Merge pull request #4 from machinelearningZH/prepare_publication

Prepare publication

.Rbuildignore

@@ -2,3 +2,18 @@
 ^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^README\.Rmd$
+^\.ccache$
+^\.github$
+^tic\.R$
+^LICENSE\.md$
+^plausi\.Rcheck$
+^plausi.*\.tar\.gz$
+^plausi.*\.tgz$
+^doc$
+^Meta$
+^vignettes
+^data-raw$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/tic.yml

@@ -0,0 +1,102 @@
+## tic GitHub Actions template: linux-macos-windows-deploy
+## revision date: 2023-12-15
+on:
+  workflow_dispatch:
+  push:
+    branches:
+    - main
+    - cran-*
+    - develop
+    - prepare_publication
+  pull_request:
+    branches:
+    - main
+    - develop
+  # for now, CRON jobs only run on the default branch of the repo (i.e. usually on master)
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron: "0 4 * * *"
+
+name: tic
+
+jobs:
+  all:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # use a different tic template type if you do not want to build on all listed platforms
+          - { os: windows-latest, r: "release" }
+          - { os: macOS-latest, r: "release", pkgdown: "true", latex: "true" }
+          - { os: ubuntu-latest, r: "devel" }
+          - { os: ubuntu-latest, r: "release" }
+
+    env:
+      # make sure to run `tic::use_ghactions_deploy()` to set up deployment
+      TIC_DEPLOY_KEY: ${{ secrets.TIC_DEPLOY_KEY }}
+      # prevent rgl issues because no X11 display is available
+      RGL_USE_NULL: true
+      # if you use bookdown or blogdown, replace "PKGDOWN" by the respective
+      # capitalized term. This also might need to be done in tic.R
+      BUILD_PKGDOWN: ${{ matrix.config.pkgdown }}
+      # use GITHUB_TOKEN from GitHub to workaround rate limits in {remotes}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          Ncpus: 4
+
+      - uses: r-lib/actions/setup-tinytex@v2
+        if: matrix.config.latex == 'true'
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install sys deps for Ubuntu
+        if: runner.os == 'Linux'
+        run: sudo apt update && sudo apt install -y libgit2-dev libcurl4-openssl-dev
+
+      # set date/week for use in cache creation
+      # https://github.community/t5/GitHub-Actions/How-to-set-and-access-a-Workflow-variable/m-p/42970
+      # - cache R packages daily
+      - name: "[Cache] Prepare daily timestamp for cache"
+        if: runner.os != 'Windows'
+        id: date
+        run: echo "date=$(date '+%d-%m')" >> $GITHUB_OUTPUT
+
+      - name: "[Cache] Restore R package cache"
+        if: runner.os != 'Windows'
+        uses: actions/cache/restore@v3
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
+
+      - name: "[Stage] Install"
+        run: Rscript -e "install.packages('tic', repos = c('https://ropensci.r-universe.dev', if (grepl('Ubuntu', Sys.info()[['version']])) {sprintf('https://packagemanager.rstudio.com/all/__linux__/%s/latest', system('lsb_release -cs', intern = TRUE))} else {'https://cloud.r-project.org'}))" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
+
+      - name: "[Cache] Save R package cache"
+        if: runner.os != 'Windows' && always()
+        uses: actions/cache/save@v3
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
+
+      - name: "[Stage] Script"
+        run: Rscript -e 'tic::script()'
+
+      - name: "[Stage] After Success"
+        run: Rscript -e "tic::after_success()"
+
+      - name: "[Stage] Upload R CMD check artifacts"
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.gitignore

@@ -3,3 +3,9 @@
 .RData
 .Ruserdata
 inst/doc
+plausi.Rcheck/
+plausi*.tar.gz
+plausi*.tgz
+/doc/
+/Meta/
+docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: plausi
 Type: Package
 Title: popular vote forensics
-Version: 0.1.0.9999
+Version: 0.2.0
 Authors@R: c(person(given = "Thomas",
              family = "Lo Russo",
              role = c("aut", "cre"),
@@ -11,21 +11,26 @@ Authors@R: c(person(given = "Thomas",
              role = c("aut"),
              email = "[email protected]"))
 Description: Toolkit for vote and election forensics in R that allows to identify statistical anomalies in vote results.
-License: GPL-2
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports: 
-     purrr,
-     dplyr,
-     tidyr,
-     caret,
-     stats
+    caret,
+    stats
 Depends: 
     R (>= 2.10)
 Remotes: 
-     r-lib/cli
+    r-lib/cli
+Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    devtools,
+    kernlab,
+    ggplot2,
+    dplyr,
+    tidyr,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Config/testthat/edition: 3

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: plausi authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 plausi authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,31 +1,26 @@
 # Generated by roxygen2: do not edit by hand
 
-export(DoubleMAD)
-export(DoubleMADsFromMedian)
-export(RMSE)
 export(cross_fun)
+export(double_mad)
+export(double_mad_from_median)
 export(get_differences)
 export(is_outlier_double_mad)
-export(isnt_out_mad)
-export(isnt_out_turkey)
-export(isnt_out_z)
+export(is_outlier_single_mad)
+export(is_outlier_turkey)
+export(is_outlier_z)
 export(outlier_range)
 export(predict_single_vote)
 export(predict_votes)
+export(rmse)
+export(train_prediction_model)
 importFrom(caret,train)
 importFrom(caret,trainControl)
-importFrom(dplyr,"%>%")
-importFrom(dplyr,bind_cols)
-importFrom(dplyr,contains)
-importFrom(dplyr,ends_with)
-importFrom(dplyr,mutate)
-importFrom(dplyr,select)
-importFrom(purrr,map2)
-importFrom(purrr,map_dfr)
+importFrom(stats,IQR)
 importFrom(stats,as.formula)
 importFrom(stats,mad)
 importFrom(stats,median)
+importFrom(stats,na.omit)
 importFrom(stats,predict)
 importFrom(stats,quantile)
+importFrom(stats,reshape)
 importFrom(stats,sd)
-importFrom(tidyr,drop_na)

R/data.R

@@ -1,12 +1,52 @@
-#' Test data containing past results and incomplete results for two votes
+#' Test data containing past results and incomplete results for two votes.
+#'
+#' @description
+#' Test data containing past results covering 5 years of federal and cantonal
+#' votes in the canton of Zurich as well as incomplete results of two current
+#' issues.
+#'
+#' The units presented are counting circles. Counting circles usually correspond
+#' to municipalities, with the exception of the cities Zürich and Winterthur,
+#' which are divided into and published as sub units.
 #'
 #'
 #' @format A dataframe with 171 rows and 79 columns.
 #' \describe{
-#'   \item{gemeinde}{municipality name}
-#'   \item{v_gemwkid}{vote id}
-#'   \item{Eidg1}{Yes-Share of an on going federal vote}
-#'   \item{Kant1}{Yes-Share of an on going  cantonal vote}
-#'   \item{v_....}{yes shares of past votes}
+#'   \item{gemeinde}{name of counting circle}
+#'   \item{v_gemwkid}{FSO number of the municipality (for the counting circles
+#'   of Zürich and Winterthur, this consists of a numeric, a zero and the FSO
+#'   number of the municipality)}
+#'   \item{Eidg1}{yes-share of the current incomplete federal vote}
+#'   \item{Kant1}{yes-share of the current incomplete cantonal vote}
+#'   \item{v_....}{yes-shares of past votes}
 #'}
-"votedata"
+#'
+
+"vote_data"
+
+
+
+#' Test data containing results for national votes from the canton of Zurich for
+#' all Sundays from 2017-03-01 to 2020-09-27.
+#'
+#' @format A dataframe with 3864 rows and 16 columns.
+#' \describe{
+#'   \item{name}{Name of the referendum.}
+#'   \item{id}{ID of the referendum.}
+#'   \item{canton_id}{ID of the canton.}
+#'   \item{canton_name}{Name of the canton.}
+#'   \item{mun_name}{Name of the municipality.}
+#'   \item{geoLevelParentnummer}{Geo level number of the parent geo unit, in the case of municipalities that means district number.}
+#'   \item{gebietAusgezaehlt}{Indicator for finalised counting status.}
+#'   \item{jaStimmenInProzent}{Percentage of yes-votes.}
+#'   \item{jaStimmenAbsolut}{Absolut number of yes-votes.}
+#'   \item{neinStimmenAbsolut}{Absolut number of no-votes.}
+#'   \item{stimmbeteiligungInProzent}{Turnout.}
+#'   \item{eingelegteStimmzettel}{Total number of submitted ballots.}
+#'   \item{anzahlStimmberechtigte}{Number of elligable voters.}
+#'   \item{gueltigeStimmen}{Total number of valid yes- and no-votes.}
+#'   \item{votedate}{Date of the vote.}
+#'}
+#'
+
+"result_data"