Feature try GitHub actions

.Rbuildignore

@@ -10,3 +10,6 @@ cran-comments.md
 ^appveyor\.yml$
 ^\.travis\.yml$
 vignettes/REndo-introduction_cache
+^\.github$
+^/Users/patrik/StudentAssi/REndo/GIT/pschil/REndo/_pkgdown\.yml$
+^_pkgdown\.yml$

.github/.gitignore

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

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

@@ -0,0 +1,74 @@
+name: R-CMD-checks
+on: [push, pull_request]
+jobs:
+  # job for R CMD checks on win, mac, ubuntu
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: R-CMD-check-${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: '3.6.2'}
+          - {os: macOS-latest,   r: '3.6.2'}
+          - {os: ubuntu-16.04,   r: '3.6.2', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+    env:
+        R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+        RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+        - uses: actions/checkout@v2
+
+        - uses: r-lib/actions/setup-r@master
+          with:
+            r-version: ${{ matrix.config.r }}
+            rtools-version: '../testing/rtools40-x86_64.exe'
+
+        - name: Query dependencies
+          run: |
+            install.packages('remotes')
+            saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+          shell: Rscript {0}
+
+        - name: Cache R packages
+          if: runner.os != 'Windows'
+          uses: actions/cache@v1
+          with:
+            path: ${{ env.R_LIBS_USER }}
+            key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
+            restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+
+        - name: Install system dependencies
+          if: runner.os == 'Linux'
+          env:
+            RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+          run: |
+            Rscript -e "remotes::install_github('r-hub/sysreqs')"
+            sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+            sudo -s eval "$sysreqs"
+            sudo apt-get install -y qpdf
+
+        - name: Install gsl for mac
+          if: runner.os == 'macOS'
+          run: |
+            brew install gsl
+
+        - name: Install dependencies
+          run: |
+            remotes::install_deps(dependencies = TRUE)
+            remotes::install_cran("rcmdcheck")
+            # install from source for ubuntu, binary does not work
+            remotes::install_cran("RcppGSL", repos = "https://cran.rstudio.com/")
+            print(RcppGSL::LdFlags())
+            print(RcppGSL::CFlags())
+            if(file.exists('depends.Rds')) {file.remove('depends.Rds')}
+            # check if can build a rcppgsl package from source
+            install.packages("flan", type="source", repos="https://cran.rstudio.com/")
+            library(flan)
+          shell: Rscript {0}
+
+        - name: Check
+          run: rcmdcheck::rcmdcheck(args = c("--no-tests", "--as-cran", "--no-manual"), error_on = "warning", check_dir = "check")
+          shell: Rscript {0}
+

.github/workflows/pkgdown.yaml

@@ -0,0 +1,43 @@
+on:
+  push:
+    branches: feature-try-github-actions
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: macOS-r-4.0-${{ hashFiles('depends.Rds') }}
+          restore-keys: macOS-r-4.0-
+
+      - name: Install dependencies
+        run: |
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_dev("pkgdown")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: pkgdown::deploy_to_branch(new_process = FALSE)
+        shell: Rscript {0}
+

.github/workflows/test-and-coverage.yml

@@ -0,0 +1,46 @@
+name: test-and-coverage
+on: pull_request
+jobs:
+  # job for test on ubunutu only
+  tests-and-coverage-ubuntu-16-04-R-3-6:
+    runs-on: ubuntu-16.04
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      # to install binaries on ubuntu
+      RSPM: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 3.6
+      - name: Install system dependencies
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "install.packages(c('remotes', 'rcmdcheck'))"
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+      - name: Install package dependencies
+        # RcppGSL and stringi can currently not load or link when installed from RSPM,
+        #   therefore install from cran (source)
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          print(getOption("repos"))
+          remotes::install_cran("testthat", repos = "https://cran.rstudio.com/")
+          remotes::install_cran("devtools", repos = "https://cran.rstudio.com/")
+          remotes::install_cran("covr", repos = "https://cran.rstudio.com/")
+        shell: Rscript {0}
+
+      - name: Run tests
+        run: |
+          library(testthat)
+          library(devtools)
+          devtools::test(reporter=RstudioReporter)
+        shell: Rscript {0}
+
+      - name: Test coverage, if tests succeeded
+        if: success()
+        # run: covr::codecov()
+        run: covr::package_coverage(type = "tests", quiet = FALSE)
+        shell: Rscript {0}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: REndo
 Title: Fitting Linear Models with Endogenous Regressors using Latent Instrumental Variables
-Version: 2.3.1
-Date: 2020-02-15
+Version: 2.3.2
+Date: 2020-03-28
 Authors@R: c(
     person(given="Raluca", family="Gui",         email = "[email protected]", role = c("cre","aut")),
     person(given="Markus", family="Meierer",     email = "[email protected]", role = "aut"),
@@ -35,7 +35,8 @@ Imports:
 Suggests:
     testthat,
     covr,
-    R.rsp
+    R.rsp, 
+    bookdown
 Encoding: UTF-8
 RoxygenNote: 7.0.2
 VignetteBuilder: R.rsp

NEWS.md

@@ -1,45 +1,45 @@
-# CHANGES IN REndo 2.3.1
+# REndo 2.3.1
 * None. Version bump in order to resubmit to CRAN after package was archived.
 
 
-# CHANGES IN REndo 2.3.0
+# REndo 2.3.0
 
-## SIGNIFICANT USER-VISIBLE CHANGES
+#### SIGNIFICANT USER-VISIBLE CHANGES
 * Add support for predictions through method `predict` for every model
 
-## BUG FIXES
+#### BUG FIXES
 * Fix wrong calculations for the fitted values and residuals in the enhanced OLS cases of `copulaCorrection`
 * Improved documentation
 
 
 
-# CHANGES IN REndo 2.2.1
+# REndo 2.2.1
 
-## SIGNIFICANT USER-VISIBLE CHANGES
+#### SIGNIFICANT USER-VISIBLE CHANGES
 * To tweak the lmer model fit in `multilevelIV` to their linking, users can supply a parameter `lmer.control`
 
-## NEW FEATURES
+#### NEW FEATURES
 * Warning in `confint` if there are NAs in the bootstrapped estimates for `copulaCorrection`
 * Updated vignette
 
-## BUG FIXES
+#### BUG FIXES
 * The coefficient estimates for `multilevelIV` are more consistent and independent of data sorting due to different standard settings for fitting `lmer`
 * Bootstrapped parameter estimates for `copualCorrection` result in fewer NAs when using L-BFGS-B as optimization method
 
 
 
-# CHANGES IN REndo 2.2.0
+# REndo 2.2.0
 
-## SIGNIFICANT USER-VISIBLE CHANGES
+#### SIGNIFICANT USER-VISIBLE CHANGES
 * The augmented OLS method in `copulaCorrection` also bootstraps parameter estimates
 * The summary output for results from `copulaCorrection` was adapted to reflect that standard errors are bootstrapped
 * Removed support for the S3 method `labels` because of inconsistent behavior across methods
 
-## NEW FEATURES
+#### NEW FEATURES
 * Bootstrapping for `copulaCorrection` case 1 is now considerably faster
 * New data was generated for `dataMultilevelIV`
 
-## BUG FIXES
+#### BUG FIXES
 * The sigma matrix in `latentIV` is constructed as in the paper by Ebbes et al. what improves results. Special thanks to Jordan Henderson for investigating and pointing this out!
 * In `latentIV`, the parameter for group membership (`theta5`) is now transformed back and reported correctly.
 * The vcov matrix for `latentIV` is corrected for the transformation in `theta5`.
@@ -48,43 +48,43 @@
 
 
 
-# CHANGES IN REndo 2.1.0
+# REndo 2.1.0
 
-## SIGNIFICANT USER-VISIBLE CHANGES
+#### SIGNIFICANT USER-VISIBLE CHANGES
 * The reworked method `multilevelIV` and accompanying data was added back to the package
 * Vignette `REndo-introduction` was added to showcase package usage
 * Users can supply a parameter `optimx.args` to tweak the LL optimization to their liking
 
-## NEW FEATURES
+#### NEW FEATURES
 * Method `confint` was added for methods `latentIV` and `copulaCorrection`
 * Examples and documentation were improved for all methods
 * New data was generated for `dataHetIV`
 * The default number of iterations for all optimizations was increased to 100'000
 
-## BUG FIXES
+#### BUG FIXES
 * To avoid infrequent warnings, the parameter `sigma` used in `copulaCorrection` was constrained to > 0
 * Various spelling mistakes were fixed
 
 
 
-# CHANGES IN REndo 2.0.0
+# REndo 2.0.0
 
-## SIGNIFICANT USER-VISIBLE CHANGES
+#### SIGNIFICANT USER-VISIBLE CHANGES
 * Remodeled all methods' user-interface
 * Added detailed input checks for every provided parameter
 * Adapted all visible outputs
 * Parameter `verbose` allows to turn on or off printing
 * Updated documentation to reflect all changes and added theoretical background
 
-## NEW FEATURES
+#### NEW FEATURES
 * Formulas support transformations
 * Improve all code to be more reliable and stable
 * Provide new example datasets and accompanying documentation for all methods
 * Added extensive testing for all aspects of the package
 * Increased numerical stability for log-likelihood optimization methods `latentIV` and `copualCorrection`
 
-## BUG FIXES
+#### BUG FIXES
 * Many
 
-# DEPRECATED AND DEFUNCT
+#### DEPRECATED AND DEFUNCT
 * The multilevel function is temporarily removed from the package due to ongoing work on it

R/REndo-package.R

@@ -17,6 +17,7 @@
 #' \item{\code{multilevelIV()}}{multilevel GMM method proposed by Kim and Frees (2007)}
 #' }
 #'
+#'
 #' \strong{Differences between current (2.0.0) and previous version of REndo}
 #'
 #' Note that with version 2.0.0 sweeping changes were which greatly improve functionality but break backwards compatibility.

_pkgdown.yml

@@ -0,0 +1,3 @@
+template:
+  params:
+    bootswatch: cerulean