merge 0.6.0

NAMESPACE

@@ -43,6 +43,8 @@ S3method(as_item,item)
 S3method(as_item,itm)
 S3method(as_item,list)
 S3method(as_item,rec_cncpt)
+S3method(as_ptype,data.frame)
+S3method(as_ptype,data.table)
 S3method(as_ptype,default)
 S3method(as_ptype,id_tbl)
 S3method(as_src_cfg,default)
@@ -251,6 +253,7 @@ S3method(set_callback,default)
 S3method(set_callback,itm)
 S3method(set_target,cncpt)
 S3method(set_target,concept)
+S3method(set_target,default)
 S3method(set_target,item)
 S3method(set_target,itm)
 S3method(setup_src_data,character)

NEWS.md

@@ -4,6 +4,11 @@
 * MIMIC-IV (`miiv` in `ricu`) version bumped to 2.2
 * fixed the usage of `round()` and `trunc()`; both replaced by `floor()` throughout
 
+# ricu 0.5.6
+
+* maintenance release: fixes non-character numeric version input issues
+>>>>>>> 3c72261c4f049b49e7040a588b28eeb974a2f177
+
 # ricu 0.5.5
 
 * maintenance release: fixes an issue introduced by pillar 1.9.0 via an update

R/assertions.R

@@ -1,4 +1,3 @@
-
 #' @importFrom assertthat see_if on_failure<- validate_that
 #' @importFrom assertthat is.string is.flag is.dir is.count is.scalar
 #' @importFrom assertthat has_name has_attr are_equal is.number

R/callback-cncpt.R

@@ -1,4 +1,3 @@
-
 collect_dots <- function(concepts, interval, ..., merge_dat = FALSE) {
 
   assert_that(is.character(concepts))

R/callback-itm.R

@@ -1,4 +1,3 @@
-
 vent_flag <- function(x, val_var, ...) {
   x <- x[as.logical(get(val_var)), ]
   set(x, j = c(index_var(x), val_var),

R/callback-scores.R

@@ -1,4 +1,3 @@
-
 #' SIRS score label
 #'
 #' The SIRS (Systemic Inflammatory Response Syndrome) score is a commonly used

R/callback-sep3.R

@@ -1,4 +1,3 @@
-
 #' Sepsis 3 label
 #'
 #' The sepsis 3 label consists of a suspected infection combined with an acute

R/callback-sofa.R

@@ -1,4 +1,3 @@
-
 #' SOFA score label
 #'
 #' The SOFA (Sequential Organ Failure Assessment) score is a commonly used

R/concept-load.R

@@ -1,4 +1,3 @@
-
 #' Load concept data
 #'
 #' Concept objects are used in `ricu` as a way to specify how a clinical

R/concept-utils.R

@@ -1,4 +1,3 @@
-
 #' Data items
 #'
 #' Item objects are used in `ricu` as a way to specify how individual data
@@ -806,6 +805,7 @@ set_target.concept <- function(x, target) {
   new_concept(lapply(x, set_target, target))
 }
 
+#' @export
 set_target.default <- function(x, target) stop_generic(x, .Generic)
 
 #' @rdname item_utils

R/config-class.R

@@ -1,4 +1,3 @@
-
 #' Internal utilities for working with data source configurations
 #'
 #' Data source configuration objects store information on data sources used

R/config-utils.R

@@ -1,4 +1,3 @@
-
 #' @param x Object to coerce/query
 #'
 #' @rdname src_cfg

R/data-env.R

@@ -1,4 +1,3 @@
-
 #' ICU datasets
 #'
 #' The [Laboratory for Computational Physiology

R/data-load.R

@@ -1,4 +1,3 @@
-
 #' Low level functions for loading data
 #'
 #' Data loading involves a cascade of S3 generic functions, which can

R/data-utils.R

@@ -1,4 +1,3 @@
-
 #' Data loading utilities
 #'
 #' Two important tools for smoothing out differences among used datasets are

R/ricu.R

@@ -1,4 +1,3 @@
-
 #' @keywords internal
 #' @importFrom data.table setattr setcolorder set setnames setorderv
 #' @importFrom data.table setDT setDF fifelse rbindlist data.table

R/setup-attach.R

@@ -1,4 +1,3 @@
-
 #' Data attach utilities
 #'
 #' Making a dataset available to `ricu` consists of 3 steps: downloading

R/setup-download.R

@@ -1,4 +1,3 @@
-
 #' Data download utilities
 #'
 #' Making a dataset available to `ricu` consists of 3 steps: downloading
@@ -228,7 +227,7 @@ download_src.aumc_cfg <- function(x, data_dir = src_data_dir(x),
       fil <- file.path(tmp, name)
 
       if (isTRUE(verbose)) {
-        prg <- progress_init(size, msg = "Donwloading `aumc` data",
+        prg <- progress_init(size, msg = "Downloading `aumc` data",
                              what = FALSE)
       } else {
         prg <- FALSE

R/setup-import.R

@@ -1,4 +1,3 @@
-
 #' Data import utilities
 #'
 #' Making a dataset available to `ricu` consists of 3 steps: downloading

R/tbl-base.R

@@ -1,4 +1,3 @@
-
 #' @export
 `[.id_tbl` <- function(x, ...) wrap_ptype(as_ptype(x), NextMethod())
 

R/tbl-class.R

@@ -1,4 +1,3 @@
-
 #' Tabular ICU data classes
 #'
 #' In order to simplify handling or tabular ICU data, `ricu` provides
@@ -636,11 +635,11 @@ as_ptype.id_tbl <- function(x) {
   reclass_tbl(as.data.table(lapply(x, `[`, 0L)[meta_vars(x)]), x)
 }
 
-#' @method reclass_tbl data.table
+#' @method as_ptype data.table
 #' @export
 as_ptype.data.table <- function(x) data.table()
 
-#' @method reclass_tbl data.frame
+#' @method as_ptype data.frame
 #' @export
 as_ptype.data.frame <- function(x) data.frame()
 

R/tbl-utils.R

@@ -1,4 +1,3 @@
-
 #' ICU class meta data utilities
 #'
 #' The two data classes `id_tbl` and `ts_tbl`, used by `ricu` to represent ICU

R/utils-cli.R

@@ -1,4 +1,3 @@
-
 is_interactive <- function() {
   !isTRUE(getOption('knitr.in.progress')) && interactive()
 }

R/utils-export.R

@@ -1,4 +1,3 @@
-
 #' Read and write utilities
 #'
 #' Support for reading from and writing to pipe separated values (`.psv`)

R/utils-file.R

@@ -1,4 +1,3 @@
-
 #' File system utilities
 #'
 #' Determine the location where to place data meant to persist between

R/utils-misc.R

@@ -1,4 +1,3 @@
-
 agg_or_na <- function(agg_fun) {
   function(x) {
     if (all(is.na(x))) return(x[1L])

R/utils-ts.R

@@ -1,4 +1,3 @@
-
 #' Time series utility functions
 #'
 #' ICU data as handled by `ricu` is mostly comprised of time series data and as
@@ -64,6 +63,7 @@
 #' `has_gaps()`/`has_no_gaps()`/`is_regular()`, which return logical flags.
 #'
 #' @examples
+#' if (FALSE) {
 #' tbl <- ts_tbl(x = 1:5, y = hours(1:5), z = hours(2:6), val = rnorm(5),
 #'               index_var = "y")
 #' exp <- expand(tbl, "y", "z", step_size = 1L, new_index = "y",
@@ -89,6 +89,7 @@
 #' tbl[6, 2] <- hours(2)
 #' has_no_gaps(tbl)
 #' is_regular(tbl)
+#' }
 #'
 #' @rdname ts_utils
 #' @export

R/zzz.R

@@ -1,4 +1,3 @@
-
 .onLoad <- function(libname, pkgname) { # nocov start
 
   fix_base_fun <- function(fun, fix) {

README.md

@@ -1,4 +1,3 @@
-
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # [ricu](https://eth-mds.github.io/ricu/)

_pkgdown.yml

@@ -1,4 +1,3 @@
-
 title: ICU data with R
 
 url: https://eth-mds.github.io/ricu

cran-comments.md

@@ -10,5 +10,4 @@
 
 0 errors | 0 warnings | 0 notes
 
-* Maintenance release (fixes an issue introduced by pillar 1.9.0 via an update
-  to 0.2.0 of prt)
+* Maintenance release (fixes non-character numeric version input issues)