Issues 19 and 21 fixed

+ codecov added + Issues [#19](#19) and [#21](#21) fixed
rpact-com · Feb 22, 2024 · 404472f · 404472f
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -47,3 +47,4 @@ testthat-problems\.rds
 ^.*\.gcno$
 ^inst/\.covrignore$
 ^README\.html$
+^codecov\.yml$
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,57 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          Sys.setenv("RPACT_COMPLETE_UNIT_TEST_SET_ENABLED" = TRUE)
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: rpact-com/rpact
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rpact
 Title: Confirmatory Adaptive Clinical Trial Design and Analysis
-Version: 3.5.1.9231
-Date: 2024-02-09
+Version: 3.5.1
+Date: 2024-02-16
 Authors@R: c(
 	person(
 		given = "Gernot", 

diff --git a/NEWS.md b/NEWS.md
@@ -2,7 +2,20 @@
 # rpact 3.5.1
 
 * The fields `.parameterNames` and `.parameterFormatFunctions` were removed from all rpact result objects in favor of a more efficient solution
-* Issues [15](https://github.com/rpact-com/rpact/issues/15), [16](https://github.com/rpact-com/rpact/issues/16), and [17](https://github.com/rpact-com/rpact/issues/17) fixed
+* Issues [#15](https://github.com/rpact-com/rpact/issues/15), [#16](https://github.com/rpact-com/rpact/issues/16), [#17](https://github.com/rpact-com/rpact/issues/17), and [#19](https://github.com/rpact-com/rpact/issues/19) fixed
+* Fixed inconsistent naming of variables and class fields (issue [#21](https://github.com/rpact-com/rpact/issues/21))
+    - `getSampleSizeSurvival()` / `getPowerSurvival()`:
+       + Field `eventsPerStage` replaced by `cumulativeEventsPerStage`
+       + Field `singleEventsPerStage` added
+    - `getSimulationSurvival()`: 
+       + Field `eventsPerStage` replaced by `singleEventsPerStage` 
+       + Field `overallEventsPerStage` replaced by `cumulativeEventsPerStage` 
+    - `getSimulationMultiArmSurvival()`: 
+       + Field `eventsPerStage` replaced by `cumulativeEventsPerStage` 
+       + Field `singleNumberOfEventsPerStage` replaced by `singleEventsPerArmAndStage` 
+       + Field `singleEventsPerStage` added
+    - `getSimulationEnrichmentSurvival()`: 
+       + field `singleNumberOfEventsPerStage` replaced by `singleEventsPerPopulationAndStage` 
 
 
 # rpact 3.5.0

diff --git a/R/class_analysis_dataset.R b/R/class_analysis_dataset.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 7620 $
-## |  Last changed: $Date: 2024-02-09 12:57:37 +0100 (Fr, 09 Feb 2024) $
+## |  File version: $Revision: 7645 $
+## |  Last changed: $Date: 2024-02-16 16:12:34 +0100 (Fr, 16 Feb 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -615,19 +615,19 @@ writeDatasets <- function(datasets, file, ..., append = FALSE, quote = TRUE, sep
 #'
 #' For enrichment designs, the comparison of two samples is provided for an unstratified
 #' (sub-population wise) or stratified data input.\cr
-#' For unstratified (sub-population wise) data input the data sets are defined for the sub-populations
+#' For non-stratified (sub-population wise) data input the data sets are defined for the sub-populations
 #' S1, S2, ..., F, where F refers to the full populations. Use of \code{getDataset(S1 = , S2, ..., F = )}
 #' defines the data set to be used in \code{\link[=getAnalysisResults]{getAnalysisResults()}} (see examples)\cr
 #' For stratified data input the data sets are defined for the strata S1, S12, S2, ..., R, where R
 #' refers to the remainder of the strata such that the union of all sets is the full population.
 #' Use of \code{getDataset(S1 = , S12 = , S2, ..., R = )} defines the data set to be used in
 #' \code{\link[=getAnalysisResults]{getAnalysisResults()}} (see examples)\cr
-#' For survival data, for enrichment designs the log-rank statistics should be entered as stratified
+#' For survival data, for enrichment designs the log-rank statistics can only be entered as stratified
 #' log-rank statistics in order to provide strong control of Type I error rate. For stratified data input,
-#' the variables to be specified in \code{getDataset()} are \code{events}, \code{expectedEvents},
-#' \code{varianceEvents}, and \code{allocationRatios} or \code{overallEvents}, \code{overallExpectedEvents},
-#' \code{overallVarianceEvents}, and \code{overallAllocationRatios}. From this, (stratified) log-rank tests are
-#' calculated.
+#' the variables to be specified in \code{getDataset()} are \code{cumEvents}, \code{cumExpectedEvents},
+#' \code{cumVarianceEvents}, and \code{cumAllocationRatios} or \code{overallEvents}, \code{overallExpectedEvents},
+#' \code{overallVarianceEvents}, and \code{overallAllocationRatios}. From this, (stratified) log-rank tests and
+#' and the independent increments are calculated.
 #'
 #' @template return_object_dataset
 #'
@@ -1463,7 +1463,7 @@ Dataset <- setRefClass("Dataset",
 
             if (any(grepl("^subsets?\\d*$", colnames(dataFrame)))) {
                 numberOfTreatmentGroups <- .getNumberOfGroups(dataFrame, c(C_KEY_WORDS_SAMPLE_SIZES, C_KEY_WORDS_LOG_RANKS))
-                subsets <<- character(0)
+                subsets <<- character()
                 for (group in 1:numberOfTreatmentGroups) {
                     suffix <- ifelse(any(grepl("^subsets?\\d+$", colnames(dataFrame))), group, "")
                     subsets <<- c(subsets, .getValuesByParameterName(dataFrame, C_KEY_WORDS_SUBSETS, suffix = suffix))
@@ -1729,7 +1729,7 @@ Dataset <- setRefClass("Dataset",
         getNumberOfStages = function(naOmitEnabled = TRUE) {
             if (naOmitEnabled) {
                 colNames <- colnames(.data)
-                validColNames <- character(0)
+                validColNames <- character()
                 for (colName in colNames) {
                     colValues <- .data[, colName]
                     if (length(colValues) > 0 && !all(is.na(colValues))) {
@@ -3755,10 +3755,10 @@ DatasetEnrichmentSurvival <- setRefClass("DatasetEnrichmentSurvival",
             if (.paramExists(dataFrame, C_KEY_WORDS_OVERALL_EXPECTED_EVENTS) ||
                     .paramExists(dataFrame, C_KEY_WORDS_OVERALL_VARIANCE_EVENTS)) {
                 if (!.paramExists(dataFrame, C_KEY_WORDS_OVERALL_EXPECTED_EVENTS)) {
-                    stop(C_EXCEPTION_TYPE_MISSING_ARGUMENT, "'overallExpectedEvents' is missing")
+                    stop(C_EXCEPTION_TYPE_MISSING_ARGUMENT, "'overallExpectedEvents' or 'cumExpectedEvents' is missing")
                 }
                 if (!.paramExists(dataFrame, C_KEY_WORDS_OVERALL_VARIANCE_EVENTS)) {
-                    stop(C_EXCEPTION_TYPE_MISSING_ARGUMENT, "'overallVarianceEvents' is missing")
+                    stop(C_EXCEPTION_TYPE_MISSING_ARGUMENT, "'overallVarianceEvents' or 'cumVarianceEvents' is missing")
                 }
 
                 .inputType <<- "overall"
@@ -4012,7 +4012,7 @@ summary.Dataset <- function(object, ..., type = 1, digits = NA_integer_) {
     digitsGeneral <- digitSettings$digitsGeneral
     digitsProbabilities <- digitSettings$digitsProbabilities
 
-    paramsToCheck <- character(0)
+    paramsToCheck <- character()
     if (object$isDatasetMeans() || object$isDatasetRates()) {
         paramsToCheck <- c(paramsToCheck, "sampleSizes")
         if (kMax > 1) {
@@ -4143,7 +4143,7 @@ summary.Dataset <- function(object, ..., type = 1, digits = NA_integer_) {
 
 .getDatasetArgumentsRCodeLines <- function(x, complete = FALSE, digits = 4) {
     m <- getWideFormat(x)
-    lines <- character(0)
+    lines <- character()
     paramNames <- colnames(m)
     if (!complete) {
         if (x$.inputType == "stagewise") {

diff --git a/R/class_analysis_stage_results.R b/R/class_analysis_stage_results.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 7620 $
-## |  Last changed: $Date: 2024-02-09 12:57:37 +0100 (Fr, 09 Feb 2024) $
+## |  File version: $Revision: 7645 $
+## |  Last changed: $Date: 2024-02-16 16:12:34 +0100 (Fr, 16 Feb 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -1437,7 +1437,7 @@ plot.StageResults <- function(x, y, ..., type = 1L,
         data <- data.frame(
             xValues = numeric(0),
             yValues = numeric(0),
-            categories = character(0),
+            categories = character(),
             treatmentArms = numeric(0)
         )
         for (treatmentArm in treatmentArmsToShow) {
@@ -1486,7 +1486,7 @@ plot.StageResults <- function(x, y, ..., type = 1L,
         data <- data.frame(
             xValues = numeric(0),
             yValues = numeric(0),
-            categories = character(0),
+            categories = character(),
             populations = numeric(0)
         )
         for (population in populationsToShow) {

diff --git a/R/class_core_parameter_set.R b/R/class_core_parameter_set.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 7620 $
-## |  Last changed: $Date: 2024-02-09 12:57:37 +0100 (Fr, 09 Feb 2024) $
+## |  File version: $Revision: 7650 $
+## |  Last changed: $Date: 2024-02-20 14:37:26 +0100 (Di, 20 Feb 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -45,7 +45,8 @@ FieldSet <- setRefClass("FieldSet",
     fields = list(
         .parameterTypes = "list",
         .showParameterTypeEnabled = "logical",
-        .catLines = "character"
+        .catLines = "character",
+        .deprecatedFieldNames = "character"
     ),
     methods = list(
         .getFieldNames = function() {
@@ -54,10 +55,11 @@ FieldSet <- setRefClass("FieldSet",
         .getVisibleFieldNames = function() {
             fieldNames <- names(.self$getRefClass()$fields())
             fieldNames <- fieldNames[!startsWith(fieldNames, ".")]
+            fieldNames <- fieldNames[!(fieldNames %in% .deprecatedFieldNames)]
             return(fieldNames)
         },
         .resetCat = function() {
-            .catLines <<- character(0)
+            .catLines <<- character()
         },
         .cat = function(..., file = "", sep = "", fill = FALSE, labels = NULL,
                 append = FALSE, heading = 0, tableColumns = 0, consoleOutputEnabled = TRUE,
@@ -199,7 +201,8 @@ ParameterSet <- setRefClass("ParameterSet",
                 .showParameterTypeEnabled = .showParameterTypeEnabled
             )
             .parameterTypes <<- list()
-            .catLines <<- character(0)
+            .catLines <<- character()
+            .deprecatedFieldNames <<- character()
         },
         clone = function() {
             paramNames <- names(.self$getRefClass()$fields())
@@ -605,7 +608,7 @@ ParameterSet <- setRefClass("ParameterSet",
                 paramCaption <- paste0("%", paramName, "%")
             }
             if (!is.null(category) && !is.na(category)) {
-                if (.isMultiArmSimulationResults(.self) && paramName == "singleNumberOfEventsPerStage") {
+                if (.isMultiArmSimulationResults(.self) && paramName == "singleEventsPerArmAndStage") {
                     if (!inherits(.self, "SimulationResultsEnrichmentSurvival") &&
                             !is.na(numberOfCategories) && numberOfCategories == category) {
                         category <- "control"
@@ -1112,7 +1115,7 @@ ParameterSet <- setRefClass("ParameterSet",
     names(dataFrame) <- stagesCaption
 
     if (parameterSet$.isEnrichmentObject()) {
-        populations <- character(0)
+        populations <- character()
         for (i in 1:numberOfVariants) {
             populations <- c(populations, ifelse(i == numberOfVariants, "F", paste0("S", i)))
         }
@@ -1139,7 +1142,7 @@ ParameterSet <- setRefClass("ParameterSet",
         }
     )
 
-    usedParameterNames <- character(0)
+    usedParameterNames <- character()
     for (parameterName in parameterNames) {
         tryCatch(
             {
@@ -1284,7 +1287,7 @@ ParameterSet <- setRefClass("ParameterSet",
         includeAllParameters = FALSE,
         handleParameterNamesAsToBeExcluded = FALSE,
         returnParametersAsCharacter = FALSE,
-        mandatoryParameterNames = character(0)) {
+        mandatoryParameterNames = character()) {
     parameterNamesToBeExcluded <- c()
     if (handleParameterNamesAsToBeExcluded) {
         parameterNamesToBeExcluded <- parameterNames
@@ -1297,7 +1300,7 @@ ParameterSet <- setRefClass("ParameterSet",
     }
     parameterNames <- parameterNames[!grepl("^\\.", parameterNames)]
 
-    parametersToIgnore <- character(0)
+    parametersToIgnore <- character()
     if (!is.null(parameterSet[[".piecewiseSurvivalTime"]]) &&
             parameterSet$.piecewiseSurvivalTime$piecewiseSurvivalEnabled) {
         parametersToIgnore <- c(
@@ -1354,7 +1357,7 @@ ParameterSet <- setRefClass("ParameterSet",
 
 .getCategoryCaptionEnrichment <- function(parameterSet, parameterName, categoryNumber) {
     categoryCaption <- categoryNumber
-    if (parameterName %in% c("sampleSizes", "singleNumberOfEventsPerStage")) {
+    if (parameterName %in% c("sampleSizes", "singleEventsPerPopulationAndStage")) {
         categoryCaption <- parameterSet$effectList$subGroups[categoryNumber]
         maxNumberOfDigits <- max(nchar(sub("\\D*", "", parameterSet$effectList$subGroups)))
         if (parameterSet$populations > 2 && grepl(paste0("^S\\d{1,", maxNumberOfDigits - 1, "}$"), categoryCaption)) {

diff --git a/R/class_core_plot_settings.R b/R/class_core_plot_settings.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 7620 $
-## |  Last changed: $Date: 2024-02-09 12:57:37 +0100 (Fr, 09 Feb 2024) $
+## |  File version: $Revision: 7645 $
+## |  Last changed: $Date: 2024-02-16 16:12:34 +0100 (Fr, 16 Feb 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -103,7 +103,7 @@ PlotSubTitleItems <- setRefClass("PlotSubTitleItems",
                 return(NA_character_)
             }
 
-            s <- character(0)
+            s <- character()
             for (item in items) {
                 s <- c(s, item$toString())
             }

diff --git a/R/class_design_plan.R b/R/class_design_plan.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 7620 $
-## |  Last changed: $Date: 2024-02-09 12:57:37 +0100 (Fr, 09 Feb 2024) $
+## |  File version: $Revision: 7651 $
+## |  Last changed: $Date: 2024-02-20 15:45:44 +0100 (Di, 20 Feb 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -699,6 +699,8 @@ TrialDesignPlanRates <- setRefClass("TrialDesignPlanRates",
 #' @template field_studyDuration
 #' @template field_maxStudyDuration
 #' @template field_eventsPerStage
+#' @template field_singleEventsPerStage
+#' @template field_cumulativeEventsPerStage
 #' @template field_expectedEventsH0
 #' @template field_expectedEventsH01
 #' @template field_expectedEventsH1
@@ -715,7 +717,7 @@ TrialDesignPlanRates <- setRefClass("TrialDesignPlanRates",
 #' @template field_futilityBoundsEffectScaleLower
 #' @template field_futilityBoundsEffectScaleUpper
 #' @template field_futilityBoundsPValueScale
-#'
+#' 
 #' @details
 #' This object cannot be created directly; use \code{\link[=getSampleSizeSurvival]{getSampleSizeSurvival()}}
 #' with suitable arguments to create a design plan for a dataset of survival data.
@@ -783,7 +785,9 @@ TrialDesignPlanSurvival <- setRefClass("TrialDesignPlanSurvival",
         studyDurationH1 = "numeric",
         studyDuration = "numeric",
         maxStudyDuration = "numeric",
-        eventsPerStage = "matrix",
+        eventsPerStage = "matrix", # deprecated
+        singleEventsPerStage = "matrix",
+        cumulativeEventsPerStage = "matrix",
         expectedEventsH0 = "numeric",
         expectedEventsH01 = "numeric",
         expectedEventsH1 = "numeric",
@@ -826,6 +830,8 @@ TrialDesignPlanSurvival <- setRefClass("TrialDesignPlanSurvival",
             .setParameterType("futilityBoundsEffectScale", C_PARAM_NOT_APPLICABLE)
             .setParameterType("futilityBoundsEffectScaleLower", C_PARAM_NOT_APPLICABLE)
             .setParameterType("futilityBoundsEffectScaleUpper", C_PARAM_NOT_APPLICABLE)
+
+            .setParameterType("singleEventsPerStage", C_PARAM_NOT_APPLICABLE)
 
             # set default values
             for (parameterName in c(