options for strict tests; few enhancements (#295)

- part of insightsengineering/coredev-tasks#478 - please read this for more info about the implementation: insightsengineering/coredev-tasks#478 (comment) - removed unnecessary empty first line in examples as this is actually being rendered - removed `library(random.cdisc.data)` as it's redundant Please review the changes carefully and let me know if there is something you don't like. --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
insightsengineering · Mar 4, 2024 · fad0aae · fad0aae
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -31,7 +31,8 @@ Suggests:
     diffdf,
     knitr (>= 1.42),
     rmarkdown (>= 2.19),
-    testthat (>= 3.0.4)
+    testthat (>= 3.0.4),
+    withr (>= 2.0.0)
 VignetteBuilder:
     knitr
 RdMacros:
@@ -40,7 +41,7 @@ Config/Needs/verdepcheck: mllg/checkmate, tidyverse/dplyr,
     r-lib/lifecycle, tidyverse/lubridate, tidyverse/magrittr, r-lib/rlang,
     tidyverse/stringr, tidyverse/tibble, tidyverse/tidyr,
     yaml=vubiostat/r-yaml, gowerc/diffdf, yihui/knitr, rstudio/rmarkdown,
-    r-lib/testthat
+    r-lib/testthat, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3
 Encoding: UTF-8

diff --git a/R/radab.R b/R/radab.R
@@ -17,7 +17,6 @@
 #' @details One record per study per subject per parameter per time point: "R1800000", "RESULT1", "R1800001", "RESULT2".
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #' adpc <- radpc(adsl, seed = 2, duration = 9 * 7)
 #'
@@ -245,34 +244,25 @@ radab <- function(adsl,
   adab_subj <- adab %>%
     dplyr::group_by(USUBJID) %>%
     dplyr::mutate(
-      pos_bl = any(PARAM == "ADA interpreted per sample result" &
-        !is.na(ABLFL) & AVALC == "POSITIVE"),
-      pos_bl_nab = any(PARAM == "NAB interpreted per sample result" &
-        !is.na(ABLFL) & AVALC == "POSITIVE"),
-      any_pos_postbl = any(PARAM == "ADA interpreted per sample result" &
-        is.na(ABLFL) & AVALC == "POSITIVE"),
-      any_pos_postbl_nab = any(PARAM == "NAB interpreted per sample result" &
-        is.na(ABLFL) & AVALC == "POSITIVE"),
-      pos_last_postbl = any(PARAM == "ADA interpreted per sample result" &
-        NFRLT == max(NFRLT) & AVALC == "POSITIVE"),
+      pos_bl = any(PARAM == "ADA interpreted per sample result" & !is.na(ABLFL) & AVALC == "POSITIVE"),
+      pos_bl_nab = any(PARAM == "NAB interpreted per sample result" & !is.na(ABLFL) & AVALC == "POSITIVE"),
+      any_pos_postbl = any(PARAM == "ADA interpreted per sample result" & is.na(ABLFL) & AVALC == "POSITIVE"),
+      any_pos_postbl_nab = any(PARAM == "NAB interpreted per sample result" & is.na(ABLFL) & AVALC == "POSITIVE"),
+      pos_last_postbl = any(PARAM == "ADA interpreted per sample result" & NFRLT == max(NFRLT) & AVALC == "POSITIVE"),
       ada_bl = AVAL[PARAM == "Antibody titer units" & !is.na(ABLFL)],
       nab_bl = AVAL[PARAM == "Neutralizing Antibody titer units" & !is.na(ABLFL)]
     )
   pos_tots <- adab_subj %>%
     dplyr::summarise(
       n_pos = sum(PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"),
-      inc_postbl = sum(PARAM == "ADA interpreted per sample result" &
-        is.na(ABLFL) & (AVAL - ada_bl) > 0.60),
-      inc_postbl_nab = sum(PARAM == "NAB interpreted per sample result" &
-        is.na(ABLFL) & (AVAL - nab_bl) > 0.60),
-      onset_ada = if (any(PARAM == "ADA interpreted per sample result" &
-        AVALC == "POSITIVE")) {
+      inc_postbl = sum(PARAM == "ADA interpreted per sample result" & is.na(ABLFL) & (AVAL - ada_bl) > 0.60),
+      inc_postbl_nab = sum(PARAM == "NAB interpreted per sample result" & is.na(ABLFL) & (AVAL - nab_bl) > 0.60),
+      onset_ada = if (any(PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE")) {
         min(NFRLT[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"])
       } else {
         NA
       },
-      last_ada = if (any(PARAM == "ADA interpreted per sample result" &
-        AVALC == "POSITIVE")) {
+      last_ada = if (any(PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE")) {
         max(NFRLT[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"])
       } else {
         NA
@@ -304,6 +294,7 @@ radab <- function(adsl,
   adab[!(adab$PARAM %in% visit_lvl_params), ] <- adab %>%
     dplyr::filter(!(PARAM %in% visit_lvl_params)) %>%
     dplyr::mutate(
+      # nolint start indentation_linter
       AVALC = dplyr::case_when(
         (PARAM == "ADA Status of a patient" & any_pos_postbl) ~ "POSITIVE",
         (PARAM == "ADA Status of a patient" & !any_pos_postbl) ~ "NEGATIVE",
@@ -366,6 +357,7 @@ radab <- function(adsl,
           !((!pos_bl_nab & any_pos_postbl_nab) | (pos_bl_nab & inc_postbl_nab > 0))) ~ 1,
         TRUE ~ 0
       ),
+      # nolint end indentation_linter
       PARCAT1 = dplyr::case_when(
         PARAM %in% c(
           "Neutralizing Antibody titer units", "NAB interpreted per sample result",

diff --git a/R/radae.R b/R/radae.R
@@ -18,7 +18,6 @@
 #' @export
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, study_duration = 2, seed = 1)
 #'
 #' adae <- radae(adsl, seed = 2)

diff --git a/R/radaette.R b/R/radaette.R
@@ -21,7 +21,6 @@
 #' @author Xiuting Mi
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #'
 #' adaette <- radaette(adsl, seed = 2)

diff --git a/R/radcm.R b/R/radcm.R
@@ -19,7 +19,6 @@
 #' @export
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #'
 #' adcm <- radcm(adsl, seed = 2)

diff --git a/R/raddv.R b/R/raddv.R
@@ -19,7 +19,6 @@
 #' @export
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #'
 #' addv <- raddv(adsl, seed = 2)

diff --git a/R/radeg.R b/R/radeg.R
@@ -21,7 +21,6 @@
 #' @author tomlinsj, npaszty, Xuefeng Hou, dipietrc
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #'
 #' adeg <- radeg(adsl, visit_format = "WEEK", n_assessments = 7L, seed = 2)

diff --git a/R/radex.R b/R/radex.R
@@ -21,7 +21,6 @@
 #' @export
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, study_duration = 2, seed = 1)
 #'
 #' adex <- radex(adsl, seed = 2)

diff --git a/R/radhy.R b/R/radhy.R
@@ -19,7 +19,6 @@
 #' @author wojciakw
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #'
 #' adhy <- radhy(adsl, seed = 2)

diff --git a/R/radlb.R b/R/radlb.R
@@ -21,7 +21,6 @@
 #' @author tomlinsj, npaszty, Xuefeng Hou
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #'
 #' adlb <- radlb(adsl, visit_format = "WEEK", n_assessments = 7L, seed = 2)

diff --git a/R/radmh.R b/R/radmh.R
@@ -18,7 +18,6 @@
 #' @export
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, study_duration = 2, seed = 1)
 #'
 #' admh <- radmh(adsl, seed = 2)

diff --git a/R/radpc.R b/R/radpc.R
@@ -18,7 +18,6 @@
 #' @export
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #'
 #' adpc <- radpc(adsl, seed = 2)
@@ -67,8 +66,7 @@ radpc <- function(adsl,
       PCTPTNUM = if (day == 1) c(0, 0.5, 1, 1.5, 2, 3, 4, 8, 12) else 24 * (day - 1),
       PARAM = factor(c("Plasma Drug X", "Urine Drug X", "Plasma Drug Y", "Urine Drug Y"))
     )
-    adpc_day <- adpc_day[!(grepl("Urine", adpc_day$PARAM) &
-      adpc_day$PCTPTNUM %in% c(0.5, 1, 1.5, 2, 3)), ] %>%
+    adpc_day <- adpc_day[!(grepl("Urine", adpc_day$PARAM) & adpc_day$PCTPTNUM %in% c(0.5, 1, 1.5, 2, 3)), ] %>%
       dplyr::arrange(USUBJID, PARAM) %>%
       dplyr::mutate(
         VISITDY = day,
@@ -97,8 +95,11 @@ radpc <- function(adsl,
         )
       ) %>%
       dplyr::mutate(
-        PCVOL = ifelse(ASMED == "URINE", round(abs(((PCTPTNUM - 1) %% 24) *
-          A0 * ka * exp(PCTPTNUM %% 1.8 / 10)), 2), NA),
+        PCVOL = ifelse(
+          ASMED == "URINE",
+          round(abs(((PCTPTNUM - 1) %% 24) * A0 * ka * exp(PCTPTNUM %% 1.8 / 10)), 2),
+          NA
+        ),
         # PK Equation
         AVALC = ifelse(AVAL == 0, "BLQ", as.character(AVAL)),
         AVALU = avalu,

diff --git a/R/radpp.R b/R/radpp.R
@@ -17,7 +17,6 @@
 #' @export
 #'
 #' @examples
-#' library(random.cdisc.data)
 #' adsl <- radsl(N = 10, seed = 1, study_duration = 2)
 #'
 #' adpp <- radpp(adsl, seed = 2)
@@ -138,8 +137,10 @@ radpp <- function(adsl,
     dplyr::left_join(t1_t2, by = c("PARAMCD"), multiple = "all", relationship = "many-to-many")
 
   adpp <- dplyr::inner_join(adpp, adsl, by = c("STUDYID", "USUBJID")) %>%
-    dplyr::filter(ACTARM != "B: Placebo", !(ACTARM == "A: Drug X" &
-      (PPCAT == "Plasma Drug Y" | PPCAT == "Metabolite Drug Y")))
+    dplyr::filter(
+      ACTARM != "B: Placebo",
+      !(ACTARM == "A: Drug X" & (PPCAT == "Plasma Drug Y" | PPCAT == "Metabolite Drug Y"))
+    )
 
   # derive PKARMCD column for creating more cohorts
   adpp <- adpp %>%