Merge branch 'main' into load-rec-args

.Rbuildignore

@@ -10,7 +10,7 @@
 ^Meta$
 ^cran-comments\.md$
 ^CRAN-RELEASE$
-^vignettes/jss\.(aux|bbl|blg|bst|cls|knit\.md|log|out|pdf|R|tex)$
-^vignettes/(jss|uom)_(cache|files)$
+^vignettes/ricu\.(aux|bbl|blg|bst|cls|knit\.md|log|out|pdf|R|tex)$
+^vignettes/(ricu|uom)_(cache|files)$
 ^inst/local_testdata
 ^CRAN-SUBMISSION$

.github/workflows/check.yaml

@@ -49,11 +49,12 @@ jobs:
             any::rcmdcheck
             eth-mds/mimic-demo
             eth-mds/eicu-demo
-          needs: check
+            nbenn/mockthat
 
       - uses: r-lib/actions/check-r-package@v2
         env:
           _R_CHECK_CRAN_INCOMING_: false
           _R_CHECK_FORCE_SUGGESTS_: false
+          _R_CHECK_DOC_SIZES_: false
         with:
           upload-snapshots: true

.github/workflows/coverage.yaml

@@ -29,7 +29,7 @@ jobs:
             any::covr
             eth-mds/mimic-demo
             eth-mds/eicu-demo
-          needs: coverage
+            nbenn/mockthat
 
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)

.github/workflows/pkgdown.yaml

@@ -33,7 +33,7 @@ jobs:
             local::.
             eth-mds/mimic-demo
             eth-mds/eicu-demo
-          needs: website
+            nbenn/mockthat
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

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: 0.5.3
+Version: 0.5.6
 Authors@R: c(
     person(given = "Nicolas",
            family = "Bennett",
@@ -68,8 +68,9 @@ Suggests:
     kableExtra,
     units,
     pdftools,
-    magick
-RoxygenNote: 7.2.0
+    magick,
+    pillar
+RoxygenNote: 7.2.3
 Additional_repositories: https://eth-mds.github.io/physionet-demo
 VignetteBuilder: knitr
 Config/testthat/edition: 3

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)
@@ -170,10 +172,12 @@ S3method(load_concepts,cncpt)
 S3method(load_concepts,concept)
 S3method(load_concepts,default)
 S3method(load_concepts,fct_cncpt)
+S3method(load_concepts,integer)
 S3method(load_concepts,item)
 S3method(load_concepts,itm)
 S3method(load_concepts,lgl_cncpt)
 S3method(load_concepts,num_cncpt)
+S3method(load_concepts,numeric)
 S3method(load_concepts,rec_cncpt)
 S3method(load_concepts,unt_cncpt)
 S3method(load_difftime,aumc_tbl)
@@ -247,6 +251,7 @@ 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

@@ -1,3 +1,16 @@
+# ricu 0.5.6
+
+* maintenance release: fixes non-character numeric version input issues
+
+# ricu 0.5.5
+
+* maintenance release: fixes an issue introduced by pillar 1.9.0 via an update
+  to 0.2.0 of prt
+
+# ricu 0.5.4
+
+* maintenance release: tests using `mockthat` are only run when available
+
 # ricu 0.5.3
 
 * maintenance release for compatibility with an update to `prt`

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
@@ -62,7 +61,15 @@ is_intish <- function(x) {
 }
 
 on_failure(is_intish) <- function(call, env) {
-  format_assert("{as_label(call$x)} integer-values", "is_intish_assert")
+  format_assert("{as_label(call$x)} contains non integer values",
+                "is_intish_assert")
+}
+
+no_na <- function(x) !anyNA(x)
+
+on_failure(no_na) <- function(call, env) {
+  format_assert("{as_label(call$x)} contains NA values",
+                "no_na_assert")
 }
 
 has_length <- function(x, length = NA) {

R/callback-cncpt.R

@@ -1,4 +1,3 @@
-
 collect_dots <- function(concepts, interval, ..., merge_dat = FALSE) {
 
   assert_that(is.character(concepts))
@@ -89,32 +88,21 @@ rename_data_var <- function(new_name, old_name = NULL) {
 #' values might not be ideal for some datasets and/or analysis tasks.
 #'
 #' ## `pafi`
-#' In order to calculate the PaO\ifelse{latex
-#' }{\out{\textsubscript{2}}}{\ifelse{html}{\out{<sub>2</sub>}}{2}}/FiO\ifelse{
-#' latex}{\out{\textsubscript{2}}}{\ifelse{html}{\out{<sub>2</sub>}}{2}} (or
-#' Horowitz index), for a given time point, both a PaO\ifelse{
-#' latex}{\out{\textsubscript{2}}}{\ifelse{html}{\out{<sub>2</sub>}}{2}} and a
-#' FiO\ifelse{latex}{\out{\textsubscript{2}}}{\ifelse{html
-#' }{\out{<sub>2</sub>}}{2}} measurement is required. As the two are often
-#' not measured at the same time, some form of imputation or matching
-#' procedure is required. Several options are available:
+#' In order to calculate the PaO\subs{2}/FiO\subs{2} (or Horowitz index), for
+#' a given time point, both a PaO\subs{2} and an FiO\subs{2} measurement is
+#' required. As the two are often not measured at the same time, some form of
+#' imputation or matching procedure is required. Several options are available:
 #'
 #' * `match_vals` allows for a time difference of maximally `match_win`
 #'   between two measurements for calculating their ratio
-#' * `extreme_vals` uses the worst PaO\ifelse{latex
-#'   }{\out{\textsubscript{2}}}{\ifelse{html}{\out{<sub>2</sub>}}{2}} and a
-#'   FiO\ifelse{latex}{\out{\textsubscript{2}}}{\ifelse{html
-#'   }{\out{<sub>2</sub>}}{2}} values within the time window spanned by
-#'   `match_win`
+#' * `extreme_vals` uses the worst PaO\subs{2} and FiO\subs{2} values within
+#'   the time window spanned by `match_win`
 #' * `fill_gaps` represents a variation of `extreme_vals`, where ratios are
 #'   evaluated at every time-point as specified by `interval`as opposed to
-#'   only the time points where either a PaO\ifelse{latex
-#'   }{\out{\textsubscript{2}}}{\ifelse{html}{\out{<sub>2</sub>}}{2}} or a
-#'   FiO\ifelse{latex}{\out{\textsubscript{2}}}{\ifelse{html
-#'   }{\out{<sub>2</sub>}}{2}} measurement is available
+#'   only the time points where either a PaO\subs{2} or an FiO\subs{2}
+#'   measurement is available
 #'
-#' Finally, `fix_na_fio2` imputes all remaining missing FiO\ifelse{latex
-#' }{\out{\textsubscript{2}}}{\ifelse{html}{\out{<sub>2</sub>}}{2}} with 21,
+#' Finally, `fix_na_fio2` imputes all remaining missing FiO\subs{2} with 21,
 #' the percentage (by volume) of oxygen in (tropospheric) air.
 #'
 #' ## `vent_ind`
@@ -165,13 +153,9 @@ rename_data_var <- function(new_name, old_name = NULL) {
 #'
 #' @param ... Data input used for concept calculation
 #' @param match_win Time-span during which matching of values is allowed
-#' @param mode Method for matching PaO\ifelse{latex
-#' }{\out{\textsubscript{2}}}{\ifelse{html}{\out{<sub>2</sub>}}{2}} and
-#' FiO\ifelse{latex}{\out{\textsubscript{2}}}{\ifelse{html
-#' }{\out{<sub>2</sub>}}{2}} values
+#' @param mode Method for matching PaO\subs{2} and FiO\subs{2} values
 #' @param fix_na_fio2 Logical flag indicating whether to impute missing
-#' FiO\ifelse{latex}{\out{\textsubscript{2}}}{\ifelse{html
-#' }{\out{<sub>2</sub>}}{2}} values with 21
+#' FiO\subs{2} values with 21
 #' @param interval Expected time series step size (determined from data if
 #' `NULL`)
 #'

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
@@ -19,38 +18,88 @@
 #' increase in the SOFA score (see [sofa_score()]) of 2 points or more within
 #' the suspected infection (SI) window (see [susp_inf()]):
 #'
-#' ```{tikz sofa-sep-3, echo = FALSE}
+#' ```{tikz}
+#' #| sofa-sep-3,
+#' #| echo = FALSE,
+#' #| engine.opts = list(
+#' #|   extra.preamble = c(
+#' #|     "\\usepackage{pgfplots}", "\\pgfplotsset{compat=newest}"
+#' #|   )
+#' #| )
+#'
 #' \begin{tikzpicture}
-#'   \draw (-6,0) -- (3,0);
-#'   \draw (-6,-0.25) -- (-6,0.25);
-#'   \draw (3,-0.25) -- (3,0.25);
-#'   \draw (0,-0.25) -- (0,0.25);
-#'   \node[align = center] at (0,-0.75) {SI time};
-#'   \node[align = center] at (3,-0.75) {SI window\\ end};
-#'   \node[align = center] at (-6,-0.75) {SI window\\ start};
-#'   \filldraw  (-6, 1) circle (2pt);
-#'   \draw (-6,1) -- (-5.5, 1);
-#'   \filldraw (-5.5, 1) circle (2pt);
-#'   \draw (-5.5,1) -- (-5, 1);
-#'   \node at (-4.25, 1) {$\dots$} ;
-#'   \filldraw (-5, 1) circle (2pt);
-#'   \filldraw (-3.5, 1) circle (2pt);
-#'   \filldraw (-3, 1.5) circle (2pt);
-#'   \filldraw (-2.5, 1.5) circle (2pt);
-#'   \filldraw (-2, 2.5) circle (2pt);
-#'   \draw (-3.5,1) -- (-3, 1.5);
-#'   \draw (-3,1.5) -- (-2.5, 1.5);
-#'   \draw (-2.5,1.5) -- (-2, 2.5);
-#'   \node [black] at (-0.25, 1.75) {$\Delta$SOFA $\geq 2$};
-#'   \draw (-6.5, 1) -- (-6.5, 2.5) ;
-#'   \node at (-6.5, 3) {SOFA} ;
-#'   \draw (-6.5,1)--(-6.6,1) node[left,font=\small]{$0$};
-#'   \draw (-6.5,1.5)--(-6.6,1.5) node[left,font=\small]{$1$};
-#'   \draw (-6.5,2)--(-6.6,2) node[left,font=\small]{$2$};
-#'   \draw (-6.5,2.5)--(-6.6, 2.5) node[left,font=\small]{$3$};
-#'   \draw[red] (-2,-0.25) -- (-2,0.25);
-#'   \draw[dashed,red] (-2, 2.35) -- (-2, 0) ;
-#'   \node[red] at (-2, -0.75) {Sepsis-3 time};
+#'
+#'   \draw (-5.5, 0) -- (3.5, 0);
+#'   \draw (-5.5, -0.2) -- (-5.5, 0.2);
+#'   \draw (3.5, -0.2) -- (3.5, 0.2);
+#'   \draw (0.5, -0.2) -- (0.5, 0.2);
+#'
+#'   \node[align = center] at (0.5, 0.5) {SI time};
+#'   \node[align = center] at (3.5, 0.5) {SI window end};
+#'   \node[align = center] at (-5.5, -0.5) {SI window start};
+#'
+#'   \draw (-1.5, -0.2) -- (-1.5, 0.2);
+#'   \draw[dashed] (-1.5, 2) -- (-1.5, 0);
+#'   \node[align = center] at (-1.5, -0.5) {Sepsis-3 time};
+#'
+#'   \node[align = center] at (-2.75, 0.5) {-48 hours};
+#'   \node[align = center] at (2, -0.5) {24 hours};
+#'
+#'   \draw[dashed] (0.5, 0) -- (0.5, -1);
+#'
+#'   \draw (0.5, -1) -- (3.5, -1);
+#'   \draw (3.5, -1.2) -- (3.5, -0.8);
+#'   \draw (0.5, -1.2) -- (0.5, -0.8);
+#'
+#'   \node at (5.25, -1) {within 24 hours};
+#'
+#'   \node[align = center] at (0.5, -1.5) {ABX};
+#'   \node[align = center] at (3.5, -1.5) {Sampling};
+#'
+#'   \draw (0.5, -2) -- (9.5, -2);
+#'   \draw (9.5, -2.2) -- (9.5, -1.8);
+#'   \draw (0.5, -2.2) -- (0.5, -1.8);
+#'
+#'   \node[align = center] at (5.25, -2.5) {within 72 hours};
+#'
+#'   \node[align = center] at (0.5, -2.5) {Sampling};
+#'   \node[align = center] at (9.5, -2.5) {ABX};
+#'
+#'   \draw [decorate, decoration = {brace, mirror, amplitude=5pt, raise=4pt},
+#'          yshift=0pt] (0, -0.9) -- (0, -2.1);
+#'   \node at (-3, -1.5) {Either option is permissible};
+#'
+#'   \filldraw  (-6, 1.5) circle (1pt);
+#'   \draw (-6, 1.5) -- (-5.5, 1.5);
+#'   \filldraw (-5.5, 1.5) circle (1pt);
+#'   \draw (-5.5, 1.5) -- (-5, 1);
+#'   \filldraw (-5, 1) circle (1pt);
+#'   \draw (-5, 1) -- (-4.5, 1);
+#'   \filldraw (-4.5, 1) circle (1pt);
+#'   \draw (-4.5, 1) -- (-4, 1);
+#'   \filldraw (-4, 1) circle (1pt);
+#'   \draw (-4, 1) -- (-3.5, 1);
+#'   \filldraw (-3.5, 1) circle (1pt);
+#'   \draw (-3.5, 1) -- (-3, 1.5);
+#'   \filldraw (-3, 1.5) circle (1pt);
+#'   \draw (-3, 1.5) -- (-2.5, 1.5);
+#'   \filldraw (-2.5, 1.5) circle (1pt);
+#'   \draw (-2.5, 1.5) -- (-2, 1.5);
+#'   \filldraw (-2, 1.5) circle (1pt);
+#'   \draw (-2, 1.5) -- (-1.5, 2.0);
+#'   \filldraw (-1.5, 2.0) circle (1pt);
+#'
+#'   \draw [decorate, decoration = {brace, amplitude=5pt, mirror, raise=4pt},
+#'          yshift=0pt] (-1.25, 1) -- (-1.25, 2);
+#'   \node [black] at (0.25, 1.5) {$\Delta$SOFA $\geq 2$};
+#'
+#'   \draw (-6.5, 1) -- (-6.5, 2.5);
+#'   \node at (-6.5, 3) {SOFA};
+#'   \draw (-6.5, 1) -- (-6.6, 1) node[left]{0};
+#'   \draw (-6.5, 1.5) -- (-6.6, 1.5) node[left]{1};
+#'   \draw (-6.5, 2) -- (-6.6, 2) node[left]{2};
+#'   \draw (-6.5, 2.5) -- (-6.6, 2.5) node[left]{3};
+#'
 #' \end{tikzpicture}
 #' ```
 #'

R/callback-sofa.R

@@ -1,4 +1,3 @@
-
 #' SOFA score label
 #'
 #' The SOFA (Sequential Organ Failure Assessment) score is a commonly used
@@ -38,40 +37,26 @@
 #' | **SOFA score**              |     1     |     2     |     3    |    4   |
 #' | --------------------------- | --------- | --------- | -------- | ------ |
 #' | **Respiration**             |           |           |          |        |
-#' | PaO\ifelse{latex}{\out{\textsubscript{2}}}{\ifelse{html
-#'   }{\out{<sub>2</sub>}}{2}}/FiO\ifelse{latex
-#'   }{\out{\textsubscript{2}}}{\ifelse{html
-#'   }{\out{<sub>2</sub>}}{2}} \[mmHg\] | < 400 | < 300  |   < 200  |  < 100 |
+#' | PaO\subs{2}/FiO\subs{2} \[mmHg\] | < 400 | < 300    |   < 200  |  < 100 |
 #' | and mechanical ventilation  |           |           |    yes   |   yes  |
 #' | **Coagulation**             |           |           |          |        |
-#' | Platelets \[\ifelse{latex}{\out{$\times$}}{\ifelse{html
-#'   }{\out{&times;}}{x}}10\ifelse{latex}{\out{\textsuperscript{3}}}{\ifelse{
-#'   html}{\out{<sup>3</sup>}}{3}}/mm\ifelse{latex
-#'   }{\out{\textsuperscript{3}}}{\ifelse{html
-#'   }{\out{<sup>3</sup>}}{3}}\] | < 150     |   < 100   |   < 50   |  < 20  |
+#' | Platelets \[\tims{}10\sups{3}/mm\sups{3}\] | < 150 | < 100 | < 50 | < 20 |
 #' | **Liver**                   |           |           |          |        |
 #' | Bilirubin \[mg/dl\]         |  1.2-1.9  |  2.0-5.9  | 6.0-11.9 | > 12.0 |
-#' | **Cardiovascular**\ifelse{latex}{\out{\textsuperscript{a}}}{\ifelse{html
-#'   }{\out{<sup>a</sup>}}{a}}   |           |           |          |        |
+#' | **Cardiovascular**\sups{a}  |           |           |          |        |
 #' | MAP                         | < 70 mmHg |           |          |        |
-#' | or dopamine                 |           | \ifelse{latex}{\out{$\le$}}{\ifelse{html
-#'   }{\out{&leq;}}{<=}}                           5     |    > 5   |   > 15 |
+#' | or dopamine                 |           | \leq{}5   |    > 5   |   > 15 |
 #' | or dobutamine               |           |  any dose |          |        |
-#' | or epinephrine              |           |           | \ifelse{latex}{\out{$\le$}}{\ifelse{html
-#'   }{\out{&leq;}}{<=}}                                      0.1   |  > 0.1 |
-#' | or norepinephrine           |           |           | \ifelse{latex}{\out{$\le$}}{\ifelse{html
-#'   }{\out{&leq;}}{<=}}                                      0.1   |  > 0.1 |
+#' | or epinephrine              |           |          | \leq{}0.1 |  > 0.1 |
+#' | or norepinephrine           |           |          | \leq{}0.1 |  > 0.1 |
 #' | **Central nervous system**  |           |           |          |        |
 #' | Glasgow Coma Score          | 13-14     |   10-12   |    6-9   |   < 6  |
 #' | **Renal**                   |           |           |          |        |
 #' | Creatinine \[mg/dl\]        |  1.2-1.9  |  2.0-3.4  |  3.5-4.9 |  > 5.0 |
 #' | or urine output \[ml/day\]  |           |           |   < 500  |  < 200 |
 #'
-#' \ifelse{latex}{\out{\textsuperscript{a}}}{\ifelse{html
-#' }{\out{<sup>a</sup>}}{a}}Adrenergic agents administered for at least 1h
-#' (doses given are in \[\ifelse{latex}{\out{$\mu$}}{\ifelse{html
-#' }{\out{&mu;}}{u}}g/kg \ifelse{latex}{\out{$\cdot$}}{\ifelse{html
-#' }{\out{&middot;}}{.}} min\]
+#' Adrenergic\sups{a} agents administered for at least 1h
+#' (doses given are in \[\smu{}g/kg \dotm{} min\]
 #'
 #' At default, for each patient, a score is calculated for every time step,
 #' from the first available measurement to the last. In instead of a regularly