Fix build issues and R CMD check warnings (#1)

* Fix build and modernize

* roxygen2md::roxygen2md()

* Add GitHub actions check and basic pkgdown

* Fix more docs

* Remove superfluous dependencies

.Rbuildignore

@@ -1,2 +1,9 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^pvm\.Rproj$
+^LICENSE\.md$
+^man-roxygen$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# 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: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.gitignore

@@ -3,3 +3,4 @@
 .RData
 *.DS_Store*
 *.Rproj
+docs

DESCRIPTION

@@ -1,25 +1,25 @@
 Package: pvm
-Title: PharmacoVigilance Methods 
+Title: PharmacoVigilance Methods
 Version: 1.0
-Date: 2018-07-01
 Author: Louis Dijkstra [aut, cre], Marco Garling [ctb]
 Maintainer: Louis Dijkstra <[email protected]>
-Description: A collection of methods used in the field 
-	of pharmacovigilance for the dectection of 'interesting'
-	drug-adverse event pairs from spontaneous reporting 
-	data.
-Imports: 
+Description: A collection of methods used in the field of
+    pharmacovigilance for the dectection of 'interesting' drug-adverse
+    event pairs from spontaneous reporting data.
+License: GPL (>= 3)
+URL: https://github.com/bips-hb/pvm
+BugReports: https://github.com/bips-hb/pvm/issues
 Depends: 
-	R (>= 3.2.3), 
-	Rcpp,
-	glmnet,
-	ggplot2, 
-	MCMCpack,
-	PhViD
-LinkingTo: Rcpp
-License: GPL-3
+    R (>= 3.2.3)
+Imports: 
+    glmnet,
+    MCMCpack,
+    PhViD,
+    Rcpp,
+    stats
+LinkingTo: 
+    Rcpp
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
-URL: https://github.com/bips-hb/pvm
-BugReports: https://github.com/bips-hb/pvm/issues
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1