updated documentation and citation

.Rbuildignore

@@ -1,4 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
-^appveyor\.yml$
+^gitignore$
+^\.github$

.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 }}

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: pseudorank
 Title: Pseudo-Ranks
-Version: 1.0.2
-Date: 2021-12-21
-Authors@R: c(person("Martin Happ", role = c("aut", "cre"),
-                      email = "martin.happ@aon.at",
+Version: 1.0.3
+Date: 2025-02-15
+Authors@R: c(person("Martin","Happ", role = c("aut", "cre"),
+                      email = "[email protected].at",
                       comment = c(ORCID = "0000-0003-0009-2665")),
-	      person("Georg Zimmermann", role = "aut"),
-	      person("Arne C. Bathke", role = "aut"),
-	      person("Edgar Brunner", role = "aut"))
-Maintainer: Martin Happ <martin.happ@aon.at>
+	      person("Georg", "Zimmermann", role = "aut"),
+	      person("Arne C.", "Bathke", role = "aut"),
+	      person("Edgar", "Brunner", role = "aut"))
+Maintainer: Martin Happ <[email protected].at>
 Description: Efficient calculation of pseudo-ranks and (pseudo)-rank based test statistics. In case of equal sample sizes, pseudo-ranks and mid-ranks are equal. When used for inference mid-ranks may lead to paradoxical results. Pseudo-ranks are in general not affected by such a problem <doi:10.18637/jss.v095.c01>.
 License: GPL-3
 Encoding: UTF-8
@@ -19,5 +19,5 @@ LinkingTo: Rcpp
 SystemRequirements: C++11
 URL: https://github.com/happma/pseudorank/
 BugReports: https://github.com/happma/pseudorank/issues/
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2
 Suggests: testthat

NEWS.md

@@ -1,3 +1,6 @@
+# pseudorank 1.0.3
+* Updated documentation
+
 # pseudorank 1.0.2
 * Fixed problem with the Kepner-Robinson-test
 

R/kepner_robinson.R

@@ -2,11 +2,11 @@
 #'
 #' @description This function calculates the Kepner-Robinsin test under the null hypothesis H0F: F_1 = ... F_k.
 #' @param data numeric vector containing the data
-#' @param group ordered factor vector for the groups
-#' @param alternative either decreasing or increasing
+#' @param time factor vector containing time points
+#' @param subject factor vector containing subjects
+#' @param distribution specified distribution, either Chisq or F
 #' @param na.rm a logical value indicating if NA values should be removed
 #' @param formula formula object
-#' @param trend custom numeric vector indicating the trend for the custom alternative, only used if alternative = "custom"
 #' @param ... further arguments are ignored
 #' @return Returns a data.frame with the results
 #' @example R/example_4.txt

README.md

@@ -1,9 +1,8 @@
-# pseudorank 1.0.2
+# pseudorank 1.0.3
 
 [![CRANstatus](https://www.r-pkg.org/badges/version/pseudorank)](https://cran.r-project.org/package=pseudorank/)
 [![](https://cranlogs.r-pkg.org/badges/pseudorank)](https://cran.r-project.org/package=pseudorank/)
-[![Travis-CI Build Status](https://travis-ci.org/happma/pseudorank.svg?branch=master)](https://travis-ci.org/happma/pseudorank/)
-[![Build status](https://ci.appveyor.com/api/projects/status/queq8aa7cpct3j16?svg=true)](https://ci.appveyor.com/project/happma/pseudorank/)
+[![DOI](https://img.shields.io/badge/DOI-10.18637%2Fjss.v095.c01-blue.svg)](https://dx.doi.org/10.18637/jss.v095.c01)
 
 This R package provides a function written in C++ to calculate pseudo-ranks in R and some rank statistics which can opionally use pseudo-ranks instead of ranks.
 For a definition and discussion of pseudo-ranks, see for example 

inst/CITATION

@@ -1,24 +1,14 @@
-bibentry(bibtype = "Article",
+bibentry("Article",
   title        = "Pseudo-Ranks: How to Calculate Them Efficiently in {R}",
-  author       = c(person(given = "Martin",
-                          family = "Happ",
-                          email = "[email protected]"),
-                   person(given = "Georg",
-                          family = "Zimmermann",
-                          email = "[email protected]"),
-                   person(given = "Edgar",
-                          family = "Brunner",
-                          email = "[email protected]"),
-                   person(given = c("Arne", "C."),
-                          family = "Bathke",
-                          email = "[email protected]")),
+  author       = c(as.person("Martin Happ"),
+                   as.person("Georg Zimmermann"),
+                   as.person("Edgar Brunner"),
+                   as.person("Arne C. Bathke")),
   journal      = "Journal of Statistical Software, Code Snippets",
   year         = "2020",
   volume       = "95",
   number       = "1",
   pages        = "1--22",
   doi          = "10.18637/jss.v095.c01",
-
-  header       = "To cite pseudorank in publications use:"
 )
 

src/RcppExports.cpp

@@ -5,6 +5,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // order_vec
 Rcpp::NumericVector order_vec(Rcpp::NumericVector& data);
 RcppExport SEXP _pseudorank_order_vec(SEXP dataSEXP) {