add rhub workflow (#436)

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mmrm
 Title: Mixed Models for Repeated Measures
-Version: 0.3.11
+Version: 0.3.11.9000
 Authors@R: c(
     person("Daniel", "Sabanes Bove", , "daniel.sabanes_bove@roche.com", role = c("aut", "cre")),
     person("Liming", "Li", , "liming.li@roche.com", role = "aut"),

NEWS.md

@@ -1,3 +1,5 @@
+# mmrm 0.3.11.9000
+
 # mmrm 0.3.11
 
 ### Bug Fixes

vignettes/empirical_wls.Rmd

@@ -246,7 +246,7 @@ We follow the following logic (see the corresponding `C++` function `pseudoInver
 otherwise replace the value with 0.
 3. Reconstruct the pseudo inverse matrix from modified singular values and U/V matrix.
 
-In `Eigen` package, the pseudo inverse method is already implemented in [`Eigen::CompleteOrthogonalDecomposition< MatrixType_ >::pseudoInverse`](https://eigen.tuxfamily.org/dox/classEigen_1_1CompleteOrthogonalDecomposition.html#ab5e8b3f2c7b602772e1f1d7ce63d446e),
+In `Eigen` package, the pseudo inverse method is already implemented in [`Eigen::CompleteOrthogonalDecomposition< MatrixType_ >::pseudoInverse`](https://libeigen.gitlab.io/docs/classEigen_1_1CompleteOrthogonalDecomposition.html#a6260bd1050a28dd59733233d93eb6bed),
 but it is not used for the following reason:
 
 1. The pseudo inverse method is not stable and can lead to `NAN` in calculations.