Merge pull request #6 from rpact-com/cran/release/3.4.0

cran/release/3.4.0

.Rbuildignore

@@ -11,6 +11,7 @@
 ^_version$
 ^doc$
 ^docs$
+^man-raw$
 ^bin$
 ^cran-comments\.md$
 ^README\.Rmd$
@@ -35,3 +36,6 @@ index\.txt
 lastMiKTeXException
 ^\.github$
 ^CRAN-SUBMISSION$
+^_pkgdown\.yml$
+^pkgdown$
+^rpact-tests$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -1,5 +1,6 @@
 Meta
 doc
+/man-raw
 .Rproj.user
 .Rhistory
 .RData
@@ -20,3 +21,5 @@ lastMiKTeXException
 /data-raw
 /.cproject
 /.project
+docs
+rpact-tests

DESCRIPTION

@@ -1,25 +1,42 @@
 Package: rpact
 Title: Confirmatory Adaptive Clinical Trial Design and Analysis
-Version: 3.3.4
-Date: 2023-02-14
+Version: 3.4.0
+Date: 2023-07-03
 Authors@R: c(
 	person(
 		given = "Gernot", 
 		family = "Wassmer", 
 		email = "[email protected]", 
-		role = c("aut")),
+		comment = c(ORCID = "0000-0001-9397-1794"), 
+		role = c("aut")
+	),
     person(
     	given = "Friedrich", 
     	family = "Pahlke", 
     	email = "[email protected]",
     	comment = c(ORCID = "0000-0003-2105-2582"), 
-    	role = c("aut", "cre"))
-    )
+    	role = c("aut", "cre")
+    ),
+    person(
+    	given = "Till", 
+    	family = "Jensen", 
+    	email = "[email protected]",
+    	role = c("ctb")
+	),
+    person(
+    	given = "Stephen", 
+    	family = "Schueuerhuis", 
+    	email = "[email protected]",
+    	role = c("ctb")
+	))
 Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
 License: LGPL-3
 Encoding: UTF-8
 LazyData: true
-URL: https://www.rpact.org, https://www.rpact.com, https://github.com/rpact-com/rpact
+URL: https://www.rpact.org,
+    https://www.rpact.com,
+    https://github.com/rpact-com/rpact,
+    https://rpact-com.github.io/rpact/
 BugReports: https://github.com/rpact-com/rpact/issues
 Language: en-US
 Depends: 
@@ -31,14 +48,13 @@ Imports:
 	graphics,
 	tools,
 	rlang,
+	knitr (>= 1.19), 
 	Rcpp (>= 1.0.3)
 LinkingTo: Rcpp
 Suggests: 
-	parallel,
 	ggplot2 (>= 2.2.0),	
 	testthat (>= 3.0.0),
 	mnormt (>= 1.5-7),
-	knitr (>= 1.19), 
 	rmarkdown (>= 1.10)
 VignetteBuilder: knitr, rmarkdown
 RoxygenNote: 7.2.3
@@ -58,6 +74,7 @@ Collate:
     'class_core_plot_settings.R'
     'f_core_plot.R'
     'class_design.R'
+    'f_object_r_code.R'
     'f_analysis_base.R'
     'class_analysis_dataset.R'
     'class_analysis_stage_results.R'
@@ -71,6 +88,7 @@ Collate:
     'f_simulation_utilities.R'
     'f_simulation_base_survival.R'
     'class_simulation_results.R'
+    'class_performance_score.R'
     'class_summary.R'
     'data.R'
     'f_analysis_base_means.R'

NAMESPACE

@@ -9,6 +9,7 @@ S3method(as.data.frame,TrialDesignCharacteristics)
 S3method(as.data.frame,TrialDesignPlan)
 S3method(as.data.frame,TrialDesignSet)
 S3method(as.matrix,FieldSet)
+S3method(knit_print,ParameterSet)
 S3method(length,TrialDesignSet)
 S3method(names,AnalysisResults)
 S3method(names,FieldSet)
@@ -24,17 +25,19 @@ S3method(plot,SimulationResults)
 S3method(plot,StageResults)
 S3method(plot,SummaryFactory)
 S3method(plot,TrialDesign)
+S3method(plot,TrialDesignCharacteristics)
 S3method(plot,TrialDesignPlan)
 S3method(plot,TrialDesignSet)
 S3method(print,Dataset)
 S3method(print,FieldSet)
 S3method(print,ParameterSet)
 S3method(print,SimulationResults)
+S3method(print,SummaryFactory)
+S3method(print,TrialDesignCharacteristics)
 S3method(summary,AnalysisResults)
 S3method(summary,Dataset)
 S3method(summary,ParameterSet)
 S3method(summary,TrialDesignSet)
-export(.getAnalysisResultsMeansParallelComputing)
 export(getAccrualTime)
 export(getAnalysisResults)
 export(getAvailablePlotTypes)
@@ -88,7 +91,6 @@ export(getRepeatedPValues)
 export(getSampleSizeMeans)
 export(getSampleSizeRates)
 export(getSampleSizeSurvival)
-export(getSimulatedRejectionsDelayedResponse)
 export(getSimulationEnrichmentMeans)
 export(getSimulationEnrichmentRates)
 export(getSimulationEnrichmentSurvival)
@@ -126,6 +128,8 @@ import(stats)
 import(tools)
 import(utils)
 importFrom(Rcpp,evalCpp)
+importFrom(knitr,kable)
+importFrom(knitr,knit_print)
 importFrom(methods,new)
 importFrom(rlang,.data)
 useDynLib(rpact, .registration = TRUE)

NEWS.md

@@ -1,4 +1,24 @@
 
+# rpact 3.4.0
+
+## New features
+
+* The new function `getPerformanceScore()` calculates the conditional performance score, its sub-scores and components according to Herrmann et al. (2020) for a given simulation result from a two-stage design
+* `allocationRatioPlanned` for simulating multi-arm and enrichment designs can be a vector of length kMax, the number of stages 
+* `getObjectRCode()` (short: `rcmd()`): with the new arguments `pipeOperator` and `output` many new output variants can be specified, e.g., the native R pipe operator or the magrittr pipe operator can be used
+* Generic function `knitr::knit_print` for all result objects implemented and automatic code chunk option `results = 'asis'` activated
+
+## Improvements, issues, and changes
+
+* Improved speed of numerical computation of group sequential designs and test characteristics
+* Multivariate t distribution restricted to `df <= 500` because of erroneous results in `mnormt` package otherwise. For `df > 500`, multivariate normal distribution is used 
+* Performance of cumulative distribution function and survival function plot improved
+* Test coverage extended and improved
+* Descriptions for all class fields added
+* Renamed field `omega` to `chi` in class `TrialDesignPlanSurvival`
+* Several minor improvements
+
+
 # rpact 3.3.4
 
 * Rcpp sugar function `sapply` removed from C++ code to stop deprecated warnings on r-devel-linux-x86_64-fedora-clang 

R/RcppExports.R

@@ -25,10 +25,6 @@ getDesignGroupSequentialPampallonaTsiatisCpp <- function(tolerance, beta, alpha,
     .Call(`_rpact_getDesignGroupSequentialPampallonaTsiatisCpp`, tolerance, beta, alpha, kMax, deltaPT0, deltaPT1, informationRates, sided, bindingFutility)
 }
 
-getSpendingValueCpp <- function(alpha, x, sided, typeOfDesign, gamma) {
-    .Call(`_rpact_getSpendingValueCpp`, alpha, x, sided, typeOfDesign, gamma)
-}
-
 getDesignGroupSequentialUserDefinedAlphaSpendingCpp <- function(kMax, userAlphaSpending, sided, informationRates, bindingFutility, futilityBounds, tolerance) {
     .Call(`_rpact_getDesignGroupSequentialUserDefinedAlphaSpendingCpp`, kMax, userAlphaSpending, sided, informationRates, bindingFutility, futilityBounds, tolerance)
 }