]] <- "apneaparms"
- info[[which(tbl)]][["cols"]] <- new
- }
-
- time_vars <- lapply(info, function(x) {
- nme <- vapply(x[["cols"]], `[[`, character(1L), "name")
- typ <- vapply(x[["cols"]], `[[`, character(1L), "spec")
- nme[typ == "col_integer" & grepl("offset$", nme)]
- })
-
- names(time_vars) <- vapply(info, `[[`, character(1L), "table_name")
-
- as_tbl_spec(files, defaults, time_vars, info, part)
-}
-
-mimic_tbl_cfg <- function(info, is_demo = FALSE) {
-
- find_entry <- function(x, what, name) {
- which(vapply(x, `[[`, character(1L), what) == name)
- }
-
- files <- c("ADMISSIONS.csv.gz",
- "CALLOUT.csv.gz",
- "CAREGIVERS.csv.gz",
- "CHARTEVENTS.csv.gz",
- "CPTEVENTS.csv.gz",
- "DATETIMEEVENTS.csv.gz",
- "DIAGNOSES_ICD.csv.gz",
- "DRGCODES.csv.gz",
- "D_CPT.csv.gz",
- "D_ICD_DIAGNOSES.csv.gz",
- "D_ICD_PROCEDURES.csv.gz",
- "D_ITEMS.csv.gz",
- "D_LABITEMS.csv.gz",
- "ICUSTAYS.csv.gz",
- "INPUTEVENTS_CV.csv.gz",
- "INPUTEVENTS_MV.csv.gz",
- "LABEVENTS.csv.gz",
- "MICROBIOLOGYEVENTS.csv.gz",
- "NOTEEVENTS.csv.gz",
- "OUTPUTEVENTS.csv.gz",
- "PATIENTS.csv.gz",
- "PRESCRIPTIONS.csv.gz",
- "PROCEDUREEVENTS_MV.csv.gz",
- "PROCEDURES_ICD.csv.gz",
- "SERVICES.csv.gz",
- "TRANSFERS.csv.gz")
- names(files) <- sub("\\.csv\\.gz", "", tolower(files))
-
- if (is_demo) {
- files <- sub("\\.gz$", "", files)
- }
-
- defaults <- list(
- admissions = list(
- val_var = "admission_type"
- ),
- callout = list(
- index_var = "outcometime",
- val_var = "callout_outcome"
- ),
- caregivers = list(
- id_var = "cgid",
- val_var = "label"
- ),
- chartevents = list(
- index_var = "charttime",
- val_var = "valuenum",
- unit_var = "valueuom"
- ),
- cptevents = list(
- index_var = "chartdate",
- val_var = "cpt_cd"
- ),
- d_cpt = list(
- id_var = "subsectionrange",
- val_var = "subsectionheader"
- ),
- d_icd_diagnoses = list(
- id_var = "icd9_code",
- val_var = "short_title"
- ),
- d_icd_procedures = list(
- id_var = "icd9_code",
- val_var = "short_title"
- ),
- d_items = list(
- id_var = "itemid",
- val_var = "label"
- ),
- d_labitems = list(
- id_var = "itemid",
- val_var = "label"
- ),
- datetimeevents = list(
- index_var = "charttime",
- val_var = "itemid"
- ),
- diagnoses_icd = list(
- val_var = "icd9_code"
- ),
- drgcodes = list(
- val_var = "drg_code"
- ),
- icustays = list(
- index_var = "intime",
- val_var = "last_careunit"
- ),
- inputevents_cv = list(
- index_var = "charttime",
- val_var = "rate",
- unit_var = "rateuom"
- ),
- inputevents_mv = list(
- index_var = "starttime",
- val_var = "rate",
- unit_var = "rateuom"
- ),
- labevents = list(
- index_var = "charttime",
- val_var = "valuenum",
- unit_var = "valueuom"
- ),
- microbiologyevents = list(
- index_var = "chartdate",
- val_var = "isolate_num"
- ),
- noteevents = list(
- index_var = "chartdate",
- val_var = "text"
- ),
- outputevents = list(
- index_var = "charttime",
- val_var = "value",
- unit_var = "valueuom"
- ),
- patients = list(
- val_var = "expire_flag"
- ),
- prescriptions = list(
- index_var = "startdate",
- val_var = "dose_val_rx",
- unit_var = "dose_unit_rx"
- ),
- procedureevents_mv = list(
- index_var = "starttime",
- val_var = "value",
- unit_var = "valueuom"
- ),
- procedures_icd = list(
- val_var = "icd9_code"
- ),
- services = list(
- index_var = "transfertime",
- val_var = "curr_service"
- ),
- transfers = list(
- index_var = "intime",
- val_var = "curr_careunit"
- )
- )
-
- part <- list(
- chartevents = list(
- itemid = `if`(is_demo,
- 100000L,
- c( 127L, 210L, 425L, 549L, 643L, 741L, 1483L,
- 3458L, 3695L, 8440L, 8553L, 220274L, 223921L, 224085L,
- 224859L, 227629L
- )
- )
- )
- )
-
- info <- info[
- !grepl("^chartevents_", vapply(info, `[[`, character(1L), "table_name"))
- ]
-
- if (is_demo) {
-
- info <- lapply(info, `[[<-`, "num_rows", NULL)
-
- info <- info[
- vapply(info, `[[`, character(1L), "table_name") != "noteevents"
- ]
-
- } else {
-
- info <- lapply(info, function(x) {
- x[["cols"]] <- Map(`[[<-`, x[["cols"]], "col",
- toupper(vapply(x[["cols"]], `[[`, character(1L), "col"))
- )
- x
- })
-
- icd_diag <- find_entry(info, "table_name", "d_icd_diagnoses")
- info[[icd_diag]]$num_rows <- 14567L
-
- icd_proc <- find_entry(info, "table_name", "d_icd_procedures")
- info[[icd_proc]]$num_rows <- 3882L
-
- note <- find_entry(info, "table_name", "noteevents")
- date <- find_entry(info[[note]]$cols, "name", "chartdate")
- info[[note]]$cols[[date]]$format <- "%Y-%m-%d"
- }
-
- time_vars <- lapply(info, function(x) {
- nme <- vapply(x[["cols"]], `[[`, character(1L), "name")
- typ <- vapply(x[["cols"]], `[[`, character(1L), "spec")
- nme[typ == "col_datetime"]
- })
-
- names(time_vars) <- vapply(info, `[[`, character(1L), "table_name")
-
- as_tbl_spec(files, defaults, time_vars, info, part)
-}
-
-hirid_tbl_cfg <- function() {
-
- info <- list(
- general = list(
- patientid = list(spec = "col_integer"),
- admissiontime = list(spec = "col_datetime",
- format = "%Y-%m-%d %H:%M:%S"),
- sex = list(spec = "col_character"),
- age = list(spec = "col_integer"),
- discharge_status = list(spec = "col_character")
- ),
- observations = list(
- patientid = list(spec = "col_integer"),
- datetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- entertime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- status = list(spec = "col_integer"),
- stringvalue = list(spec = "col_character"),
- type = list(spec = "col_character"),
- value = list(spec = "col_double"),
- variableid = list(spec = "col_integer")
- ),
- ordinal = list(
- variableid = list(spec = "col_integer"),
- code = list(spec = "col_integer"),
- stringvalue = list(spec = "col_character")
- ),
- pharma = list(
- patientid = list(spec = "col_integer"),
- pharmaid = list(spec = "col_integer"),
- givenat = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- enteredentryat = list(spec = "col_datetime",
- format = "%Y-%m-%d %H:%M:%S"),
- givendose = list(spec = "col_double"),
- cumulativedose = list(spec = "col_double"),
- fluidamount_calc = list(spec = "col_double"),
- cumulfluidamount_calc = list(spec = "col_double"),
- doseunit = list(spec = "col_character"),
- route = list(spec = "col_character"),
- infusionid = list(spec = "col_integer"),
- typeid = list(spec = "col_integer"),
- subtypeid = list(spec = "col_double"),
- recordstatus = list(spec = "col_integer")
- ),
- variables = list(
- `Source Table` = list(spec = "col_character"),
- ID = list(spec = "col_integer"),
- `Variable Name` = list(spec = "col_character"),
- Unit = list(spec = "col_character"),
- `Additional information` = list(spec = "col_character")
- )
- )
-
- files <- list(
- general = "general_table.csv",
- observations = file.path(
- "observation_tables", "csv", paste0("part-", 0L:249L, ".csv")
- ),
- ordinal = "ordinal_vars_ref.csv",
- pharma = file.path(
- "pharma_records", "csv", paste0("part-", 0L:249L, ".csv")
- ),
- variables = "hirid_variable_reference.csv"
- )
-
- defaults <- list(
- general = list(
- index_var = "admissiontime"
- ),
- observations = list(
- index_var = "datetime",
- val_var = "value"
- ),
- ordinal = list(
- id_var = "variableid"
- ),
- pharma = list(
- index_var = "givenat",
- val_var = "givendose",
- unit_var = "doseunit"
- ),
- variables = list(
- id_var = "id"
- )
- )
-
- n_row <- list(
- general = 33905L,
- variables = 712L,
- ordinal = 72L,
- pharma = 16270399L,
- observations = 776921131L
- )
-
- zip_files <- list(
- general = "reference_data.tar.gz",
- variables = "reference_data.tar.gz",
- ordinal = "reference_data.tar.gz",
- pharma = "raw_stage/pharma_records_csv.tar.gz",
- observations = "raw_stage/observation_tables_csv.tar.gz"
- )
-
- part <- list(
- observations = list(variableid = c(
- 110L, 120L, 200L, 210L, 211L, 300L, 620L,
- 2010L, 2610L, 3110L, 4000L, 5685L, 15001565L, 30005075L)
- ),
- pharma = list(pharmaid = 431L)
- )
-
- info <- lapply(info, function(x) {
- Map(c, Map(list, name = sub(" ", "_", tolower(names(x))),
- col = names(x)), x)
- })
-
- info <- Map(list, table_name = names(info), cols = info,
- num_rows = n_row[names(info)],
- zip_file = zip_files[names(info)])
-
- time_vars <- lapply(info, function(x) {
- nme <- vapply(x[["cols"]], `[[`, character(1L), "name")
- typ <- vapply(x[["cols"]], `[[`, character(1L), "spec")
- nme[typ == "col_datetime"]
- })
-
- names(time_vars) <- vapply(info, `[[`, character(1L), "table_name")
-
- as_tbl_spec(files, defaults, time_vars, info, part)
-}
-
-aumc_tbl_cfg <- function() {
-
- info <- list(
- admissions = list(
- patientid = list(spec = "col_integer"),
- admissionid = list(spec = "col_integer"),
- admissioncount = list(spec = "col_integer"),
- location = list(spec = "col_character"),
- urgency = list(spec = "col_logical"),
- origin = list(spec = "col_character"),
- admittedat = list(spec = "col_double"),
- admissionyeargroup = list(spec = "col_character"),
- dischargedat = list(spec = "col_double"),
- lengthofstay = list(spec = "col_integer"),
- destination = list(spec = "col_character"),
- gender = list(spec = "col_character"),
- agegroup = list(spec = "col_character"),
- dateofdeath = list(spec = "col_double"),
- weightgroup = list(spec = "col_character"),
- weightsource = list(spec = "col_character"),
- specialty = list(spec = "col_character")
- ),
- drugitems = list(
- admissionid = list(spec = "col_integer"),
- orderid = list(spec = "col_integer"),
- ordercategoryid = list(spec = "col_integer"),
- ordercategory = list(spec = "col_character"),
- itemid = list(spec = "col_integer"),
- item = list(spec = "col_character"),
- isadditive = list(spec = "col_logical"),
- isconditional = list(spec = "col_logical"),
- rate = list(spec = "col_double"),
- rateunit = list(spec = "col_character"),
- rateunitid = list(spec = "col_integer"),
- ratetimeunitid = list(spec = "col_integer"),
- doserateperkg = list(spec = "col_logical"),
- dose = list(spec = "col_double"),
- doseunit = list(spec = "col_character"),
- doserateunit = list(spec = "col_character"),
- doseunitid = list(spec = "col_integer"),
- doserateunitid = list(spec = "col_integer"),
- administered = list(spec = "col_double"),
- administeredunit = list(spec = "col_character"),
- administeredunitid = list(spec = "col_integer"),
- action = list(spec = "col_character"),
- start = list(spec = "col_double"),
- stop = list(spec = "col_double"),
- duration = list(spec = "col_integer"),
- solutionitemid = list(spec = "col_integer"),
- solutionitem = list(spec = "col_character"),
- solutionadministered = list(spec = "col_double"),
- solutionadministeredunit = list(spec = "col_character"),
- fluidin = list(spec = "col_double"),
- iscontinuous = list(spec = "col_logical")
- ),
- freetextitems = list(
- admissionid = list(spec = "col_integer"),
- itemid = list(spec = "col_integer"),
- item = list(spec = "col_character"),
- value = list(spec = "col_character"),
- comment = list(spec = "col_character"),
- measuredat = list(spec = "col_double"),
- registeredat = list(spec = "col_double"),
- registeredby = list(spec = "col_character"),
- updatedat = list(spec = "col_double"),
- updatedby = list(spec = "col_character"),
- islabresult = list(spec = "col_logical")
- ),
- listitems = list(
- admissionid = list(spec = "col_integer"),
- itemid = list(spec = "col_integer"),
- item = list(spec = "col_character"),
- valueid = list(spec = "col_integer"),
- value = list(spec = "col_character"),
- measuredat = list(spec = "col_double"),
- registeredat = list(spec = "col_double"),
- registeredby = list(spec = "col_character"),
- updatedat = list(spec = "col_double"),
- updatedby = list(spec = "col_character"),
- islabresult = list(spec = "col_logical")
- ),
- numericitems = list(
- admissionid = list(spec = "col_integer"),
- itemid = list(spec = "col_integer"),
- item = list(spec = "col_character"),
- tag = list(spec = "col_character"),
- value = list(spec = "col_double"),
- unitid = list(spec = "col_integer"),
- unit = list(spec = "col_character"),
- comment = list(spec = "col_character"),
- measuredat = list(spec = "col_double"),
- registeredat = list(spec = "col_double"),
- registeredby = list(spec = "col_character"),
- updatedat = list(spec = "col_double"),
- updatedby = list(spec = "col_character"),
- islabresult = list(spec = "col_logical"),
- fluidout = list(spec = "col_double")
- ),
- procedureorderitems = list(
- admissionid = list(spec = "col_integer"),
- orderid = list(spec = "col_integer"),
- ordercategoryid = list(spec = "col_integer"),
- ordercategoryname = list(spec = "col_character"),
- itemid = list(spec = "col_integer"),
- item = list(spec = "col_character"),
- registeredat = list(spec = "col_double"),
- registeredby = list(spec = "col_character")
- ),
- processitems = list(
- admissionid = list(spec = "col_integer"),
- itemid = list(spec = "col_integer"),
- item = list(spec = "col_character"),
- start = list(spec = "col_double"),
- stop = list(spec = "col_double"),
- duration = list(spec = "col_integer")
- )
- )
-
- tables <- names(info)
-
- cols <- lapply(info, function(tbl) {
- Map(function(name, spec) c(list(name = name), spec), names(tbl), tbl)
- })
-
- defaults <- list(
- admissions = list(
- index_var = "admittedat",
- time_vars = c("admittedat", "dischargedat", "dateofdeath")
- ),
- drugitems = list(
- index_var = "start",
- val_var = "dose",
- unit_var = "doseunit",
- time_vars = c("start", "stop")
- ),
- freetextitems = list(
- index_var = "measuredat",
- id_var = "value",
- time_vars = c("measuredat", "registeredat", "updatedat")
- ),
- listitems = list(
- index_var = "measuredat",
- val_var = "value",
- time_vars = c("measuredat", "registeredat", "updatedat")
- ),
- numericitems = list(
- index_var = "measuredat",
- val_var = "value",
- unit_var = "unit",
- time_vars = c("measuredat", "registeredat", "updatedat")
- ),
- procedureorderitems = list(
- index_var = "registeredat",
- val_var = "item",
- time_vars = "registeredat"
- ),
- processitems = list(
- index_var = "start",
- val_var = "item",
- time_vars = c("start", "stop")
- )
- )
-
- n_row <- list(
- admissions = 23106L,
- drugitems = 4907269L,
- freetextitems = 651248L,
- listitems = 30744065L,
- numericitems = 977625612L,
- procedureorderitems = 2188626L,
- processitems = 256715L
- )
-
- part <- list(
- listitems = list(col = "itemid", breaks = 12290L),
- numericitems = list(col = "itemid", breaks = c(
- 6641L, 6642L, 6643L, 6664L, 6666L, 6667L, 6669L, 6672L, 6673L,
- 6675L, 6707L, 6709L, 8874L, 12270L, 12275L, 12278L, 12281L, 12286L,
- 12303L, 12561L, 12576L, 12804L, 14841L)
- )
- )
-
- tables <- Map(list, files = setNames(paste0(tables, ".csv"), tables),
- defaults = defaults[tables], num_rows = n_row[tables],
- cols = cols[tables])
-
- tables[names(part)] <- Map(`[[<-`, tables[names(part)], "partitioning", part)
-
- tables
-}
-
-miiv_tbl_cfg <- function() {
-
- info <- list(
- admissions = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- admittime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- dischtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- deathtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- admission_type = list(spec = "col_character"),
- admission_location = list(spec = "col_character"),
- discharge_location = list(spec = "col_character"),
- insurance = list(spec = "col_character"),
- language = list(spec = "col_character"),
- marital_status = list(spec = "col_character"),
- ethnicity = list(spec = "col_character"),
- edregtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- edouttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- hospital_expire_flag = list(spec = "col_integer")
- ),
- patients = list(
- subject_id = list(spec = "col_integer"),
- gender = list(spec = "col_character"),
- anchor_age = list(spec = "col_integer"),
- anchor_year = list(spec = "col_integer"),
- anchor_year_group = list(spec = "col_character"),
- dod = list(spec = "col_datetime", format = "%Y-%m-%d")
- ),
- transfers = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- transfer_id = list(spec = "col_integer"),
- eventtype = list(spec = "col_character"),
- careunit = list(spec = "col_character"),
- intime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- outtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S")
- ),
- d_hcpcs = list(
- code = list(spec = "col_character"),
- category = list(spec = "col_integer"),
- long_description = list(spec = "col_character"),
- short_description = list(spec = "col_character")
- ),
- diagnoses_icd = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- seq_num = list(spec = "col_integer"),
- icd_code = list(spec = "col_character"),
- icd_version = list(spec = "col_integer")
- ),
- d_icd_diagnoses = list(
- icd_code = list(spec = "col_character"),
- icd_version = list(spec = "col_integer"),
- long_title = list(spec = "col_character")
- ),
- d_icd_procedures = list(
- icd_code = list(spec = "col_character"),
- icd_version = list(spec = "col_integer"),
- long_title = list(spec = "col_character")
- ),
- d_labitems = list(
- itemid = list(spec = "col_integer"),
- label = list(spec = "col_character"),
- fluid = list(spec = "col_character"),
- category = list(spec = "col_character"),
- loinc_code = list(spec = "col_character")
- ),
- drgcodes = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- drg_type = list(spec = "col_character"),
- drg_code = list(spec = "col_character"),
- description = list(spec = "col_character"),
- drg_severity = list(spec = "col_integer"),
- drg_mortality = list(spec = "col_integer")
- ),
- emar_detail = list(
- subject_id = list(spec = "col_integer"),
- emar_id = list(spec = "col_character"),
- emar_seq = list(spec = "col_integer"),
- parent_field_ordinal = list(spec = "col_double"),
- administration_type = list(spec = "col_character"),
- pharmacy_id = list(spec = "col_integer"),
- barcode_type = list(spec = "col_character"),
- reason_for_no_barcode = list(spec = "col_character"),
- complete_dose_not_given = list(spec = "col_character"),
- dose_due = list(spec = "col_character"),
- dose_due_unit = list(spec = "col_character"),
- dose_given = list(spec = "col_character"),
- dose_given_unit = list(spec = "col_character"),
- will_remainder_of_dose_be_given = list(spec = "col_character"),
- product_amount_given = list(spec = "col_character"),
- product_unit = list(spec = "col_character"),
- product_code = list(spec = "col_character"),
- product_description = list(spec = "col_character"),
- product_description_other = list(spec = "col_character"),
- prior_infusion_rate = list(spec = "col_character"),
- infusion_rate = list(spec = "col_character"),
- infusion_rate_adjustment = list(spec = "col_character"),
- infusion_rate_adjustment_amount = list(spec = "col_character"),
- infusion_rate_unit = list(spec = "col_character"),
- route = list(spec = "col_character"),
- infusion_complete = list(spec = "col_character"),
- completion_interval = list(spec = "col_character"),
- new_iv_bag_hung = list(spec = "col_character"),
- continued_infusion_in_other_location = list(spec = "col_character"),
- restart_interval = list(spec = "col_character"),
- side = list(spec = "col_character"),
- site = list(spec = "col_character"),
- non_formulary_visual_verification = list(spec = "col_character")
- ),
- emar = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- emar_id = list(spec = "col_character"),
- emar_seq = list(spec = "col_integer"),
- poe_id = list(spec = "col_character"),
- pharmacy_id = list(spec = "col_integer"),
- charttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- medication = list(spec = "col_character"),
- event_txt = list(spec = "col_character"),
- scheduletime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S")
- ),
- hcpcsevents = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- chartdate = list(spec = "col_datetime", format = "%Y-%m-%d"),
- hcpcs_cd = list(spec = "col_character"),
- seq_num = list(spec = "col_integer"),
- short_description = list(spec = "col_character")
- ),
- labevents = list(
- labevent_id = list(spec = "col_integer"),
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- specimen_id = list(spec = "col_integer"),
- itemid = list(spec = "col_integer"),
- charttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- value = list(spec = "col_character"),
- valuenum = list(spec = "col_double"),
- valueuom = list(spec = "col_character"),
- ref_range_lower = list(spec = "col_double"),
- ref_range_upper = list(spec = "col_double"),
- flag = list(spec = "col_character"),
- priority = list(spec = "col_character"),
- comments = list(spec = "col_character")
- ),
- microbiologyevents = list(
- microevent_id = list(spec = "col_integer"),
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- micro_specimen_id = list(spec = "col_integer"),
- chartdate = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- charttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- spec_itemid = list(spec = "col_integer"),
- spec_type_desc = list(spec = "col_character"),
- test_seq = list(spec = "col_integer"),
- storedate = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- test_itemid = list(spec = "col_integer"),
- test_name = list(spec = "col_character"),
- org_itemid = list(spec = "col_integer"),
- org_name = list(spec = "col_character"),
- isolate_num = list(spec = "col_integer"),
- quantity = list(spec = "col_character"),
- ab_itemid = list(spec = "col_integer"),
- ab_name = list(spec = "col_character"),
- dilution_text = list(spec = "col_character"),
- dilution_comparison = list(spec = "col_character"),
- dilution_value = list(spec = "col_double"),
- interpretation = list(spec = "col_character"),
- comments = list(spec = "col_character")
- ),
- pharmacy = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- pharmacy_id = list(spec = "col_integer"),
- poe_id = list(spec = "col_character"),
- starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- stoptime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- medication = list(spec = "col_character"),
- proc_type = list(spec = "col_character"),
- status = list(spec = "col_character"),
- entertime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- verifiedtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- route = list(spec = "col_character"),
- frequency = list(spec = "col_character"),
- disp_sched = list(spec = "col_character"),
- infusion_type = list(spec = "col_character"),
- sliding_scale = list(spec = "col_character"),
- lockout_interval = list(spec = "col_character"),
- basal_rate = list(spec = "col_double"),
- one_hr_max = list(spec = "col_character"),
- doses_per_24_hrs = list(spec = "col_double"),
- duration = list(spec = "col_double"),
- duration_interval = list(spec = "col_character"),
- expiration_value = list(spec = "col_integer"),
- expiration_unit = list(spec = "col_character"),
- expirationdate = list(spec = "col_datetime",
- format = "%Y-%m-%d %H:%M:%S"),
- dispensation = list(spec = "col_character"),
- fill_quantity = list(spec = "col_character")
- ),
- poe_detail = list(
- poe_id = list(spec = "col_character"),
- poe_seq = list(spec = "col_integer"),
- subject_id = list(spec = "col_integer"),
- field_name = list(spec = "col_character"),
- field_value = list(spec = "col_character")
- ),
- poe = list(
- poe_id = list(spec = "col_character"),
- poe_seq = list(spec = "col_integer"),
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- ordertime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- order_type = list(spec = "col_character"),
- order_subtype = list(spec = "col_character"),
- transaction_type = list(spec = "col_character"),
- discontinue_of_poe_id = list(spec = "col_character"),
- discontinued_by_poe_id = list(spec = "col_character"),
- order_status = list(spec = "col_character")
- ),
- prescriptions = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- pharmacy_id = list(spec = "col_integer"),
- starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- stoptime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- drug_type = list(spec = "col_character"),
- drug = list(spec = "col_character"),
- gsn = list(spec = "col_character"),
- ndc = list(spec = "col_character"),
- prod_strength = list(spec = "col_character"),
- form_rx = list(spec = "col_character"),
- dose_val_rx = list(spec = "col_character"),
- dose_unit_rx = list(spec = "col_character"),
- form_val_disp = list(spec = "col_character"),
- form_unit_disp = list(spec = "col_character"),
- doses_per_24_hrs = list(spec = "col_double"),
- route = list(spec = "col_character")
- ),
- procedures_icd = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- seq_num = list(spec = "col_integer"),
- chartdate = list(spec = "col_datetime", format = "%Y-%m-%d"),
- icd_code = list(spec = "col_character"),
- icd_version = list(spec = "col_integer")
- ),
- services = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- transfertime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- prev_service = list(spec = "col_character"),
- curr_service = list(spec = "col_character")
- ),
- chartevents = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- stay_id = list(spec = "col_integer"),
- charttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- itemid = list(spec = "col_integer"),
- value = list(spec = "col_character"),
- valuenum = list(spec = "col_double"),
- valueuom = list(spec = "col_character"),
- warning = list(spec = "col_integer")
- ),
- datetimeevents = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- stay_id = list(spec = "col_integer"),
- charttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- itemid = list(spec = "col_integer"),
- value = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- valueuom = list(spec = "col_character"),
- warning = list(spec = "col_integer")
- ),
- d_items = list(
- itemid = list(spec = "col_integer"),
- label = list(spec = "col_character"),
- abbreviation = list(spec = "col_character"),
- linksto = list(spec = "col_character"),
- category = list(spec = "col_character"),
- unitname = list(spec = "col_character"),
- param_type = list(spec = "col_character"),
- lownormalvalue = list(spec = "col_double"),
- highnormalvalue = list(spec = "col_double")
- ),
- icustays = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- stay_id = list(spec = "col_integer"),
- first_careunit = list(spec = "col_character"),
- last_careunit = list(spec = "col_character"),
- intime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- outtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- los = list(spec = "col_double")
- ),
- inputevents = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- stay_id = list(spec = "col_integer"),
- starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- endtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- itemid = list(spec = "col_integer"),
- amount = list(spec = "col_double"),
- amountuom = list(spec = "col_character"),
- rate = list(spec = "col_double"),
- rateuom = list(spec = "col_character"),
- orderid = list(spec = "col_integer"),
- linkorderid = list(spec = "col_integer"),
- ordercategoryname = list(spec = "col_character"),
- secondaryordercategoryname = list(spec = "col_character"),
- ordercomponenttypedescription = list(spec = "col_character"),
- ordercategorydescription = list(spec = "col_character"),
- patientweight = list(spec = "col_double"),
- totalamount = list(spec = "col_double"),
- totalamountuom = list(spec = "col_character"),
- isopenbag = list(spec = "col_integer"),
- continueinnextdept = list(spec = "col_integer"),
- cancelreason = list(spec = "col_integer"),
- statusdescription = list(spec = "col_character"),
- originalamount = list(spec = "col_double"),
- originalrate = list(spec = "col_double")
- ),
- outputevents = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- stay_id = list(spec = "col_integer"),
- charttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- itemid = list(spec = "col_integer"),
- value = list(spec = "col_double"),
- valueuom = list(spec = "col_character")
- ),
- procedureevents = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- stay_id = list(spec = "col_integer"),
- starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- endtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- itemid = list(spec = "col_integer"),
- value = list(spec = "col_double"),
- valueuom = list(spec = "col_character"),
- location = list(spec = "col_character"),
- locationcategory = list(spec = "col_character"),
- orderid = list(spec = "col_integer"),
- linkorderid = list(spec = "col_integer"),
- ordercategoryname = list(spec = "col_character"),
- secondaryordercategoryname = list(spec = "col_character"),
- ordercategorydescription = list(spec = "col_character"),
- patientweight = list(spec = "col_double"),
- totalamount = list(spec = "col_double"),
- totalamountuom = list(spec = "col_character"),
- isopenbag = list(spec = "col_integer"),
- continueinnextdept = list(spec = "col_integer"),
- cancelreason = list(spec = "col_integer"),
- statusdescription = list(spec = "col_character"),
- comments_date = list(spec = "col_datetime",
- format = "%Y-%m-%d %H:%M:%S"),
- originalamount = list(spec = "col_double"),
- originalrate = list(spec = "col_double")
- ),
- omr = list(
- subject_id = list(spec = "col_integer"),
- chartdate = list(spec = "col_datetime", format = "%Y-%m-%d"),
- seq_num = list(spec = "col_integer"),
- result_name = list(spec = "col_character"),
- result_value = list(spec = "col_character")
- ),
- caregiver = list(
- caregiver_id = list(spec = "col_integer")
- ),
- provider = list(
- provider_id = list(spec = "col_character")
- ),
- ingredientevents = list(
- subject_id = list(spec = "col_integer"),
- hadm_id = list(spec = "col_integer"),
- stay_id = list(spec = "col_integer"),
- starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- endtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
- itemid = list(spec = "col_integer"),
- amount = list(spec = "col_double"),
- amountuom = list(spec = "col_character"),
- rate = list(spec = "col_double"),
- rateuom = list(spec = "col_character"),
- orderid = list(spec = "col_integer"),
- linkorderid = list(spec = "col_integer"),
- statusdescription = list(spec = "col_character"),
- originalamount = list(spec = "col_double"),
- originalrate = list(spec = "col_double")
- )
- )
-
- tables <- names(info)
-
- cols <- lapply(info, function(tbl) {
- Map(function(name, spec) c(list(name = name), spec), names(tbl), tbl)
- })
-
- defaults <- list(
- admissions = list(
- val_var = "admission_type"
- ),
- d_hcpcs = list(
- id_var = "code",
- val_var = "short_description"
- ),
- d_icd_diagnoses = list(
- id_var = "icd_code",
- val_var = "long_title"
- ),
- d_icd_procedures = list(
- id_var = "icd_code",
- val_var = "long_title"
- ),
- d_labitems = list(
- id_var = "itemid",
- val_var = "label"
- ),
- diagnoses_icd = list(
- val_var = "icd_code"
- ),
- drgcodes = list(
- val_var = "drg_code"
- ),
- emar_detail = list(
- id_var = "emar_id"
- ),
- emar = list(
- index_var = "charttime"
- ),
- hcpcsevents = list(
- index_var = "chartdate"
- ),
- labevents = list(
- index_var = "charttime",
- val_var = "valuenum",
- unit_var = "valueuom"
- ),
- microbiologyevents = list(
- index_var = "chartdate",
- val_var = "isolate_num"
- ),
- pharmacy = list(
- id_var = "pharmacy_id",
- index_var = "starttime",
- val_var = "duration",
- unit_var = "duration_interval"
- ),
- poe_detail = list(
- id_var = "poe_id"
- ),
- poe = list(
- index_var = "ordertime"
- ),
- prescriptions = list(
- index_var = "starttime",
- val_var = "dose_val_rx",
- unit_var = "dose_unit_rx"
- ),
- procedures_icd = list(
- index_var = "chartdate",
- val_var = "icd_code"
- ),
- services = list(
- index_var = "transfertime",
- val_var = "curr_service"
- ),
- chartevents = list(
- index_var = "charttime",
- val_var = "valuenum",
- unit_var = "valueuom"
- ),
- d_items = list(
- id_var = "itemid",
- val_var = "label"
- ),
- datetimeevents = list(
- index_var = "charttime",
- val_var = "itemid"
- ),
- icustays = list(
- index_var = "intime",
- val_var = "last_careunit"
- ),
- inputevents = list(
- index_var = "starttime",
- val_var = "rate",
- unit_var = "rateuom"
- ),
- outputevents = list(
- index_var = "charttime",
- val_var = "value",
- unit_var = "valueuom"
- ),
- procedureevents = list(
- index_var = "starttime",
- val_var = "value",
- unit_var = "valueuom"
- ),
- omr = list(
- index_var = "chartdate",
- val_var = "result_value"
- ),
- caregiver = list(),
- provider = list(),
- ingredientevents = list(
- index_var = "starttime",
- val_var = "rate",
- unit_var = "rateuom"
- )
- )
-
- defaults <- Map(function(cl, df) {
- nme <- vapply(cl, `[[`, character(1L), "name")
- typ <- vapply(cl, `[[`, character(1L), "spec")
- tim <- nme[typ == "col_datetime"]
- if (length(tim)) c(df, list(time_vars = tim)) else df
- }, cols[tables], defaults[tables])
-
- n_row <- c(
- admissions = 431231L,
- patients = 299712L,
- transfers = 1890972L,
- d_hcpcs = 89200L,
- d_icd_diagnoses = 109775L,
- d_icd_procedures = 85257L,
- d_labitems = 1622L,
- diagnoses_icd = 4756326L,
- drgcodes = 604377L,
- emar_detail = 54744789L,
- emar = 26850359L,
- hcpcsevents = 150771L,
- labevents = 118171367L,
- microbiologyevents = 3228713L,
- pharmacy = 13584514L,
- poe_detail = 3879418L,
- poe = 39366291L,
- prescriptions = 15416708L,
- procedures_icd = 669186L,
- services = 468029L,
- chartevents = 313645063L,
- d_items = 4014L,
- datetimeevents = 7112999L,
- icustays = 73181L,
- inputevents = 8978893L,
- outputevents = 4234967L,
- procedureevents = 696092L,
- omr = 6439169L,
- caregiver = 15468L,
- provider = 40508L,
- ingredientevents = 11627821L
- )
-
- files <- c(
- admissions = "hosp/admissions.csv.gz",
- patients = "hosp/patients.csv.gz",
- transfers = "hosp/transfers.csv.gz",
- d_hcpcs = "hosp/d_hcpcs.csv.gz",
- d_icd_diagnoses = "hosp/d_icd_diagnoses.csv.gz",
- d_icd_procedures = "hosp/d_icd_procedures.csv.gz",
- d_labitems = "hosp/d_labitems.csv.gz",
- diagnoses_icd = "hosp/diagnoses_icd.csv.gz",
- drgcodes = "hosp/drgcodes.csv.gz",
- emar_detail = "hosp/emar_detail.csv.gz",
- emar = "hosp/emar.csv.gz",
- hcpcsevents = "hosp/hcpcsevents.csv.gz",
- labevents = "hosp/labevents.csv.gz",
- microbiologyevents = "hosp/microbiologyevents.csv.gz",
- pharmacy = "hosp/pharmacy.csv.gz",
- poe_detail = "hosp/poe_detail.csv.gz",
- poe = "hosp/poe.csv.gz",
- prescriptions = "hosp/prescriptions.csv.gz",
- procedures_icd = "hosp/procedures_icd.csv.gz",
- services = "hosp/services.csv.gz",
- chartevents = "icu/chartevents.csv.gz",
- d_items = "icu/d_items.csv.gz",
- datetimeevents = "icu/datetimeevents.csv.gz",
- icustays = "icu/icustays.csv.gz",
- inputevents = "icu/inputevents.csv.gz",
- outputevents = "icu/outputevents.csv.gz",
- procedureevents = "icu/procedureevents.csv.gz",
- omr = "hosp/omr.csv.gz",
- caregiver = "hosp/caregiver.csv.gz",
- provider = "hosp/provider.csv.gz",
- ingredientevents = "icu/ingredientevents.csv.gz"
- )
-
- part <- list(
- labevents = list(
- col = "itemid",
- breaks = c(
- 50868L, 50902L, 50943L, 50983L, 51146L, 51248L, 51256L, 51279L,
- 51491L
- )
- ),
- chartevents = list(
- col = "itemid",
- breaks = c(
- 220048L, 220059L, 220181L, 220228L, 220615L, 223782L, 223835L,
- 223905L, 223962L, 223990L, 224015L, 224055L, 224082L, 224093L,
- 224328L, 224650L, 224701L, 224850L, 225072L, 226104L, 227240L,
- 227467L, 227950L, 227960L, 228004L, 228397L, 228594L, 228924L,
- 229124L
- )
- ),
- poe = list(
- col = "subject_id",
- breaks = c(12017899L, 13999829L, 15979442L, 17994364L)
- )
- )
-
- tables <- Map(list, files = files[tables],
- defaults = defaults[tables], num_rows = n_row[tables],
- cols = cols[tables])
-
- tables[names(part)] <- Map(`[[<-`, tables[names(part)], "partitioning", part)
-
- tables
-}
-
-sic_tbl_cfg <- function() {
-
- info <- list(
- cases = list(
- caseid = list(name = "CaseID", spec = "col_integer"),
- patientid = list(name = "PatientID", spec = "col_integer"),
- admissionyear = list(name = "AdmissionYear", spec = "col_integer"),
- timeofstay = list(name = "TimeOfStay", spec = "col_integer"),
- icuoffset = list(name = "ICUOffset", spec = "col_integer"),
- saps3 = list(name = "saps3", spec = "col_double"),
- hospitaldischargetype = list(name = "HospitalDischargeType",
- spec = "col_integer"),
- dischargestate = list(name = "DischargeState",
- spec = "col_integer"),
- dischargeunit = list(name = "DischargeUnit",
- spec = "col_integer"),
- offsetofdeath = list(name = "OffsetOfDeath",
- spec = "col_integer"),
- estimatedsurvivalobservationtime = list(name = "EstimatedSurvivalObservationTime",
- spec = "col_integer"),
- sex = list(name = "Sex", spec = "col_integer"),
- weightonadmission = list(name = "WeightOnAdmission", spec = "col_double"),
- heightonadmission = list(name = "HeightOnAdmission", spec = "col_double"),
- ageonadmission = list(name = "AgeOnAdmission", spec = "col_integer"),
- hospitalunit = list(name = "HospitalUnit", spec = "col_integer"),
- referringunit = list(name = "ReferringUnit", spec = "col_integer"),
- icd10main = list(name = "ICD10Main", spec = "col_character"),
- icd10maintext = list(name = "ICD10MainText", spec = "col_character"),
- diagnosist2 = list(name = "DiagnosisT2", spec = "col_character"),
- surgicalsite = list(name = "SurgicalSite", spec = "col_integer"),
- hoursofcrrt = list(name = "HoursOfCRRT", spec = "col_integer"),
- admissionformhassepsis = list(name = "AdmissionFormHasSepsis", spec = "col_integer"),
- orbisdataavailable = list(name = "OrbisDataAvailable", spec = "col_character"),
- heartsurgeryadditionaldata = list(name = "HeartSurgeryAdditionalData",
- spec = "col_integer"),
- heartsurgerycrossclamptime = list(name = "HeartSurgeryCrossClampTime",
- spec = "col_integer"),
- heartsurgerybeginoffset = list(name = "HeartSurgeryBeginOffset",
- spec = "col_integer"),
- heartsurgeryendoffset = list(name = "HeartSurgeryEndOffset",
- spec = "col_integer"),
- offsetafterfirstadmission = list(name = "OffsetAfterFirstAdmission",
- spec = "col_integer")
- ),
- d_references = list(
- referenceglobalid = list(name = "ReferenceGlobalID",
- spec = "col_integer"),
- referencevalue = list(name = "ReferenceValue",
- spec = "col_character"),
- referencename = list(name = "ReferenceName",
- spec = "col_character"),
- referencedescription = list(name = "ReferenceDescription", spec = "col_character"),
- referenceunit = list(name = "ReferenceUnit", spec = "col_character"),
- referenceorder = list(name = "ReferenceOrder", spec = "col_integer"),
- referencetype = list(name = "ReferenceType", spec = "col_integer"),
- data = list(name = "Data", spec = "col_character")
- ),
- data_float_h = list(
- id = list(name = "id", spec = "col_integer"),
- caseid = list(name = "CaseID",
- spec = "col_integer"),
- dataid = list(name = "DataID",
- spec = "col_integer"),
- offset = list(name = "Offset",
- spec = "col_integer"),
- val = list(name = "Val", spec = "col_double"),
- cnt = list(name = "cnt", spec = "col_integer"),
- rawdata = list(name = "rawdata", spec = "col_double")
- ),
- data_ref = list(
- id = list(name = "id", spec = "col_integer"),
- caseid = list(name = "CaseID", spec = "col_integer"),
- refid = list(name = "RefID", spec = "col_integer"),
- customfieldid = list(name = "CustomFieldID", spec = "col_integer")
- ),
- laboratory = list(
- id = list(name = "id", spec = "col_integer"),
- caseid = list(name = "CaseID", spec = "col_integer"),
- laboratoryid = list(name = "LaboratoryID", spec = "col_integer"),
- offset = list(name = "Offset", spec = "col_integer"),
- laboratoryvalue = list(name = "LaboratoryValue", spec = "col_double"),
- laboratorytype = list(name = "LaboratoryType", spec = "col_integer")
- ),
- medication = list(
- id = list(name = "id", spec = "col_integer"),
- caseid = list(name = "CaseID",
- spec = "col_integer"),
- patientid = list(name = "PatientID",
- spec = "col_integer"),
- drugid = list(name = "DrugID",
- spec = "col_integer"),
- offset = list(name = "Offset",
- spec = "col_integer"),
- offsetdrugend = list(name = "OffsetDrugEnd",
- spec = "col_integer"),
- issingledose = list(name = "IsSingleDose",
- spec = "col_logical"),
- amount = list(name = "Amount",
- spec = "col_double"),
- amountperminute = list(name = "AmountPerMinute",
- spec = "col_double"),
- givenstate = list(name = "GivenState",
- spec = "col_integer")
- ),
- data_range = list(
- id = list(name = "id",
- spec = "col_integer"),
- caseid = list(name = "CaseID",
- spec = "col_integer"),
- dataid = list(name = "DataID",
- spec = "col_integer"),
- offset = list(name = "Offset",
- spec = "col_integer"),
- offsetend = list(name = "OffsetEnd",
- spec = "col_integer"),
- data = list(name = "Data",
- spec = "col_character")
- ),
- unitlog = list(
- id = list(name = "id",
- spec = "col_integer"),
- caseid = list(name = "CaseID",
- spec = "col_integer"),
- patientid = list(name = "PatientID",
- spec = "col_integer"),
- logstate = list(name = "LogState",
- spec = "col_integer"),
- offset = list(name = "Offset",
- spec = "col_integer"),
- hospitalunit = list(name = "HospitalUnit",
- spec = "col_integer")
- )
- )
-
- tables <- names(info)
- cols <- info
-
- defaults <- list(
- cases = list(
- index_var = "ICUOffset"
- ),
- d_references = list(),
- data_float_h = list(
- index_var = "Offset",
- val_var = "Val"
- ),
- data_ref = list(
- index_var = "OffsetAfterFirstAdmission"
- ),
- laboratory = list(
- index_var = "Offset",
- val_var = "LaboratoryValue"
- ),
- medication = list(
- index_var = "Offset",
- val_var = "Amount"
- ),
- data_range = list(
- index_var = "Offset"
- ),
- unitlog = list(
- index_var = "Offset"
- )
- )
-
- defaults <- Map(function(cl, df) {
- nme <- vapply(cl, `[[`, character(1L), "name")
- typ <- vapply(cl, `[[`, character(1L), "spec")
- tim <- nme[grep("offset", names(nme), ignore.case = TRUE)]
- if (length(tim)) c(df, list(time_vars = tim)) else df
- }, cols[tables], defaults[tables])
-
- n_row <- c(
- cases = 27386L,
- d_references = 1608L,
- data_float_h = 36785241L,
- data_range = 183339L,
- data_ref = 354157L,
- laboratory = 17572279L,
- medication = 5141346L,
- unitlog = 139968L
- )
-
- files <- c(
- cases = "cases.csv.gz",
- d_references = "d_references.csv.gz",
- data_float_h = "data_float_h.csv.gz",
- data_range = "data_range.csv.gz",
- data_ref = "data_ref.csv.gz",
- laboratory = "laboratory.csv.gz",
- medication = "medication.csv.gz",
- unitlog = "unitlog.csv.gz"
- )
-
- part <- list(
- data_float_h = list(
- col = "dataid",
- breaks = c(
- 1L, 2L, 3L, 4L, 7L, 28L, 29L, 702L, 703L, 705L, 708L, 709L, 710L, 715L,
- 717L, 719L, 724L, 725L, 731L, 773L, 2018L, 2274L, 2278L, 2280L, 2283L,
- 2290L, 3056L, 3059L, 3071L
- )
- )
- )
-
- tables <- Map(list, files = files[tables],
- defaults = defaults[tables], num_rows = n_row[tables],
- cols = cols[tables])
-
- tables[names(part)] <- Map(`[[<-`, tables[names(part)], "partitioning", part)
-
- tables
-}
-
-pkg_dir <- rprojroot::find_root(rprojroot::is_r_package)
-cfg_dir <- file.path(pkg_dir, "inst", "extdata", "config")
-
-eicu_id_cfg <- list(
- hadm = list(id = "patienthealthsystemstayid", position = 1L,
- start = "hospitaladmitoffset",
- end = "hospitaldischargeoffset", table = "patient"),
- icustay = list(id = "patientunitstayid", position = 2L,
- start = "unitadmitoffset", end = "unitdischargeoffset",
- table = "patient")
-)
-
-mimic_id_cfg <- list(
- patient = list(id = "subject_id", position = 1L, start = "dob",
- end = "dod", table = "patients"),
- hadm = list(id = "hadm_id", position = 2L, start = "admittime",
- end = "dischtime", table = "admissions"),
- icustay = list(id = "icustay_id", position = 3L, start = "intime",
- end = "outtime", table = "icustays")
-)
-
-eicu <- get_table_info(
- "https://mit-lcp.github.io/eicu-schema-spy/eicu.eicu_crd.xml"
-)
-
-mimic <- get_table_info(
- "https://mit-lcp.github.io/mimic-schema-spy/mimic.mimiciii.xml"
-)
-
-eicu_demo_tbls <- eicu_tbl_cfg(eicu, is_demo = TRUE)
-mimic_demo_tbls <- mimic_tbl_cfg(mimic, is_demo = TRUE)
-
-cfg <- list(
- list(
- name = "eicu",
- url = "https://physionet.org/files/eicu-crd/2.0",
- id_cfg = eicu_id_cfg,
- tables = eicu_tbl_cfg(eicu, is_demo = FALSE)
- ),
- list(
- name = "eicu_demo",
- class_prefix = c("eicu_demo", "eicu"),
- url = "https://physionet.org/files/eicu-crd-demo/2.0.1",
- id_cfg = eicu_id_cfg,
- tables = eicu_demo_tbls
- ),
- list(
- name = "mimic",
- url = "https://physionet.org/files/mimiciii/1.4",
- id_cfg = mimic_id_cfg,
- tables = mimic_tbl_cfg(mimic, is_demo = FALSE)
- ),
- list(
- name = "mimic_demo",
- class_prefix = c("mimic_demo", "mimic"),
- url = "https://physionet.org/files/mimiciii-demo/1.4",
- id_cfg = mimic_id_cfg,
- tables = mimic_demo_tbls
- ),
- list(
- name = "miiv",
- url = "https://physionet.org/files/mimiciv/2.2",
- id_cfg = list(
- patient = list(id = "subject_id", position = 1L, start = "anchor_year",
- end = "dod", table = "patients"),
- hadm = list(id = "hadm_id", position = 2L, start = "admittime",
- end = "dischtime", table = "admissions"),
- icustay = list(id = "stay_id", position = 3L, start = "intime",
- end = "outtime", table = "icustays")
- ),
- tables = miiv_tbl_cfg()
- ),
- list(
- name = "hirid",
- url = "https://physionet.org/files/hirid/1.1.1",
- id_cfg = list(
- icustay = list(id = "patientid", position = 1L, start = "admissiontime",
- table = "general")
- ),
- tables = hirid_tbl_cfg()
- ),
- list(
- name = "aumc",
- id_cfg = list(
- patient = list(id = "patientid", position = 1L,
- start = "firstadmittedat", end = "dateofdeath",
- table = "admissions"),
- icustay = list(id = "admissionid", position = 2L, start = "admittedat",
- end = "dischargedat", table = "admissions")
- ),
- unit_mapping = list(
- list(symbol = "uur", def = "1 hour"),
- list(symbol = "dag", def = "1 day")
- ),
- tables = aumc_tbl_cfg()
- ),
- list(
- name = "sic",
- url = "https://physionet.org/files/sicdb/1.0.6",
- id_cfg = list(
- patient = list(id = "PatientID", position = 1L,
- start = "ICUOffset", end = "OffsetOfDeath",
- table = "cases"),
- icustay = list(id = "CaseID", position = 2L, start = "ICUOffset",
- end = "TimeOfStay",
- table = "cases")
- ),
- tables = sic_tbl_cfg()
- )
-)
-
-ricu::set_config(cfg, "data-sources", cfg_dir)
-
-cfg <- list(
- list(
- name = "eicu_test",
- class_prefix = c("eicu_test", "eicu_demo", "eicu"),
- id_cfg = eicu_id_cfg,
- tables = lapply(eicu_demo_tbls, as_minimal_tbl_spec)
- ),
- list(
- name = "mimic_test",
- class_prefix = c("mimic_test", "mimic_demo", "mimic"),
- id_cfg = mimic_id_cfg,
- tables = lapply(mimic_demo_tbls, as_minimal_tbl_spec)
- )
-)
-
-ricu::set_config(cfg, "data-sources", file.path(pkg_dir, "inst", "testdata"))
-
-devtools::install(pkg_dir)
diff --git a/inst/extdata/config/data-sources/picdb.json b/inst/extdata/config/data-sources/picdb.json
new file mode 100644
index 00000000..adce0b71
--- /dev/null
+++ b/inst/extdata/config/data-sources/picdb.json
@@ -0,0 +1,847 @@
+[
+ {
+ "name": "picdb",
+ "url": "https://physionet.org/files/picdb/1.1.0",
+ "id_cfg": {
+ "patient": {
+ "id": "subject_id",
+ "position": 1,
+ "start": "dob",
+ "end": "dod",
+ "table": "patients"
+ },
+ "hadm": {
+ "id": "hadm_id",
+ "position": 2,
+ "start": "admittime",
+ "end": "dischtime",
+ "table": "admissions"
+ },
+ "icustay": {
+ "id": "icustay_id",
+ "position": 3,
+ "start": "intime",
+ "end": "outtime",
+ "table": "icustays"
+ }
+ },
+ "tables": {
+ "admissions": {
+ "files": "V1.1.0/ADMISSIONS.csv",
+ "defaults": {
+ "time_vars": [
+ "admittime",
+ "dischtime",
+ "deathtime",
+ "edregtime",
+ "edouttime"
+ ]
+ },
+ "num_rows": 13449,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "admittime": {
+ "name": "ADMITTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "dischtime": {
+ "name": "DISCHTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "deathtime": {
+ "name": "DEATHTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "admission_department": {
+ "name": "ADMISSION_DEPARTMENT",
+ "spec": "col_character"
+ },
+ "discharge_department": {
+ "name": "DISCHARGE_DEPARTMENT",
+ "spec": "col_character"
+ },
+ "insurance": {
+ "name": "INSURANCE",
+ "spec": "col_character"
+ },
+ "language": {
+ "name": "LANGUAGE",
+ "spec": "col_character"
+ },
+ "religion": {
+ "name": "RELIGION",
+ "spec": "col_character"
+ },
+ "marital_status": {
+ "name": "MARITAL_STATUS",
+ "spec": "col_character"
+ },
+ "ethnicity": {
+ "name": "ETHNICITY",
+ "spec": "col_character"
+ },
+ "edregtime": {
+ "name": "EDREGTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "edouttime": {
+ "name": "EDOUTTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "diagnosis": {
+ "name": "DIAGNOSIS",
+ "spec": "col_character"
+ },
+ "icd10_code_cn": {
+ "name": "ICD10_CODE_CN",
+ "spec": "col_character"
+ },
+ "hospital_expire_flag": {
+ "name": "HOSPITAL_EXPIRE_FLAG",
+ "spec": "col_integer"
+ },
+ "has_chartevents_data": {
+ "name": "HAS_CHARTEVENTS_DATA",
+ "spec": "col_integer"
+ }
+ }
+ },
+ "chartevents": {
+ "files": "V1.1.0/CHARTEVENTS.csv",
+ "defaults": {
+ "time_vars": [
+ "charttime",
+ "storetime"
+ ],
+ "index_var": "charttime",
+ "val_var": "valuenum",
+ "unit_var": "valueuom"
+ },
+ "num_rows": 2278978,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "icustay_id": {
+ "name": "ICUSTAY_ID",
+ "spec": "col_double"
+ },
+ "itemid": {
+ "name": "ITEMID",
+ "spec": "col_integer"
+ },
+ "charttime": {
+ "name": "CHARTTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "storetime": {
+ "name": "STORETIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "value": {
+ "name": "VALUE",
+ "spec": "col_double"
+ },
+ "valuenum": {
+ "name": "VALUENUM",
+ "spec": "col_double"
+ },
+ "valueuom": {
+ "name": "VALUEUOM",
+ "spec": "col_character"
+ }
+ }
+ },
+ "diagnoses_icd": {
+ "files": "V1.1.0/DIAGNOSES_ICD.csv",
+ "defaults": {
+ "val_var": "ICD10_CODE_CN"
+ },
+ "num_rows": 22712,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "seq_num": {
+ "name": "SEQ_NUM",
+ "spec": "col_integer"
+ },
+ "icd10_code_cn": {
+ "name": "ICD10_CODE_CN",
+ "spec": "col_character"
+ },
+ "diag_category": {
+ "name": "Diag_Category",
+ "spec": "col_character"
+ }
+ }
+ },
+ "d_icd_diagnoses": {
+ "files": "V1.1.0/D_ICD_DIAGNOSES.csv",
+ "defaults": {
+ },
+ "num_rows": 25379,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "icd10_code_cn": {
+ "name": "ICD10_CODE_CN",
+ "spec": "col_character"
+ },
+ "icd10_code": {
+ "name": "ICD10_CODE",
+ "spec": "col_character"
+ },
+ "title_cn": {
+ "name": "TITLE_CN",
+ "spec": "col_character"
+ },
+ "title": {
+ "name": "TITLE",
+ "spec": "col_character"
+ }
+ }
+ },
+ "d_items": {
+ "files": "V1.1.0/D_ITEMS.csv",
+ "defaults": {
+ },
+ "num_rows": 479,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "itemid": {
+ "name": "ITEMID",
+ "spec": "col_character"
+ },
+ "label_cn": {
+ "name": "LABEL_CN",
+ "spec": "col_character"
+ },
+ "label": {
+ "name": "LABEL",
+ "spec": "col_character"
+ },
+ "linksto": {
+ "name": "LINKSTO",
+ "spec": "col_character"
+ },
+ "category": {
+ "name": "CATEGORY",
+ "spec": "col_character"
+ },
+ "unitname": {
+ "name": "UNITNAME",
+ "spec": "col_character"
+ }
+ }
+ },
+ "d_labitems": {
+ "files": "V1.1.0/D_LABITEMS.csv",
+ "defaults": {
+ },
+ "num_rows": 832,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "itemid": {
+ "name": "ITEMID",
+ "spec": "col_integer"
+ },
+ "label_cn": {
+ "name": "LABEL_CN",
+ "spec": "col_character"
+ },
+ "label": {
+ "name": "LABEL",
+ "spec": "col_character"
+ },
+ "fluid": {
+ "name": "FLUID",
+ "spec": "col_character"
+ },
+ "category": {
+ "name": "CATEGORY",
+ "spec": "col_character"
+ },
+ "loinc_code": {
+ "name": "LOINC_CODE",
+ "spec": "col_character"
+ }
+ }
+ },
+ "emr_symptoms": {
+ "files": "V1.1.0/EMR_SYMPTOMS.csv",
+ "defaults": {
+ "time_vars": [
+ "recordtime"
+ ]
+ },
+ "num_rows": 402142,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "emr_id": {
+ "name": "EMR_ID",
+ "spec": "col_integer"
+ },
+ "recordtime": {
+ "name": "RECORDTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "symptom_name_cn": {
+ "name": "SYMPTOM_NAME_CN",
+ "spec": "col_character"
+ },
+ "symptom_name": {
+ "name": "SYMPTOM_NAME",
+ "spec": "col_character"
+ },
+ "symptom_attribute": {
+ "name": "SYMPTOM_ATTRIBUTE",
+ "spec": "col_character"
+ }
+ }
+ },
+ "icustays": {
+ "files": "V1.1.0/ICUSTAYS.csv",
+ "defaults": {
+ "time_vars": [
+ "intime",
+ "outtime"
+ ],
+ "index_var": "intime",
+ "val_var": "last_careunit"
+ },
+ "num_rows": 13941,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "icustay_id": {
+ "name": "ICUSTAY_ID",
+ "spec": "col_integer"
+ },
+ "first_careunit": {
+ "name": "FIRST_CAREUNIT",
+ "spec": "col_character"
+ },
+ "last_careunit": {
+ "name": "LAST_CAREUNIT",
+ "spec": "col_character"
+ },
+ "first_wardid": {
+ "name": "FIRST_WARDID",
+ "spec": "col_integer"
+ },
+ "last_wardid": {
+ "name": "LAST_WARDID",
+ "spec": "col_integer"
+ },
+ "intime": {
+ "name": "INTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "outtime": {
+ "name": "OUTTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "los": {
+ "name": "LOS",
+ "spec": "col_double"
+ }
+ }
+ },
+ "inputevents": {
+ "files": "V1.1.0/INPUTEVENTS.csv",
+ "defaults": {
+ "time_vars": [
+ "charttime",
+ "storetime"
+ ],
+ "index_var": "charttime",
+ "val_var": "amount",
+ "unit_var": "amountuom"
+ },
+ "num_rows": 26884,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "icustay_id": {
+ "name": "ICUSTAY_ID",
+ "spec": "col_double"
+ },
+ "charttime": {
+ "name": "CHARTTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "amount": {
+ "name": "AMOUNT",
+ "spec": "col_double"
+ },
+ "amountuom": {
+ "name": "AMOUNTUOM",
+ "spec": "col_character"
+ },
+ "storetime": {
+ "name": "STORETIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ }
+ }
+ },
+ "labevents": {
+ "files": "V1.1.0/LABEVENTS.csv",
+ "defaults": {
+ "time_vars": [
+ "charttime"
+ ],
+ "index_var": "charttime",
+ "val_var": "valuenum",
+ "unit_var": "valueuom"
+ },
+ "num_rows": 10094117,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "itemid": {
+ "name": "ITEMID",
+ "spec": "col_integer"
+ },
+ "charttime": {
+ "name": "CHARTTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "value": {
+ "name": "VALUE",
+ "spec": "col_character"
+ },
+ "valuenum": {
+ "name": "VALUENUM",
+ "spec": "col_double"
+ },
+ "valueuom": {
+ "name": "VALUEUOM",
+ "spec": "col_character"
+ },
+ "flag": {
+ "name": "FLAG",
+ "spec": "col_character"
+ }
+ }
+ },
+ "microbiologyevents": {
+ "files": "V1.1.0/MICROBIOLOGYEVENTS.csv",
+ "defaults": {
+ "time_vars": [
+ "charttime"
+ ],
+ "index_var": "charttime"
+ },
+ "num_rows": 183869,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "charttime": {
+ "name": "CHARTTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "spec_itemid": {
+ "name": "SPEC_ITEMID",
+ "spec": "col_character"
+ },
+ "spec_type_desc": {
+ "name": "SPEC_TYPE_DESC",
+ "spec": "col_character"
+ },
+ "org_itemid": {
+ "name": "ORG_ITEMID",
+ "spec": "col_character"
+ },
+ "org_name": {
+ "name": "ORG_NAME",
+ "spec": "col_character"
+ },
+ "ab_itemid": {
+ "name": "AB_ITEMID",
+ "spec": "col_character"
+ },
+ "ab_name": {
+ "name": "AB_NAME",
+ "spec": "col_character"
+ },
+ "dilution_text": {
+ "name": "DILUTION_TEXT",
+ "spec": "col_character"
+ },
+ "dilution_comparison": {
+ "name": "DILUTION_COMPARISON",
+ "spec": "col_character"
+ },
+ "dilution_value": {
+ "name": "DILUTION_VALUE",
+ "spec": "col_double"
+ },
+ "interpretation": {
+ "name": "INTERPRETATION",
+ "spec": "col_character"
+ }
+ }
+ },
+ "or_exam_reports": {
+ "files": "V1.1.0/OR_EXAM_REPORTS.csv",
+ "defaults": {
+ "time_vars": [
+ "examtime",
+ "reporttime"
+ ]
+ },
+ "num_rows": 183809,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "examtime": {
+ "name": "EXAMTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "reporttime": {
+ "name": "REPORTTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "exam_item_type_name": {
+ "name": "EXAM_ITEM_TYPE_NAME",
+ "spec": "col_character"
+ },
+ "exam_item_name": {
+ "name": "EXAM_ITEM_NAME",
+ "spec": "col_character"
+ },
+ "exam_part_name": {
+ "name": "EXAM_PART_NAME",
+ "spec": "col_character"
+ }
+ }
+ },
+ "outputevents": {
+ "files": "V1.1.0/OUTPUTEVENTS.csv",
+ "defaults": {
+ "time_vars": [
+ "charttime",
+ "storetime"
+ ],
+ "index_var": "charttime",
+ "val_var": "value",
+ "unit_var": "valueuom"
+ },
+ "num_rows": 39891,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "icustay_id": {
+ "name": "ICUSTAY_ID",
+ "spec": "col_double"
+ },
+ "charttime": {
+ "name": "CHARTTIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "itemid": {
+ "name": "ITEMID",
+ "spec": "col_integer"
+ },
+ "value": {
+ "name": "VALUE",
+ "spec": "col_double"
+ },
+ "valueuom": {
+ "name": "VALUEUOM",
+ "spec": "col_character"
+ },
+ "storetime": {
+ "name": "STORETIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ }
+ }
+ },
+ "patients": {
+ "files": "V1.1.0/PATIENTS.csv",
+ "defaults": {
+ "time_vars": [
+ "dob",
+ "dod"
+ ],
+ "val_var": "expire_flag"
+ },
+ "num_rows": 12881,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "gender": {
+ "name": "GENDER",
+ "spec": "col_character"
+ },
+ "dob": {
+ "name": "DOB",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "dod": {
+ "name": "DOD",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "expire_flag": {
+ "name": "EXPIRE_FLAG",
+ "spec": "col_integer"
+ }
+ }
+ },
+ "prescriptions": {
+ "files": "V1.1.0/PRESCRIPTIONS.csv",
+ "defaults": {
+ "time_vars": [
+ "startdate",
+ "enddate"
+ ],
+ "index_var": "startdate",
+ "val_var": "dose_val_rx",
+ "unit_var": "dose_unit_rx"
+ },
+ "num_rows": 1256591,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "icustay_id": {
+ "name": "ICUSTAY_ID",
+ "spec": "col_double"
+ },
+ "startdate": {
+ "name": "STARTDATE",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "enddate": {
+ "name": "ENDDATE",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "drug_name": {
+ "name": "DRUG_NAME",
+ "spec": "col_character"
+ },
+ "drug_name_en": {
+ "name": "DRUG_NAME_EN",
+ "spec": "col_character"
+ },
+ "prod_strength": {
+ "name": "PROD_STRENGTH",
+ "spec": "col_character"
+ },
+ "drug_name_generic": {
+ "name": "DRUG_NAME_GENERIC",
+ "spec": "col_character"
+ },
+ "dose_val_rx": {
+ "name": "DOSE_VAL_RX",
+ "spec": "col_double"
+ },
+ "dose_unit_rx": {
+ "name": "DOSE_UNIT_RX",
+ "spec": "col_character"
+ },
+ "drug_form": {
+ "name": "DRUG_FORM",
+ "spec": "col_character"
+ }
+ }
+ },
+ "surgery_vital_signs": {
+ "files": "V1.1.0/SURGERY_VITAL_SIGNS.csv",
+ "defaults": {
+ "time_vars": [
+ "monitor_time"
+ ],
+ "index_var": "oper_id",
+ "val_var": "value"
+ },
+ "num_rows": 1944187,
+ "cols": {
+ "row_id": {
+ "name": "ROW_ID",
+ "spec": "col_integer"
+ },
+ "subject_id": {
+ "name": "SUBJECT_ID",
+ "spec": "col_integer"
+ },
+ "hadm_id": {
+ "name": "HADM_ID",
+ "spec": "col_integer"
+ },
+ "visit_id": {
+ "name": "VISIT_ID",
+ "spec": "col_integer"
+ },
+ "oper_id": {
+ "name": "OPER_ID",
+ "spec": "col_integer"
+ },
+ "item_no": {
+ "name": "ITEM_NO",
+ "spec": "col_integer"
+ },
+ "monitor_time": {
+ "name": "MONITOR_TIME",
+ "spec": "col_datetime",
+ "format": "%Y-%m-%d %H:%M:%S"
+ },
+ "itemid": {
+ "name": "ITEMID",
+ "spec": "col_character"
+ },
+ "value": {
+ "name": "VALUE",
+ "spec": "col_double"
+ }
+ }
+ }
+ }
+ }
+]
\ No newline at end of file
diff --git a/inst/extdata/config/data-sources/sic.json b/inst/extdata/config/data-sources/sic.json
index 760b50fc..5d527e36 100644
--- a/inst/extdata/config/data-sources/sic.json
+++ b/inst/extdata/config/data-sources/sic.json
@@ -4,17 +4,17 @@
"url": "https://physionet.org/files/sicdb/1.0.6",
"id_cfg": {
"patient": {
- "id": "PatientID",
+ "id": "patientid",
"position": 1,
- "start": "ICUOffset",
- "end": "OffsetOfDeath",
+ "start": "firstadmission",
+ "end": "offsetofdeath",
"table": "cases"
},
"icustay": {
- "id": "CaseID",
+ "id": "caseid",
"position": 2,
- "start": "ICUOffset",
- "end": "TimeOfStay",
+ "start": "offsetafterfirstadmission",
+ "end": "timeofstay",
"table": "cases"
}
},
@@ -22,13 +22,13 @@
"cases": {
"files": "cases.csv.gz",
"defaults": {
- "index_var": "ICUOffset",
+ "index_var": "icuoffset",
"time_vars": [
- "ICUOffset",
- "OffsetOfDeath",
- "HeartSurgeryBeginOffset",
- "HeartSurgeryEndOffset",
- "OffsetAfterFirstAdmission"
+ "icuoffset",
+ "heartsurgerybeginoffset",
+ "heartsurgeryendoffset",
+ "offsetafterfirstadmission",
+ "offsetofdeath"
]
},
"num_rows": 27386,
@@ -193,16 +193,12 @@
"data_float_h": {
"files": "data_float_h.csv.gz",
"defaults": {
- "index_var": "Offset",
- "val_var": "Val",
- "time_vars": "Offset"
+ "index_var": "offset",
+ "val_var": "val",
+ "time_vars": "offset"
},
"num_rows": 36785241,
"cols": {
- "id": {
- "name": "id",
- "spec": "col_integer"
- },
"caseid": {
"name": "CaseID",
"spec": "col_integer"
@@ -225,48 +221,22 @@
},
"rawdata": {
"name": "rawdata",
- "spec": "col_double"
+ "spec": "col_character"
}
},
"partitioning": {
"col": "dataid",
"breaks": [
- 1,
- 2,
- 3,
- 4,
- 7,
- 28,
- 29,
- 702,
- 703,
- 705,
- 708,
- 709,
- 710,
- 715,
- 717,
- 719,
- 724,
- 725,
- 731,
- 773,
- 2018,
- 2274,
- 2278,
- 2280,
- 2283,
- 2290,
- 3056,
- 3059,
- 3071
- ]
- }
+ 702, 703, 705, 708, 709, 710, 715, 717, 719, 724, 725,
+ 731, 773, 2018, 2274, 2278, 2280, 2283, 2290, 3056, 3059, 3071]
+ },
+ "callback": "sic_data_float_h"
},
"data_ref": {
"files": "data_ref.csv.gz",
"defaults": {
- "index_var": "OffsetAfterFirstAdmission"
+ "index_var": "offsetafterfirstadmission",
+ "time_vars": ["offsetafterfirstadmission"]
},
"num_rows": 354157,
"cols": {
@@ -282,8 +252,8 @@
"name": "RefID",
"spec": "col_integer"
},
- "customfieldid": {
- "name": "CustomFieldID",
+ "fieldid": {
+ "name": "FieldID",
"spec": "col_integer"
}
}
@@ -291,9 +261,9 @@
"laboratory": {
"files": "laboratory.csv.gz",
"defaults": {
- "index_var": "Offset",
- "val_var": "LaboratoryValue",
- "time_vars": "Offset"
+ "index_var": "offset",
+ "val_var": "laboratoryvalue",
+ "time_vars": "offset"
},
"num_rows": 17572279,
"cols": {
@@ -326,11 +296,11 @@
"medication": {
"files": "medication.csv.gz",
"defaults": {
- "index_var": "Offset",
+ "index_var": "offset",
"val_var": "Amount",
"time_vars": [
- "Offset",
- "OffsetDrugEnd"
+ "offset",
+ "offsetdrugend"
]
},
"num_rows": 5141346,
@@ -380,10 +350,10 @@
"data_range": {
"files": "data_range.csv.gz",
"defaults": {
- "index_var": "Offset",
+ "index_var": "offset",
"time_vars": [
- "Offset",
- "OffsetEnd"
+ "offset",
+ "offsetend"
]
},
"num_rows": 183339,
@@ -417,8 +387,8 @@
"unitlog": {
"files": "unitlog.csv.gz",
"defaults": {
- "index_var": "Offset",
- "time_vars": "Offset"
+ "index_var": "offset",
+ "time_vars": "offset"
},
"num_rows": 139968,
"cols": {
diff --git a/man/change_id.Rd b/man/change_id.Rd
index 8c3fa01e..6193adf5 100644
--- a/man/change_id.Rd
+++ b/man/change_id.Rd
@@ -57,34 +57,19 @@ and \code{downgrade_id()} when the target ID system is of lower cardinality
}
\details{
In order to provide ID system conversion for a data source, the (internal)
-function \code{\link[=id_map]{id_map()}} must be able to construct an ID mapping for that data
+function [id_map()] must be able to construct an ID mapping for that data
source. Constructing such a mapping can be expensive w.r.t. the frequency
-it might be re-used and therefore, \code{\link[=id_map]{id_map()}} provides caching
+it might be re-used and therefore, [id_map()] provides caching
infrastructure. The mapping itself is constructed by the (internal)
-function \code{\link[=id_map_helper]{id_map_helper()}}, which is expected to provide source and
+function [id_map_helper()], which is expected to provide source and
destination ID columns as well as start and end columns corresponding to
the destination ID, relative to the source ID system. In the following
-example, we request for \code{mimic_demo}, with ICU stay IDs as source and
+example, we request for `mimic_demo`, with ICU stay IDs as source and
hospital admissions as destination IDs.
-\if{html}{\out{}}\preformatted{id_map_helper(mimic_demo, "icustay_id", "hadm_id")
-#> # An `id_tbl`: 136 x 4
-#> # Id var: `icustay_id`
-#> icustay_id hadm_id hadm_id_start hadm_id_end
-#>
-#> 1 201006 198503 -3290 mins 9114 mins
-#> 2 201204 114648 -2 mins 6949 mins
-#> 3 203766 126949 -1336 mins 8818 mins
-#> 4 204132 157609 -1 mins 10103 mins
-#> 5 204201 177678 -368 mins 9445 mins
-#> ...
-#> 132 295043 170883 -10413 mins 31258 mins
-#> 133 295741 176805 -1 mins 3153 mins
-#> 134 296804 110244 -1294 mins 4599 mins
-#> 135 297782 167612 -1 mins 207 mins
-#> 136 298685 151323 -1 mins 19082 mins
-#> # i 131 more rows
-}\if{html}{\out{
}}
+```{r, eval = is_data_avail("mimic_demo")}
+id_map_helper(mimic_demo, "icustay_id", "hadm_id")
+```
Both start and end columns encode the hospital admission windows relative
to each corresponding ICU stay start time. It therefore comes as no
@@ -93,21 +78,22 @@ occurs before ICU stay start time), while end times are often days in the
future (as hospital discharge typically occurs several days after ICU
admission).
-In order to use the ID conversion infrastructure offered by \code{ricu} for a
-new dataset, it typically suffices to provide an \code{id_cfg} entry in the
-source configuration (see \code{\link[=load_src_cfg]{load_src_cfg()}}), outlining the available ID
+In order to use the ID conversion infrastructure offered by `ricu` for a
+new dataset, it typically suffices to provide an `id_cfg` entry in the
+source configuration (see [load_src_cfg()]), outlining the available ID
systems alongside an ordering, as well as potentially a class specific
-implementation of \code{\link[=id_map_helper]{id_map_helper()}} for the given source class, specifying
+implementation of [id_map_helper()] for the given source class, specifying
the corresponding time windows in 1 minute resolution (for every possible
pair of IDs).
-While both up- and downgrades for \code{id_tbl} objects, as well as downgrades
-for \code{ts_tbl} objects are simple merge operations based on the ID mapping
-provided by \code{\link[=id_map]{id_map()}}, ID upgrades for \code{ts_tbl} objects are slightly more
-involved. As an example, consider the following setting: we have \code{data}
-associated with \code{hadm_id} IDs and times relative to hospital admission:
+While both up- and downgrades for `id_tbl` objects, as well as downgrades
+for `ts_tbl` objects are simple merge operations based on the ID mapping
+provided by [id_map()], ID upgrades for `ts_tbl` objects are slightly more
+involved. As an example, consider the following setting: we have `data`
+associated with `hadm_id` IDs and times relative to hospital admission:
-\if{html}{\out{}}\preformatted{ 1 2 3 4 5 6 7 8
+```
+ 1 2 3 4 5 6 7 8
data ---*------*-------*--------*-------*-------*--------*------*---
3h 10h 18h 27h 35h 43h 52h 59h
@@ -117,17 +103,17 @@ hadm_id |-------------------------------------------------------------|
icustay_id |------------------| |---------------|
0h 19h 0h 16h
ICU_1 ICU_2
-}\if{html}{\out{
}}
+```
-The mapping of data points from \code{hadm_id} to \code{icustay_id} is created as
+The mapping of data points from `hadm_id` to `icustay_id` is created as
follows: ICU stay end times mark boundaries and all data that is recorded
after the last ICU stay ended is assigned to the last ICU stay. Therefore
-data points 1-3 are assigned to \code{ICU_1}, while 4-8 are assigned to \code{ICU_2}.
+data points 1-3 are assigned to `ICU_1`, while 4-8 are assigned to `ICU_2`.
Times have to be shifted as well, as timestamps are expected to be relative
to the current ID system. Data points 1-3 therefore are assigned to time
stamps -4h, 3h and 11h, while data points 4-8 are assigned to -10h, -2h,
6h, 15h and 22h. Implementation-wise, the mapping is computed using an
-efficient \code{data.table} rolling join.
+efficient `data.table` rolling join.
}
\examples{
if (require(mimic.demo)) {
diff --git a/man/data_env.Rd b/man/data_env.Rd
index 542831df..1e4e4430 100644
--- a/man/data_env.Rd
+++ b/man/data_env.Rd
@@ -43,98 +43,57 @@ hosted data source is available as well. As with the PhysioNet datasets,
access is public but has to be granted by the data collectors.
}
\details{
-Setting up a dataset for use with \code{ricu} requires a configuration object.
+Setting up a dataset for use with `ricu` requires a configuration object.
For the included datasets, configuration can be loaded from
-\if{html}{\out{}}\preformatted{system.file("extdata", "config", "data-sources.json", package = "ricu")
-}\if{html}{\out{
}}
+```
+system.file("extdata", "config", "data-sources.json", package = "ricu")
+```
-by calling \code{\link[=load_src_cfg]{load_src_cfg()}} and for dataset that are external to \code{ricu},
+by calling [load_src_cfg()] and for dataset that are external to `ricu`,
additional configuration can be made available by setting the environment
-variable \code{RICU_CONFIG_PATH} (for more information, refer to
-\code{\link[=load_src_cfg]{load_src_cfg()}}). Using the dataset configuration object, data can be
-downloaded (\code{\link[=download_src]{download_src()}}), imported (\code{\link[=import_src]{import_src()}}) and attached
-(\code{\link[=attach_src]{attach_src()}}). While downloading and importing are one-time procedures,
+variable `RICU_CONFIG_PATH` (for more information, refer to
+[load_src_cfg()]). Using the dataset configuration object, data can be
+downloaded ([download_src()]), imported ([import_src()]) and attached
+([attach_src()]). While downloading and importing are one-time procedures,
attaching of the dataset is repeated every time the package is loaded.
Briefly, downloading loads the raw dataset from the internet (most likely
-in \code{.csv} format), importing consists of some preprocessing to make the
-data available more efficiently (by converting it to \code{\link[fst:fst]{.fst}}
+in `.csv` format), importing consists of some preprocessing to make the
+data available more efficiently (by converting it to [`.fst`][fst::fst()]
format) and attaching sets up the data for use by the package. For more
information on the individual steps, refer to the respective documentation
pages.
A dataset that has been successfully made available can interactively be
explored by typing its name into the console and individual tables can be
-inspected using the \code{$} function. For example for the MIMIC-III demo
-dataset and the \code{icustays} table, this gives
+inspected using the `$` function. For example for the MIMIC-III demo
+dataset and the `icustays` table, this gives
-\if{html}{\out{}}\preformatted{mimic_demo
-#>
-#> admissions callout caregivers chartevents
-#> [129 x 19] [77 x 24] [7,567 x 4] [758,355 x 15]
-#> cptevents d_cpt d_icd_diagnoses d_icd_procedures
-#> [1,579 x 12] [134 x 9] [14,567 x 4] [3,882 x 4]
-#> d_items d_labitems datetimeevents diagnoses_icd
-#> [12,487 x 10] [753 x 6] [15,551 x 14] [1,761 x 5]
-#> drgcodes icustays inputevents_cv inputevents_mv
-#> [297 x 8] [136 x 12] [34,799 x 22] [13,224 x 31]
-#> labevents microbiologyevents outputevents patients
-#> [76,074 x 9] [2,003 x 16] [11,320 x 13] [100 x 8]
-#> prescriptions procedureevents_mv procedures_icd services
-#> [10,398 x 19] [753 x 25] [506 x 5] [163 x 6]
-#> transfers
-#> [524 x 13]
+```{r, eval = is_data_avail("mimic_demo")}
+mimic_demo
mimic_demo$icustays
-#> # : [136 x 12]
-#> # ID options: subject_id (patient) < hadm_id (hadm) < icustay_id (icustay)
-#> # Defaults: `intime` (index), `last_careunit` (val)
-#> # Time vars: `intime`, `outtime`
-#> row_id subject_id hadm_id icustay_id dbsource first_careunit last_careunit
-#>
-#> 1 12742 10006 142345 206504 carevue MICU MICU
-#> 2 12747 10011 105331 232110 carevue MICU MICU
-#> 3 12749 10013 165520 264446 carevue MICU MICU
-#> 4 12754 10017 199207 204881 carevue CCU CCU
-#> 5 12755 10019 177759 228977 carevue MICU MICU
-#> ...
-#> 132 42676 44083 198330 286428 metavision CCU CCU
-#> 133 42691 44154 174245 217724 metavision MICU MICU
-#> 134 42709 44212 163189 239396 metavision MICU MICU
-#> 135 42712 44222 192189 238186 metavision CCU CCU
-#> 136 42714 44228 103379 217992 metavision SICU SICU
-#> # i 131 more rows
-#> # i 5 more variables: first_wardid , last_wardid , intime ,
-#> # outtime , los
-}\if{html}{\out{
}}
+```
Table subsets can be loaded into memory for example using the
-\code{\link[base:subset]{base::subset()}} function, which uses non-standard evaluation (NSE) to
+[base::subset()] function, which uses non-standard evaluation (NSE) to
determine a row-subsetting. This design choice stems form the fact that
some tables can have on the order of 10^8 rows, which makes loading full
tables into memory an expensive operation. Table subsets loaded into
-memory are represented as \code{\link[data.table:data.table]{data.table}} objects.
+memory are represented as [`data.table`][data.table::data.table()] objects.
Extending the above example, if only ICU stays corresponding to the patient
-with \code{subject_id == 10124} are of interest, the respective data can be
+with `subject_id == 10124` are of interest, the respective data can be
loaded as
-\if{html}{\out{}}\preformatted{subset(mimic_demo$icustays, subject_id == 10124)
-#> row_id subject_id hadm_id icustay_id dbsource first_careunit last_careunit
-#> 1: 12863 10124 182664 261764 carevue MICU MICU
-#> 2: 12864 10124 170883 222779 carevue MICU MICU
-#> 3: 12865 10124 170883 295043 carevue CCU CCU
-#> 4: 12866 10124 170883 237528 carevue MICU MICU
-#> first_wardid last_wardid intime outtime los
-#> 1: 23 23 2192-03-29 10:46:51 2192-04-01 06:36:00 2.8258
-#> 2: 50 50 2192-04-16 20:58:32 2192-04-20 08:51:28 3.4951
-#> 3: 7 7 2192-04-24 02:29:49 2192-04-26 23:59:45 2.8958
-#> 4: 23 23 2192-04-30 14:50:44 2192-05-15 23:34:21 15.3636
-}\if{html}{\out{
}}
+```{r, eval = is_data_avail("mimic_demo")}
+subset(mimic_demo$icustays, subject_id == 10124)
+```
-Much care has been taken to make \code{ricu} extensible to new datasets. For
-example the publicly available ICU database \href{https://amsterdammedicaldatascience.nl/amsterdamumcdb/}{AmsterdamUMCdb }
+Much care has been taken to make `ricu` extensible to new datasets. For
+example the publicly available ICU database [AmsterdamUMCdb
+](https://amsterdammedicaldatascience.nl/amsterdamumcdb/)
provided by the Amsterdam University Medical Center, currently is not part
-of the core datasets of \code{ricu}, but code for integrating this dataset is
-available on \href{https://github.com/eth-mds/aumc}{github}.
+of the core datasets of `ricu`, but code for integrating this dataset is
+available on [github](https://github.com/eth-mds/aumc).
}
\section{MIMIC-III}{
diff --git a/test_environment.yaml b/test_environment.yaml
new file mode 100644
index 00000000..9c0c12a8
--- /dev/null
+++ b/test_environment.yaml
@@ -0,0 +1,32 @@
+name: ricu-test
+channels:
+ - nodefaults
+ - conda-forge
+dependencies:
+ - r-base
+ - r-data.table
+ - r-curl
+ - r-assertthat
+ - r-fst
+ - r-readr
+ - r-jsonlite
+ - r-prt>=0.1.2
+ - r-tibble
+ - r-backports
+ - r-rlang
+ - r-vctrs
+ - r-cli>=2.1.0
+ - r-fansi
+ - r-openssl
+ - r-units
+ # optional
+ - r-rticles
+ - r-forestmodel
+ - r-ggplot2
+ - r-survival
+ - r-kableExtra
+ - r-magick
+ - r-cowplot
+ - r-knitr
+ - r-pdftools
+ - r-covr
\ No newline at end of file