restructured vignettes and added git wflows

Author: spedygiorgio

.Rbuildignore

@@ -1,5 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.Rproj\.user
 ^\.travis\.yml$
 ^data-raw$
 vignettes/jss*
@@ -8,3 +9,4 @@ vignettes/*.log
 ^TAGS$
 ^.*\.tar\.gz$
 ^LICENSE\.md$
+^\.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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

markovchain.Rproj

@@ -15,6 +15,6 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageBuildArgs: --compact-vignettes=both --resave-data
+PackageBuildArgs: --compact-vignettes=gs+qpdf --resave-data
 PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace

vignettes/gsoc_2017_additions.Rmd

@@ -2,17 +2,26 @@
 title: "Google Summer of Code 2017 Additions"
 author: "Vandit Jain"
 date: "August 2017"
-output: rmarkdown::pdf_document
+output: rmarkdown::html_vignette
 bibliography: markovchainBiblio.bib
 vignette: >
   %\VignetteIndexEntry{Google Summer of Code 2017 Additions} 
   %\VignetteEngine{knitr::rmarkdown}  
   %VignetteEncoding{UTF-8}
-pkgdown:
-  as_is: true
-  extension: pdf
 ---
 
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE,
+                      collapse = TRUE,
+                      comment = "#>")
+```
+
+```{r setup_2, include=FALSE}
+require(markovchain)
+```
+
+
+
 # Expected Hitting Time using CTMC
 
 The package provides `ExpectedTime` function to calculate average hitting time from one state to another. Let the final state be j, then for every state $i \in I$, where $I$ is the set of all possible states and holding time $q_{i} > 0$ for every $i \neq j$. Assuming the conditions to be true, expected hitting time is equal to minimal non-negative solution vector $p$ to the system of linear equations [@NorrisBook]:

vignettes/higher_order_markov_chains.Rmd

@@ -1,9 +1,10 @@
 ---
 title:
-  plain:     "Higher, possibly multivariate, Order Markov Chains in markovchain package"
-  formatted: "Higher, possibly multivariate, Order Markov Chains in \\pkg{markovchain} package"
-  short:     "Higher order (multivariate) Markov chains"
+  plain:     "Higher order Markov chains"
+  formatted: "Higher order Markov chains"
+  short:     "Higher order Markov chains"
 pagetitle: "Higher order (multivariate) Markov chains"
+output: rmarkdown::html_vignette
 author:
   - name: "Deepak Yadav"
     affiliation: B-Tech student, Computer Science and Engineering
@@ -18,7 +19,7 @@ author:
       Gainesville, FL, USA
     email: \email{tskang3@gmail.com}
   - name: "Giorgio Alfredo Spedicato"
-    affiliation: Ph.D C.Stat ACAS, UnipolSai R\&D
+    affiliation: Ph.D FCAS FSA CSPA C.Stat, Unipol Group
     address: >
       Via Firenze 11
       Paderno Dugnano 20037 Italy
@@ -33,20 +34,14 @@ preamble: >
   \setkeys{Gin}{width=0.8\textwidth}
 abstract: |
   The \pkg{markovchain} package contains functions to fit higher (possibly) multivariate order Markov chains. The functions are shown as well as simple exmaples
-output: if (rmarkdown::pandoc_version() < "2.2") function(...) { rmarkdown::pdf_document(template = "./template.tex", ...) } else function(...) { bookdown::pdf_book(base_format = rticles::jss_article, ...) } 
 vignette: >
-  %\VignetteIndexEntry{Higher order markov chains} 
+  %\VignetteIndexEntry{Higher order Markov chains} 
   %\VignetteEngine{knitr::rmarkdown}  
   %VignetteEncoding{UTF-8}
 keywords:
   plain: [Higher order Markov chains]
   formatted: [Higher order Markov chains]
-documentclass: jss
-classoption: nojss
 bibliography: markovchainBiblio.bib
-pkgdown:
-  as_is: true
-  extension: pdf
 ---
 
 ```{r global_options, include=FALSE}
@@ -72,11 +67,17 @@ The output will be a `list` which consists of
 
 Its quadratic programming problem is solved using `solnp` function of the Rsolnp package [@pkg:Rsolnp]. 
 
-```{r load, results='hide', warning=FALSE, message=FALSE}
-require(markovchain)
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE,
+                      collapse = TRUE,
+                      comment = "#>")
+```
 
+```{r setup_2, include=FALSE, message=FALSE, echo=FALSE}
+require(markovchain)
 ```
 
+
 ```{r higherOrder}
 if (requireNamespace("Rsolnp", quietly = TRUE)) {
 library(Rsolnp)