updates to R2jags

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

@@ -0,0 +1,80 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        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@v1
+        with:
+          extra-packages: rcmdcheck
+
+      - name: Install system dependencies (ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
+
+      - name: Install jags (windows-latest)
+        if: runner.os == 'Windows'
+        run: |
+          curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.2.0-Rtools33.exe
+          wjags.exe /S
+          del wjags.exe
+        shell: cmd
+
+      - name: Install jags (macOS-latest)
+        if: runner.os == 'macOS'
+        run : |
+          rm '/usr/local/bin/gfortran'
+          brew install jags
+
+      - uses: r-lib/actions/check-r-package@v1
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.travis.yml

@@ -0,0 +1,13 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+sudo: required
+cache: packages
+before_install:
+      - sudo add-apt-repository ppa:marutter/rrutter -y
+      - sudo apt-get update
+      - sudo apt-get install r-cran-rjags
+script:
+  - |
+    R CMD build .
+    travis_wait 30 R CMD check packageName*tar.gz

CRAN-RELEASE

@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2022-02-23.
+Once it is accepted, delete this file and tag the release (commit 7370f2b).

DESCRIPTION

@@ -48,6 +48,7 @@ Suggests:
     ggdist (>= 2.4.0),
     zoo (>= 1.8-8),
     lspline (>= 1.0-0),
+    formatR (>= 1.14),
     netmeta,
     knitr,
     rmarkdown

R/globals.R

@@ -9,4 +9,5 @@ if(getRversion() >= "2.15.1")  utils::globalVariables(c(".", "studyID", "agent",
                                                         "Estimate", "2.5%", "50%", "97.5%", "treatment",
                                                         "study", "arm", "mod1.mean", "mod2.mean", "argcheck",
                                                         "Comparison", "Evidence", "splinefun", "level",
+                                                        "class.effect",
                                                         "user.str"))

appveyor.yml

@@ -0,0 +1,52 @@
+# DO NOT CHANGE the "init" and "install" sections below
+
+# Download script file from GitHub
+init:
+  ps: |
+  $ErrorActionPreference = "Stop"
+  Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+  Import-Module '..\appveyor-tool.ps1'
+
+  install:
+    ps: Bootstrap
+
+  cache:
+    - C:\RLibrary
+
+  environment:
+    NOT_CRAN: true
+  # env vars that may need to be set, at least temporarily, from time to time
+  # see https://github.com/krlmlr/r-appveyor#readme for details
+  # USE_RTOOLS: true
+  # R_REMOTES_STANDALONE: true
+
+  # Adapt as necessary starting from here
+
+  build_script:
+    - travis-tool.sh install_deps
+
+  test_script:
+    - travis-tool.sh run_tests
+
+  on_failure:
+    - 7z a failure.zip *.Rcheck\*
+    - appveyor PushArtifact failure.zip
+
+  artifacts:
+    - path: '*.Rcheck\**\*.log'
+  name: Logs
+
+  - path: '*.Rcheck\**\*.out'
+  name: Logs
+
+  - path: '*.Rcheck\**\*.fail'
+  name: Logs
+
+  - path: '*.Rcheck\**\*.Rout'
+  name: Logs
+
+  - path: '\*_*.tar.gz'
+  name: Bits
+
+  - path: '\*_*.zip'
+  name: Bits

tests/testthat/test_fullset.R

@@ -8,6 +8,7 @@ testthat::context("Testing full set of functions")
 # Tests default ranking (including cumrank)
 # Tests default prediction
 # Occasionally tests get.relative
+# Includes tests for meta-regression on SSRI dataset
 
 
 # Tested datasets must have at least 5 agents - options are HF2PPIT, psoriasis, ssri, osteopain, gout(?)

vignettes/nma_in_mbnmadose.Rmd

@@ -26,7 +26,7 @@ library(dplyr)
 
 Although `MBNMAdose` is intended to be used for dose-response Model-Based Network Meta-Analysis (MBNMA), it can also be adapted to perform standard Network Meta-Analysis (NMA), and this allows users to take advantage of some of the additional features of `MBNMAdose`, such as modelling class effects, for use in standard NMA. As well as fitting class effect models, `MBNMAdose` also allows for nodes-splitting to check for consistency in these models.
 
-To illustrate how this can be done we will use a dataset of inhaled medications for Chronic Obstructive Pulmonary Disease (COPD) from the `netmeta` package (*REF*):
+To illustrate how this can be done we will use a dataset of inhaled medications for Chronic Obstructive Pulmonary Disease (COPD) from the `netmeta` package:
 
 ```{r, loaddata}
 library(netmeta)