strict testing (#202)

- added options for strict testing - add `pre-commit.yaml` - solve all lintr issues - solve all spelling issues --------- Signed-off-by: André Veríssimo <[email protected]> Signed-off-by: Pawel Rucki <[email protected]> Co-authored-by: André Veríssimo <[email protected]> Co-authored-by: Joe Zhu <[email protected]>
insightsengineering · Mar 11, 2024 · d17033f · d17033f
1 parent 2ac5374
commit d17033f
Show file tree

Hide file tree

Showing 84 changed files with 1,064 additions and 381 deletions.
diff --git a/.lintr b/.lintr
@@ -0,0 +1,13 @@
+linters: linters_with_defaults(
+  line_length_linter = line_length_linter(120L),
+  cyclocomp_linter = NULL,
+  object_usage_linter = NULL,
+  object_name_linter = object_name_linter(
+    styles = c("snake_case", "symbols"),
+    regexes = c(
+      ANL = "^ANL_?[0-9A-Z_]*$",
+      ADaM = "^r?AD[A-Z]{2,5}_?[0-9]*$",
+      ADaM_variables = "^AVAL$|^USUBJID$|^PARAMCD$|^PARAM$"
+      )
+    )
+  )
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,62 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.0
+    hooks:
+    -   id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style]
+    -   id: spell-check
+        exclude: >
+          (?x)^(
+          .*\.[rR]|
+          .*\.feather|
+          .*\.jpeg|
+          .*\.pdf|
+          .*\.png|
+          .*\.py|
+          .*\.RData|
+          .*\.rds|
+          .*\.Rds|
+          .*\.Rproj|
+          .*\.scss|
+          .*\.sh|
+          .*\.svg|
+          .*\.qmd|
+          (.*/|)\.gitignore|
+          (.*/|)\.gitlab-ci\.yml|
+          (.*/|)\.lintr|
+          (.*/|)\.pre-commit-.*|
+          (.*/|)\.Rbuildignore|
+          (.*/|)\.Renviron|
+          (.*/|)\.Rprofile|
+          (.*/|)CODEOWNERS|
+          (.*/|)DESCRIPTION|
+          (.*/|)LICENSE|
+          (.*/|)NAMESPACE|
+          (.*/|)staged_dependencies\.y[a]?ml|
+          (.*/|)renv/settings\.dcf|
+          (.*/|)renv\.lock|
+          (.*/|)WORDLIST|
+          \.github/workflows/.*|
+          (.*/|)\_quarto[-]?.*\.yml|
+          (.*/|)markdown-snaps.md|
+          data/.*
+          )$
+    -   id: lintr
+    -   id: parsable-R
+    -   id: no-browser-statement
+    -   id: no-debug-statement
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: check-added-large-files
+        args: ['--maxkb=200']
+-   repo: local
+    hooks:
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.(Rhistory|RData|Rds|rds)$'
+        # `exclude: <regex>` to allow committing specific files
diff --git a/book/_quarto.yml b/book/_quarto.yml
@@ -105,3 +105,8 @@ website:
       language: en
       loading: lazy
       mapping: pathname
+
+profile:
+  group:
+    - [stable, development]
+  default: stable
diff --git a/book/generate-index.R b/book/generate-index.R
@@ -15,7 +15,7 @@ print_ref_templates <- function(fpath) {
 
 section_header <- function(title) {
   cat(
-    paste("", "------------------------------------------------------------------------", "", # nolint
+    paste("", "------------------------------------------------------------------------", "",
       paste0("### ", "**", title, "**"), "",
       sep = "\n"
     ),
@@ -24,15 +24,15 @@ section_header <- function(title) {
 }
 
 create_subsection <- function(fpath, title) {
-  cat(paste("", paste("####", title), "", "", sep = "\n"), file = "./tlg-index.qmd", append = TRUE) # nolint
+  cat(paste("", paste("####", title), "", "", sep = "\n"), file = "./tlg-index.qmd", append = TRUE)
   all_files <- list.files(path = fpath, pattern = "*.qmd", full.names = TRUE)
   invisible(sapply(all_files, print_ref_templates))
 }
 
 # Create Index Header
 
 cat(
-  paste("---", "title: Index", "toc: true", "toc-depth: 4", "---", "", sep = "\n"), # nolint
+  paste("---", "title: Index", "toc: true", "toc-depth: 4", "---", "", sep = "\n"),
   file = "./tlg-index.qmd"
 )
 
@@ -61,9 +61,9 @@ create_subsection("./tables/vital-signs", "Vital Signs")
 section_header("Listings")
 create_subsection("./listings/ADA", "ADA")
 create_subsection("./listings/adverse-events", "Adverse Events")
-create_subsection("./listings/concomitant-medications", "Concomitant Medications") # nolint
+create_subsection("./listings/concomitant-medications", "Concomitant Medications")
 create_subsection("./listings/disposition", "Disposition")
-create_subsection("./listings/development-safety-update-report", "Development Safety Update Report") # nolint
+create_subsection("./listings/development-safety-update-report", "Development Safety Update Report")
 create_subsection("./listings/ECG", "ECG")
 create_subsection("./listings/exposure", "Exposure")
 create_subsection("./listings/lab-results", "Lab Results")

diff --git a/book/graphs/efficacy/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd
@@ -44,13 +44,14 @@ var_labels(anl_rsp_arms_ab) <- c(anl_labels, is_rsp = "Is Responder")
 
 ## Standard Plot
 
-```{r plot1, test = list(plot_v1 = "plot"), fig.width = 20, fig.height = 5}
+<!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
+```{r plot1, test = list(plot_v1 = "plot"), fig.width = 20, fig.height = 5, opts.label = c('skip_test_strict')}
 df <- extract_rsp_subgroups(
   variables = list(
     rsp = "is_rsp",
     arm = "ARM",
     subgroups = c("SEX", "BMRKR2"),
-    strata_var = "STRATA2"
+    strata = "STRATA2"
   ),
   data = anl_rsp_arms_ab,
   conf_level = 0.95
@@ -65,7 +66,8 @@ plot
 
 ## Plot Specifying Class Variables and <br/> Options for the Treatment Variable
 
-```{r plot2, test = list(plot_v2 = "plot"), fig.width = 20, fig.height = 5}
+<!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
+```{r plot2, test = list(plot_v2 = "plot"), fig.width = 20, fig.height = 5, opts.label = c('skip_test_strict')}
 anl_rsp_comb_arms_ac <- anl %>%
   mutate(is_rsp = AVALC %in% c("CR", "PR")) %>%
   filter(ARMCD %in% c("ARM B", "ARM A", "ARM C")) %>%
@@ -89,7 +91,7 @@ df <- extract_rsp_subgroups(
     rsp = "is_rsp",
     arm = "ARMCD",
     subgroups = c("SEX", "BMRKR2"),
-    strata_var = "STRATA2"
+    strata = "STRATA2"
   ),
   data = anl_rsp_comb_arms_ac,
   conf_level = 0.95
@@ -104,13 +106,14 @@ plot
 
 ## Plot Selecting Columns and <br/> Changing the Alpha Level
 
-```{r plot3, test = list(plot_v3 = "plot"), fig.width = 10, fig.height = 4}
+<!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
+```{r plot3, test = list(plot_v3 = "plot"), fig.width = 10, fig.height = 4, opts.label = c('skip_test_strict')}
 df <- extract_rsp_subgroups(
   variables = list(
     rsp = "is_rsp",
     arm = "ARM",
     subgroups = c("SEX", "BMRKR2"),
-    strata_var = "STRATA2"
+    strata = "STRATA2"
   ),
   data = anl_rsp_arms_ab,
   conf_level = 0.90
@@ -125,13 +128,14 @@ plot
 
 ## Plot with Fixed <br/> Symbol Size
 
-```{r plot4, test = list(plot_v4 = "plot"), fig.width = 20, fig.height = 5}
+<!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
+```{r plot4, test = list(plot_v4 = "plot"), fig.width = 20, fig.height = 5, opts.label = c('skip_test_strict')}
 df <- extract_rsp_subgroups(
   variables = list(
     rsp = "is_rsp",
     arm = "ARM",
     subgroups = c("SEX", "BMRKR2"),
-    strata_var = "STRATA2"
+    strata = "STRATA2"
   ),
   data = anl_rsp_arms_ab,
   conf_level = 0.95
@@ -149,7 +153,8 @@ plot
 
 ## Plot of CR Only, Setting <br/> Values Indicating Response
 
-```{r plot5, test = list(plot_v5 = "plot"), fig.width = 20, fig.height = 5}
+<!-- skip strict because of https://github.com/therneau/survival/issues/240 -->
+```{r plot5, test = list(plot_v5 = "plot"), fig.width = 20, fig.height = 5, opts.label = c('skip_test_strict')}
 anl_cr_arms_ab <- anl %>%
   mutate(is_rsp = AVALC == "CR") %>%
   filter(ARMCD %in% c("ARM B", "ARM A")) %>%
@@ -167,7 +172,7 @@ df <- extract_rsp_subgroups(
     rsp = "is_rsp",
     arm = "ARM",
     subgroups = c("SEX", "BMRKR2"),
-    strata_var = "STRATA2"
+    strata = "STRATA2"
   ),
   data = anl_cr_arms_ab,
   conf_level = 0.95

diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd
@@ -163,7 +163,7 @@ plot
 ```{r test parameters, test = list(width = "width", height = "height", plot_v3.width = "plot_v3.width"), echo=FALSE}
 width <- 15
 height <- 4
-plot_v3.width <- 8
+plot_v3.width <- 8 # nolint: object_name.
 ```
 
 {{< include ../../test-utils/save_results.qmd >}}

diff --git a/book/graphs/efficacy/kmg01.qmd b/book/graphs/efficacy/kmg01.qmd
@@ -27,7 +27,8 @@ variables <- list(tte = "AVAL", is_event = "is_event", arm = "ARMCD")
 
 ## Standard Plot
 
-```{r plot1, fig.height=8, test = list(plot_v1 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot1, fig.height=8, test = list(plot_v1 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -40,7 +41,8 @@ plot
 
 ## Plot of Failures
 
-```{r plot2, fig.height=8, test = list(plot_v2 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot2, fig.height=8, test = list(plot_v2 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -58,7 +60,8 @@ plot
 
 ## Plot Without <br/> Comparative Statistics
 
-```{r plot3, fig.height=8, test = list(plot_v3 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot3, fig.height=8, test = list(plot_v3 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -71,7 +74,8 @@ plot
 
 ## Plot Without <br/> Censoring Marks
 
-```{r plot4, fig.height=8, test = list(plot_v4 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot4, fig.height=8, test = list(plot_v4 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -85,7 +89,8 @@ plot
 
 ## Plot Modifying <br/> Censoring Marks
 
-```{r plot5, fig.height=8, test = list(plot_v5 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot5, fig.height=8, test = list(plot_v5 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_km(
   df = anl,
   variables = variables,
@@ -100,7 +105,8 @@ plot
 
 ## Plot Modifying Options for Statistics, <br/> Tie Handling, Stratification, etc.
 
-```{r plot6, test = list(plot_v6 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot6, test = list(plot_v6 = "plot"), opts.label = c('skip_test_strict')}
 variables$strata <- c("STRATA1", "STRATA2")
 plot <- g_km(
   df = anl,

diff --git a/book/graphs/efficacy/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd
@@ -46,7 +46,8 @@ mmrm_results <- fit_mmrm(
 
 ### Considering the treatment variable in the model
 
-```{r plot1, dev.args=list(pointsize=6), test = list(plot_v1 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot1, dev.args=list(pointsize=6), test = list(plot_v1 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_mmrm_lsmeans(
   mmrm_results,
   select = "estimates",
@@ -57,7 +58,8 @@ plot
 
 ### Considering the treatment variable in the model, with lines
 
-```{r plot2, dev.args=list(pointsize=6), test = list(plot_v2 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot2, dev.args=list(pointsize=6), test = list(plot_v2 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_mmrm_lsmeans(
   mmrm_results,
   select = "estimates",
@@ -69,7 +71,8 @@ plot
 
 ### Considering the treatment variable in the model, with statistics table
 
-```{r plot3, dev.args=list(pointsize=6), fig.height=7, test = list(plot_v3 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot3, dev.args=list(pointsize=6), fig.height=7, test = list(plot_v3 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_mmrm_lsmeans(
   mmrm_results,
   select = "estimates",
@@ -85,7 +88,8 @@ plot
 
 Users can choose to display both estimates and contrasts together by running `g_mmrm_lsmeans(mmrm_results)`.
 
-```{r plot4, dev.args=list(pointsize=6), test = list(plot_v4 = "plot")}
+<!-- skip strict because of https://github.com/r-lib/gtable/pull/94 -->
+```{r plot4, dev.args=list(pointsize=6), test = list(plot_v4 = "plot"), opts.label = c('skip_test_strict')}
 plot <- g_mmrm_lsmeans(
   mmrm_results,
   select = "contrasts",

diff --git a/book/graphs/efficacy/mmrmg02.qmd b/book/graphs/efficacy/mmrmg02.qmd
@@ -36,7 +36,7 @@ adqs_f <- adqs %>%
 set.seed(2)
 adqs_f_with_groups <- rbind(
   within(
-    adqs_f[sample(1:nrow(adqs_f), size = 1 / 2 * nrow(adqs_f)), ],
+    adqs_f[sample(seq_len(nrow(adqs_f)), size = 1 / 2 * nrow(adqs_f)), ],
     group <- "subpopulation 1"
   ),
   within(