Merge pull request #315 from insightsengineering/cran-release

Cran release

.Rbuildignore

@@ -7,3 +7,9 @@
 ^\.lintr$
 ^.gitignore$
 ^src/\.gitkeep$
+^.git$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^data-raw$
+

.gitattributes

@@ -0,0 +1 @@
+* text=auto

.github/workflows/build_docker.yaml

@@ -6,12 +6,12 @@ env:
 on:
   push:
     branches:
-      - develop
+      - main
     paths:
       - 'misc/docker/**'
   pull_request:
     branches:
-      - develop
+      - main
     paths:
       - 'misc/docker/**'
   workflow_dispatch:

.github/workflows/check_nightly_master.yaml → .github/workflows/check_nightly_cran.yaml

@@ -4,7 +4,7 @@ on:
   schedule:
     - cron: '0 4 * * 1'
 
-name: Check Nightly (master)
+name: Check Nightly (CRAN)
 
 jobs:
 
@@ -31,7 +31,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
         with:
-          ref: master
+          ref: cran
 
       - name: Check
         run: |

.github/workflows/check_nightly_develop.yaml → .github/workflows/check_nightly_main.yaml

@@ -4,7 +4,7 @@ on:
   schedule:
     - cron: '0 4 * * 1,2,3,4,5'
 
-name: Check Nightly (develop)
+name: Check Nightly (Main)
 
 jobs:
 
@@ -31,7 +31,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
         with:
-          ref: develop
+          ref: main
 
       - name: Check
         run: |

.github/workflows/check_pr_master.yaml → .github/workflows/check_pr_cran.yaml

@@ -5,10 +5,9 @@ on:
     paths-ignore:
       - 'misc/**'
     branches:
-      - main
-      - master
+      - cran
 
-name: Check Pull Requests (Master)
+name: Check Pull Requests (CRAN)
 
 jobs:
 

.github/workflows/on_push.yaml

@@ -0,0 +1,58 @@
+
+
+on:
+  push:
+    paths-ignore:
+      - 'misc/**'
+
+name: On Push
+
+jobs:
+
+  testthat:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/${{ github.repository_owner }}/rbmi:r404
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Build src
+        uses: ./.github/actions/build-src
+
+      - name: testthat
+        run: |
+          options(crayon.enabled = TRUE, cli.dynamic = FALSE)
+          devtools::test(stop_on_failure = TRUE, reporter = testthat::CheckReporter)
+        shell: Rscript {0}
+
+  document:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/${{ github.repository_owner }}/rbmi:r404
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Build src
+        uses: ./.github/actions/build-src
+
+      - name: Document Code
+        run: |
+          options(crayon.enabled = TRUE, cli.dynamic = FALSE)
+          devtools::document()
+        shell: Rscript {0}
+
+      - name: Check Is Clean
+        shell: bash
+        run: |
+          git status
+          if [ -z "$(git status --porcelain)" ]; then
+            echo "Is Clean"
+          else
+            echo "Changed Detected"
+            exit 2
+          fi
+

.github/workflows/packagedown.yaml

@@ -0,0 +1,16 @@
+---
+name: Docs
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  docs:
+    name: Pkgdown Docs
+    uses: insightsengineering/r.pkg.template/.github/workflows/pkgdown.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      install-system-dependencies: true

.github/workflows/validate_generic_master.yaml

@@ -9,6 +9,8 @@ jobs:
   r-pkg-validation:
     name: Create report 📃
     runs-on: ubuntu-latest
+    container:
+      image: rocker/verse:4.1.1
     # Set Github token permissions
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -21,7 +23,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Build report 🏗
-        uses: insightsengineering/thevalidatoR@v1.0
+        uses: insightsengineering/thevalidatoR@v1.1.3
 
       # Upload the validation report to the release
       - name: Upload report to release 🔼

.gitignore

@@ -49,5 +49,11 @@ src/*
 
 .DS_store
 
+nul
+
 !.gitkeep
 inst/doc
+docs
+/doc/
+/Meta/
+.github/meta.txt

.lintr

@@ -1,3 +1,4 @@
 linters: with_defaults(
-    line_length_linter(120)
+    line_length_linter(120),
+    object_name_linter = NULL
     )

DESCRIPTION

@@ -1,17 +1,17 @@
 Package: rbmi
 Title: Reference Based Multiple Imputation
-Version: 1.0.2
+Version: 1.1.0
 Authors@R: c(
-    person("Craig", "Gower-Page", email = "[email protected]", role = "aut"),
-    person("Alessandro", "Noci", email = "[email protected]", role = c("aut", "cre")),
+    person("Craig", "Gower-Page", email = "[email protected]", role = c("aut", "cre")),
+    person("Alessandro", "Noci", email = "[email protected]", role = c("aut")),
     person("Marcel", "Wolbers", email = "[email protected]", role = "ctb"),
     person("Roche", role = c("cph", "fnd"))
     )
 Description: Implements reference based multiple imputation allowing for the imputation of longditudinal datasets using pre-defined strategies.
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Suggests: 
     dplyr,
     covr,
@@ -24,7 +24,9 @@ Suggests:
     knitr,
     rmarkdown,
     bookdown,
-    lubridate
+    lubridate,
+    purrr,
+    ggplot2
 Biarch: true
 Config/testthat/edition: 3
 Imports: 

NAMESPACE

@@ -3,30 +3,38 @@
 S3method(as.data.frame,pool)
 S3method(draws,approxbayes)
 S3method(draws,bayes)
+S3method(draws,bmlmi)
 S3method(draws,condmean)
 S3method(impute,condmean)
 S3method(impute,random)
+S3method(pool_internal,bmlmi)
 S3method(pool_internal,bootstrap)
 S3method(pool_internal,jackknife)
 S3method(pool_internal,rubin)
 S3method(print,analysis)
 S3method(print,draws)
 S3method(print,imputation)
+S3method(print,imputation_df)
+S3method(print,imputation_list_df)
+S3method(print,imputation_list_single)
+S3method(print,imputation_single)
 S3method(print,pool)
 S3method(validate,analysis)
+S3method(validate,bmlmi)
 S3method(validate,bootstrap)
 S3method(validate,draws)
 S3method(validate,imputation)
-S3method(validate,imputation_list)
-S3method(validate,imputation_single)
+S3method(validate,imputation_df)
 S3method(validate,is_mar)
 S3method(validate,ivars)
 S3method(validate,jackknife)
 S3method(validate,references)
 S3method(validate,rubin)
 S3method(validate,sample_list)
 S3method(validate,sample_single)
+S3method(validate,simul_pars)
 S3method(validate,stan_data)
+export(Stack)
 export(add_class)
 export(analyse)
 export(ancova)
@@ -39,15 +47,18 @@ export(expand_locf)
 export(extract_imputed_dfs)
 export(fill_locf)
 export(getStrategies)
+export(get_example_data)
 export(has_class)
 export(impute)
 export(locf)
 export(longDataConstructor)
 export(method_approxbayes)
 export(method_bayes)
+export(method_bmlmi)
 export(method_condmean)
 export(pool)
 export(pool_internal)
+export(set_simul_pars)
 export(set_vars)
 export(simulate_data)
 export(strategy_CIR)
@@ -70,6 +81,7 @@ importFrom(rstan,extract)
 importFrom(rstan,sampling)
 importFrom(rstan,summary)
 importFrom(stats,as.formula)
+importFrom(stats,binomial)
 importFrom(stats,coef)
 importFrom(stats,df.residual)
 importFrom(stats,lm)
@@ -80,12 +92,15 @@ importFrom(stats,pt)
 importFrom(stats,qnorm)
 importFrom(stats,qt)
 importFrom(stats,quantile)
+importFrom(stats,rbinom)
 importFrom(stats,reformulate)
 importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stats,terms)
+importFrom(stats,uniroot)
 importFrom(stats,var)
 importFrom(stats,vcov)
 importFrom(utils,capture.output)
+importFrom(utils,relist)
 useDynLib(rbmi, .registration = TRUE)