Merge pull request #49 from rpact-com/dev/4.0.1

rhub workflow file added
rpact-com · Aug 21, 2024 · 0187716 · 0187716
2 parents ea3a28d + 9795e41
commit 0187716
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -49,3 +49,4 @@ testthat-problems\.rds
 ^README\.html$
 ^codecov\.yml$
 Rplots\.pdf
+^\.lintr$
diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rpact
 Title: Confirmatory Adaptive Clinical Trial Design and Analysis
-Version: 4.0.1.9247
-Date: 2024-08-15
+Version: 4.0.1.9248
+Date: 2024-08-21
 Authors@R: c(
 	person(
 		given = "Gernot", 

diff --git a/NAMESPACE b/NAMESPACE
@@ -104,6 +104,7 @@ export(getSampleSizeCounts)
 export(getSampleSizeMeans)
 export(getSampleSizeRates)
 export(getSampleSizeSurvival)
+export(getSimulationCounts)
 export(getSimulationEnrichmentMeans)
 export(getSimulationEnrichmentRates)
 export(getSimulationEnrichmentSurvival)

diff --git a/R/class_summary.R b/R/class_summary.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 8087 $
-## |  Last changed: $Date: 2024-08-15 16:34:30 +0200 (Do, 15 Aug 2024) $
+## |  File version: $Revision: 8111 $
+## |  Last changed: $Date: 2024-08-20 14:20:14 +0200 (Di, 20 Aug 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -1641,20 +1641,19 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
     return(header)
 }
 
-.addAlphaAndBetaToHeader <- function(header, design, designPlan, ..., endOfRecord = FALSE, powerEnabled = NA) {
-    header <- .concatenateSummaryText(header, paste0(
-        ifelse(design$sided == 1, "one-sided", "two-sided"),
-        ifelse(design$kMax == 1, "", " overall")
-    ))
+.addAlphaAndBetaToHeader <- function(header, design, designPlan, ..., endOfRecord = FALSE, powerEnabled = NA, sep = ", ") {
     if (is.na(powerEnabled)) {
         powerEnabled <- .isTrialDesignInverseNormalOrGroupSequential(design) && 
             (is.null(designPlan) || (!.isSimulationResults(designPlan) && 
             !identical("power", designPlan[[".objectType"]])))
     }
     header <- .concatenateSummaryText(header,
-        paste0("significance level ", round(100 * design$alpha, 2), "%", 
+        paste0(
+            ifelse(design$sided == 1, "one-sided", "two-sided"),
+            ifelse(design$kMax == 1, "", " overall"),
+            " significance level ", round(100 * design$alpha, 2), "%", 
             ifelse(!powerEnabled && endOfRecord, ".", "")),
-        sep = " "
+        sep = sep
     )
     if (powerEnabled) {
         header <- .concatenateSummaryText(header, 

diff --git a/R/f_design_general_utilities.R b/R/f_design_general_utilities.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 8087 $
-## |  Last changed: $Date: 2024-08-15 16:34:30 +0200 (Do, 15 Aug 2024) $
+## |  File version: $Revision: 8104 $
+## |  Last changed: $Date: 2024-08-19 10:30:01 +0200 (Mo, 19 Aug 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -27,7 +27,7 @@ NULL
 }
 
 .getDefaultDesign <- function(...,
-        type = c("sampleSize", "power", "simulation", "analysis", "characteristics"),
+        type = c("sampleSize", "power", "simulation", "simulationCounts", "analysis", "characteristics"),
         ignore = c()) {
     type <- match.arg(type)
 
@@ -54,7 +54,7 @@ NULL
 
     twoSidedPower <- .getOptionalArgument("twoSidedPower", ...)
     if (is.null(twoSidedPower)) {
-        if (type %in% c("power", "simulation") && sided == 2) {
+        if (type %in% c("power", "simulation", "simulationCounts") && sided == 2) {
             twoSidedPower <- TRUE
         } else {
             twoSidedPower <- C_TWO_SIDED_POWER_DEFAULT

diff --git a/R/f_design_group_sequential.R b/R/f_design_group_sequential.R
@@ -13,9 +13,9 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 7742 $
-## |  Last changed: $Date: 2024-03-22 13:46:29 +0100 (Fr, 22 Mrz 2024) $
-## |  Last changed by: $Author: pahlke $
+## |  File version: $Revision: 8112 $
+## |  Last changed: $Date: 2024-08-20 15:44:53 +0200 (Di, 20 Aug 2024) $
+## |  Last changed by: $Author: wassmer $
 ## |
 
 #' @include f_core_constants.R
@@ -38,9 +38,9 @@ NULL
 #' Given a sequence of information rates (fixing the correlation structure), and
 #' decisionMatrix with either 2 or 4 rows and kMax = length(informationRates) columns,
 #' this function calculates a probability matrix containing, for two rows, the probabilities:\cr
-#' P(Z_1 <- l_1), P(l_1 <- Z_1 < u_1, Z_2 < l_1),..., P(l_kMax-1 <- Z_kMax-1 < u_kMax-1, Z_kMax < l_l_kMax)\cr
-#' P(Z_1 <- u_1), P(l_1 <- Z_1 < u_1, Z_2 < u_1),..., P(l_kMax-1 <- Z_kMax-1 < u_kMax-1, Z_kMax < u_l_kMax)\cr
-#' P(Z_1 <- Inf), P(l_1 <- Z_1 < u_1, Z_2 < Inf),..., P(l_kMax-1 <- Z_kMax-1 < u_kMax-1, Z_kMax < Inf)\cr
+#' P(Z_1 < l_1), P(l_1 < Z_1 < u_1, Z_2 < l_2),..., P(l_kMax-1 < Z_kMax-1 < u_kMax-1, Z_kMax < l_l_kMax)\cr
+#' P(Z_1 < u_1), P(l_1 < Z_1 < u_1, Z_2 < u_2),..., P(l_kMax-1 < Z_kMax-1 < u_kMax-1, Z_kMax < u_l_kMax)\cr
+#' P(Z_1 < Inf), P(l_1 < Z_1 < u_1, Z_2 < Inf),..., P(l_kMax-1 < Z_kMax-1 < u_kMax-1, Z_kMax < Inf)\cr
 #' with continuation matrix\cr
 #' l_1,...,l_kMax\cr
 #' u_1,...,u_kMax\cr
@@ -423,6 +423,10 @@ getGroupSequentialProbabilities <- function(decisionMatrix, informationRates) {
 .getDesignGroupSequentialKMax1 <- function(design) {
     design$criticalValues <- .getOneMinusQNorm(design$alpha / design$sided)
     design$alphaSpent[1] <- design$alpha
+    design$.setParameterType("typeOfDesign", C_PARAM_NOT_APPLICABLE)
+    if (!identical(design$typeOfDesign, C_DEFAULT_TYPE_OF_DESIGN)) {
+        warning("'typeOfDesign' (", design$typeOfDesign, ") will be ignored because design is fixed", call. = FALSE)
+    }
     return(invisible(design))
 }
 

diff --git a/R/f_simulation_base_count_data.R b/R/f_simulation_base_count_data.R
@@ -13,9 +13,9 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 8052 $
-## |  Last changed: $Date: 2024-07-18 11:19:40 +0200 (Do, 18 Jul 2024) $
-## |  Last changed by: $Author: pahlke $
+## |  File version: $Revision: 8112 $
+## |  Last changed: $Date: 2024-08-20 15:44:53 +0200 (Di, 20 Aug 2024) $
+## |  Last changed by: $Author: wassmer $
 ## |
 
 .getInformationCountData <- function(lambda1,
@@ -101,18 +101,14 @@
 #' @inheritParams param_accrualTime_counts
 #' @inheritParams param_accrualIntensity_counts
 #' @inheritParams param_followUpTime_counts
-#' @inheritParams param_maxNumberOfSubjects
 #' @inheritParams param_overdispersion_counts
 #' @inheritParams param_directionUpper
 #' @inheritParams param_allocationRatioPlanned
-#' @inheritParams param_plannedSubjects
-#' @inheritParams param_minNumberOfSubjectsPerStage
-#' @inheritParams param_maxNumberOfSubjectsPerStage
-#' @inheritParams param_conditionalPowerSimulation
+#' @inheritParams param_maxNumberOfSubjects_counts
 #' @inheritParams param_maxNumberOfIterations
-#' @inheritParams param_calcSubjectsFunction
 #' @inheritParams param_seed
 #' @inheritParams param_three_dots
+#' @inheritParams param_calcSubjectsFunction
 #' @inheritParams param_showStatistics
 #'
 #' @details
@@ -156,8 +152,10 @@
 #'
 #' @template return_object_simulation_results
 #' @template how_to_get_help_for_generics
+#' 
+#' @template examples_get_simulation_counts
 #'
-#' @keywords internal
+#' @export
 #'
 getSimulationCounts <- function(design = NULL,
         ...,
@@ -183,7 +181,7 @@ getSimulationCounts <- function(design = NULL,
         directionUpper <- TRUE
     }
     if (is.null(design)) {
-        design <- .getDefaultDesign(..., type = "simulation")
+        design <- .getDefaultDesign(..., type = "simulationCounts")
         .warnInCaseOfUnknownArguments(
             functionName = "getSimulationCounts",
             ignore = .getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
@@ -192,7 +190,7 @@ getSimulationCounts <- function(design = NULL,
             )
         )
     } else {
-        .assertIsTrialDesign(design)
+        .assertIsTrialDesignGroupSequential(design)
         .warnInCaseOfUnknownArguments(
             functionName = "getSimulationCounts",
             ignore = c("showStatistics"), ...
@@ -426,7 +424,7 @@ getSimulationCounts <- function(design = NULL,
                                 dfStartStop$output[, "recruitTime"] <= plannedCalendarTime[k] &
                                 dfStartStop$output[, "stopCalendar"] <= plannedCalendarTime[k],
                         ]
-                        if (length(kthStageWithEvents) > 0 && nrow(kthStageWithEvents) > 0) {
+                        if (length(kthStageWithEvents) > 0 && is.matrix(kthStageWithEvents) && nrow(kthStageWithEvents) > 0) {
                             tab <- table(kthStageWithEvents[, "id"])
                             idx <- as.integer(names(tab))
                             counts[idx] <- as.vector(tab)

diff --git a/R/parameter_descriptions.R b/R/parameter_descriptions.R
@@ -13,9 +13,9 @@
 ## |
 ## |  Contact us for information about our services: info@rpact.com
 ## |
-## |  File version: $Revision: 7941 $
-## |  Last changed: $Date: 2024-05-28 08:44:36 +0200 (Di, 28 Mai 2024) $
-## |  Last changed by: $Author: pahlke $
+## |  File version: $Revision: 8112 $
+## |  Last changed: $Date: 2024-08-20 15:44:53 +0200 (Di, 20 Aug 2024) $
+## |  Last changed by: $Author: wassmer $
 ## |
 
 #' Parameter Description: "..."
@@ -344,7 +344,11 @@ NULL
 #' @keywords internal
 NULL
 
-
+#' Parameter Description: plannedMaxSubjects for Counts
+#' @param plannedMaxSubjects \code{plannedMaxSubjects > 0} needs to be specified.
+#' @name param_maxNumberOfSubjects_counts
+#' @keywords internal
+NULL
 
 ##
 ## Analysis

diff --git a/inst/doc/rpact_getting_started.html b/inst/doc/rpact_getting_started.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Friedrich Pahlke and Gernot Wassmer" />
 
-<meta name="date" content="2024-08-15" />
+<meta name="date" content="2024-08-19" />
 
 <title>Getting started with rpact</title>
 
@@ -239,7 +239,7 @@
 
 <h1 class="title toc-ignore">Getting started with rpact</h1>
 <h4 class="author">Friedrich Pahlke and Gernot Wassmer</h4>
-<h4 class="date">2024-08-15</h4>
+<h4 class="date">2024-08-19</h4>
 
 
 

diff --git a/man/getGroupSequentialProbabilities.Rd b/man/getGroupSequentialProbabilities.Rd
diff --git a/man/getSimulationCounts.Rd b/man/getSimulationCounts.Rd