bump to version 0.6.0

DESCRIPTION

@@ -6,7 +6,7 @@ Description: Focused on (but not exclusive to) data sets hosted on PhysioNet
     functions for running arbitrary queries against available data sets, a
     system for defining clinical concepts and encoding their representations
     in tabular ICU data is presented.
-Version: 0.5.5
+Version: 0.6.0
 Authors@R: c(
     person(given = "Nicolas",
            family = "Bennett",
@@ -29,7 +29,7 @@ URL:
     https://physionet.org
 BugReports: https://github.com/eth-mds/ricu/issues
 Depends:
-    R (>= 3.4.0)
+    R (>= 3.5.0)
 Imports:
     data.table,
     curl,

NAMESPACE

@@ -137,6 +137,7 @@ S3method(id_win_helper,eicu_env)
 S3method(id_win_helper,hirid_env)
 S3method(id_win_helper,miiv_env)
 S3method(id_win_helper,mimic_env)
+S3method(id_win_helper,sic_env)
 S3method(import_src,aumc_cfg)
 S3method(import_src,character)
 S3method(import_src,default)
@@ -185,6 +186,7 @@ S3method(load_difftime,eicu_tbl)
 S3method(load_difftime,hirid_tbl)
 S3method(load_difftime,miiv_tbl)
 S3method(load_difftime,mimic_tbl)
+S3method(load_difftime,sic_tbl)
 S3method(load_id,character)
 S3method(load_id,default)
 S3method(load_id,fun_itm)

NEWS.md

@@ -1,3 +1,9 @@
+# ricu 0.6.0
+
+* Salzburg database (SICdb, `sic` in `ricu`) added as a data source with 64 concepts available
+* MIMIC-IV (`miiv` in `ricu`) version bumped to 2.2
+* fixed the usage of `round()` and `trunc()`; both replaced by `floor()` throughout
+
 # ricu 0.5.5
 
 * maintenance release: fixes an issue introduced by pillar 1.9.0 via an update

R/callback-itm.R

@@ -618,7 +618,8 @@ sic_dur <- function (x, val_var, stop_var, grp_var = NULL, ...) {
 sic_rate_kg <- function (x, val_var, stop_var, env, ...) {
 
   res <- add_weight(x, env, "weight")
-  res[, AmountPerMinute := AmountPerMinute * 10^6 / 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))
 }
 

R/data-env.R

@@ -131,8 +131,8 @@
 #' is spread over 7 tables.
 #'
 #' @section MIMIC-IV:
-#' With the recent v1.0 release of MIMIC-IV, experimental support has been
-#' added in `ricu`. Building on the success of MIMIC-III, this next iteration
+#' The latest v2.2 release of MIMIC-IV is available in added in `ricu`. 
+#' Building on the success of MIMIC-III, this next iteration
 #' contains data on patients admitted to an ICU or the emergency department
 #' between 2008 - 2019 at BIDMC. Therefore, relative to MIMIC-III, patients
 #' admitted prior to 2008 (whose data is stored in a CareVue-based system) has
@@ -142,6 +142,12 @@
 #' of the initial v1.0 release and currently is not supported by `ricu`. For
 #' further information, please refer to the [MIMIC-III documentation
 #' ](https://mimic.mit.edu/docs/iii/).
+#' 
+#' @section SICdb:
+#' The Salzburg ICU database (SICdb) originates from the University Hospital of
+#' Salzburg. In `ricu`, version v1.0.6 is currently supported. For
+#' further information, please refer to the [SICdb documentation
+#' ](https://physionet.org/content/sicdb/1.0.6/).
 #'
 #' @format
 #' The exported `data` environment contains all datasets that have been made
@@ -230,6 +236,10 @@ NULL
 #' @rdname data_env
 NULL
 
+#' @name sic
+#' @rdname data_env
+NULL
+
 data_env <- function() get("data", envir = pkg_env(), mode = "environment")
 
 #' Data source environments

R/data-load.R

@@ -174,7 +174,7 @@ load_difftime.sic_tbl <- function(x, rows, cols = colnames(x),
                                   id_hint = id_vars(x),
                                   time_vars = ricu::time_vars(x), ...) {
 
-  sec_as_mins <- function(x) ricu:::min_as_mins(as.integer(x / 60))
+  sec_as_mins <- function(x) min_as_mins(as.integer(x / 60))
   warn_dots(...)
   load_eiau(x, {{ rows }}, cols, id_hint, time_vars, sec_as_mins)
 }

R/data-utils.R

@@ -233,7 +233,7 @@ id_win_helper.eicu_env <- function(x) {
 #' @export
 id_win_helper.sic_env <- function(x) {
 
-  sec_as_mins <- function(x) ricu:::min_as_mins(as.integer(x / 60))
+  sec_as_mins <- function(x) min_as_mins(as.integer(x / 60))
 
   cfg <- sort(as_id_cfg(x), decreasing = TRUE)
 

inst/extdata/config/concept-dict.R

@@ -2659,7 +2659,8 @@ cfg <- list(
         list(ids = 226512L, table = "chartevents", sub_var = "itemid")
       ),
       sic = list(
-        list(table = "cases", val_var = "WeightOnAdmission", class = "col_itm")
+        list(table = "cases", val_var = "WeightOnAdmission", class = "col_itm",
+             callback = "transform_fun(binary_op(`/`, 1000))")
       )
     )
   ),

inst/extdata/config/concept-dict.json

@@ -6582,7 +6582,8 @@
         {
           "table": "cases",
           "val_var": "WeightOnAdmission",
-          "class": "col_itm"
+          "class": "col_itm",
+          "callback": "transform_fun(binary_op(`/`, 1000))"
         }
       ]
     }