develop: use donttest to reduce runtime of examples (#15)

Also combine workflows that check the package into a single workflow.

Author: benesom

.github/workflows/r-cmd-check.yaml .github/workflows/check-package.yaml.github/workflows/r-cmd-check.yaml renamed to .github/workflows/check-package.yaml

@@ -3,7 +3,7 @@ on:
   pull_request:
     branches: [main, dev]
 
-name: r-cmd-check
+name: check package
 
 jobs:
   r-cmd-check:
@@ -36,11 +36,38 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
-          needs: check
+          extra-packages: |
+            any::lintr
+            any::devtools
+            any::rcmdcheck
+          needs: check, lint
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
           args: 'c("--ignore-vignettes")'
-          build_args: 'c("--no-build-vignettes")'
+          build_args: 'c("--no-build-vignettes")'
+
+      # test that committed man pages and namespace are up to date
+      - name: build roxygen documentation
+        run: |
+          cp -r man .man
+          cp -r NAMESPACE .NAMESPACE
+          make roxygen
+
+      - name: Check man pages
+        run: diff -r man .man
+
+      - name: Check NAMESPACE
+        run: diff -r NAMESPACE .NAMESPACE
+
+      - name: Lint package
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
+
+      # test examples that have not been tested with r cmd check because of
+      # \donttest
+      - name: check examples
+        run: make check-examples

.github/workflows/check-roxygen.yaml

@@ -66,6 +66,9 @@ rmd:
 check: lint
 	@_R_CHECK_FORCE_SUGGESTS_=0 echo 'future::plan("multicore"); res <- rcmdcheck::rcmdcheck(".", build_args=c("--no-build-vignettes"), args=c("--ignore-vignettes"))' | $(R)
 
+check-examples:
+	@_R_CHECK_FORCE_SUGGESTS_=0 echo 'future::plan("multicore"); devtools::run_examples(".", run_donttest = TRUE, run_dontrun = FALSE)' | $(R)
+
 check-cran: build
 	@$(R) CMD check $(BUILD_DIR)/$(PKG)_$(GETVER).tar.gz --timings --as-cran --no-multiarch --run-donttest
 

.github/workflows/lint-project.yaml

@@ -11,7 +11,7 @@
 #' for decision-making
 #' @author Klaus Kähler Holst, Benedikt Sommer
 #' @examples
-#' \dontrun{
+#' \dontrun{ # don't run because of high computational time
 #' trial <- Trial$new(
 #'   covariates = \(n) data.frame(a = rbinom(n, 1, 0.5), x = rnorm(n)),
 #'   outcome = setargs(outcome_count, par = c(1, 0.5, 1), overdispersion = 0.7)
@@ -320,6 +320,7 @@ Trial <- R6::R6Class("Trial", #nolint
     #' the simulation. The return object is also assigned to the `estimates`
     #' field of this Trial class object (see examples).
     #' @examples
+    #' \dontrun{ # don't run because of high computational time
     #' # future::plan("multicore")
     #' trial <- Trial$new(
     #'   covariates = \(n) data.frame(a = rbinom(n, 1, 0.5)),
@@ -351,6 +352,7 @@ Trial <- R6::R6Class("Trial", #nolint
     #'
     #' # supplying another estimator
     #' trial$run(n = 100, R = 50, estimators = est_glm(robust = FALSE))
+    #' }
     run = function(n, R = 100, estimators = NULL, ...) {
       return(trial_run(self, .private = private, n = n, R = R,
         estimators = estimators, ...)
@@ -364,6 +366,7 @@ Trial <- R6::R6Class("Trial", #nolint
     #' estimator. The behavior of passing arguments to lower level functions is
     #' identical to [Trial$run()][Trial].
     #' @examples
+    #' \dontrun{ # don't run because of high computational time
     #' # toy examples with small number of Monte-Carlo replicates
     #' # future::plan("multicore")
     #' trial <- Trial$new(
@@ -387,6 +390,7 @@ Trial <- R6::R6Class("Trial", #nolint
     #' # supplying estimators to overrule previously set estimators
     #' trial$estimate_power(n = 100, R = 20,
     #'  estimators = list(est_glm(), est_adj()))
+    #' }
     #' @return numeric
     estimate_power = function(n,  R = 100, estimators = NULL,
       summary.args = list(), ...) {
@@ -434,7 +438,7 @@ Trial <- R6::R6Class("Trial", #nolint
     #' @return samplesize_estimate S3 object
     #' @author Klaus Kähler Holst
     #' @examples
-    #' \dontrun{
+    #' \dontrun{ # don't run because of high computational time
     #' trial <- Trial$new(
     #'   covariates = \(n) data.frame(a = rbinom(n, 1, 0.5)),
     #'   outcome = \(data, ate, sd) with(data, rnorm(nrow(data), a * ate, sd)),
@@ -449,11 +453,11 @@ Trial <- R6::R6Class("Trial", #nolint
     #'
     #' # reduce number of iterations for bisection step but keep R = 100
     #' # (default value)
-    #' trial$estimate_samplesize(bisection.control = list(niter = 2))
+    #' # trial$estimate_samplesize(bisection.control = list(niter = 2))
     #'
     #' # reduce significance level from 0.05 to 0.025, but keep alternative as
     #' # before
-    #' trial$estimate_samplesize(summary.args = list(level = 0.025))
+    #' # trial$estimate_samplesize(summary.args = list(level = 0.025))
     #' }
     estimate_samplesize = function(
       ...,

Makefile

@@ -24,7 +24,7 @@
 #' @useDynLib carts, .registration=TRUE
 #' @author Benedikt Sommer, Klaus Holst, Foroogh Shamsi
 #' @examples
-#' \dontrun{
+#' \dontrun{ # don't run because of high computational time
 #' trial <- Trial$new(
 #'   covariates = \(n) data.frame(a = rbinom(n, 1, 0.5), x = rnorm(n)),
 #'   outcome = setargs(outcome_count, par = c(1, 0.5, 1), overdispersion = 0.7)

R/Trial.R

@@ -20,6 +20,7 @@
 #' @author Klaus Kähler Holst
 #' @export
 #' @examples
+#' \dontrun{
 #' trial <- Trial$new(
 #'     covariates = function(n) data.frame(a = rbinom(n, 1, 0.5), x = rnorm(n)),
 #'     outcome = setargs(outcome_count,
@@ -57,6 +58,7 @@
 #' # regression coefficient changes when encoding the treatment variable as a
 #' # factor
 #' est_glm(family = poisson, target.parameter = "a1")(dd_factor)
+#' }
 est_glm <- function(response = "y",
                     treatment = "a",
                     covariates = NULL,
@@ -164,6 +166,7 @@ est_glmbin <- function(...) {
 #' @author Klaus Kähler Holst
 #' @export
 #' @examples
+#' \dontrun{ # don't run because of high computational time
 #' trial <- Trial$new(
 #'     covariates = function(n) data.frame(a = rbinom(n, 1, 0.5), x = rnorm(n)),
 #'     outcome = setargs(outcome_count,
@@ -208,6 +211,7 @@ est_glmbin <- function(...) {
 #'
 #' dd_factor$a <- factor(dd_factor$a, levels = c(1, 0))
 #' estimator(dd_factor) # E[Y(1)] - E[Y(0)]
+#' }
 est_adj <- function(response = "y",
                     treatment = "a",
                     covariates = NULL,

R/carts-package.R

@@ -318,6 +318,7 @@ outcome_continuous <- function(data,
 #' @seealso [outcome_count] [outcome_lp] [outcome_binary] [outcome_continuous]
 #' @examples
 #' \dontrun{
+#' outcome_phreg <- carts:::outcome_phreg
 #' library("survival")
 #' data(pbc, package = "survival")
 #' pbc0 <- na.omit(pbc) |>