Merge pull request #60 from nickreich/add_pkgdown

Add pkgdown

.Rbuildignore

@@ -6,3 +6,6 @@ cran-comments.md
 ^\.github$
 ^CRAN-SUBMISSION$
 ^\.lintr$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.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@v3
+
+      - 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@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -39,3 +39,4 @@ vignettes/*.pdf
 # Vim and emacs files
 *~
 *.swp
+docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: coarseDataTools
-Version: 0.7
-Date: 2023-04-28
+Version: 0.7.1
+Date: 2023-07-03
 Title: Analysis of Coarsely Observed Data
 Authors@R: c(person("Nicholas G.", "Reich", email = "nick@umass.edu", role = c("aut", "cre")),
   person("Justin", "Lessler", email = "jlessler@unc.edu", role = "aut"),
@@ -9,7 +9,8 @@ Authors@R: c(person("Nicholas G.", "Reich", email = "nick@umass.edu", role = c("
   person("Hugo", "Gruson", email = "hugo.gruson@normalesup.org", role = "ctb"))
 Maintainer: Nicholas G. Reich <nick@umass.edu>
 License: GPL (>= 2)
-URL: https://cran.r-project.org/package=coarseDataTools
+URL: https://cran.r-project.org/package=coarseDataTools,
+    http://nickreich.github.io/coarseDataTools/
 Encoding: UTF-8
 Imports:
     MCMCpack,

NEWS.md

@@ -0,0 +1,53 @@
+# coarseDataTools 0.7.1
+
+* Added pkgdown, moved ChangeLog to NEWS.md
+
+# coarseDataTools 0.7 
+
+* Refactor code to align with lintr standards, adding Hugo Gruson as contributor.
+
+# coarseDataTools 0.6.6 
+
+* update vignette to Rmd, removal of plot method for cd.fit object.
+
+# coarseDataTools 0.6.5 
+
+* minor modifications to fix improper call to `class()` and other new NOTES.
+
+# coarseDataTools 0.6.4 
+
+* merged hackout3 branch to support new distributions
+
+# coarseDataTools 0.6.3 
+
+* minor modifications to address NAMESPACE issues.
+
+# coarseDataTools 0.6 
+
+* added Azman/Lessler contributions: MCMC estimation functions, ability to fit Weibull and Gamma distributions, and bootstrap confidence intervals.
+
+# coarseDataTools 0.5.1 
+
+* changed code to eliminate NOTE message in R CMD CHECK.
+
+# coarseDataTools 0.5 
+
+* added get.obs.type() function to easily generate observation types for data set up in doubly interval censored format. 
+
+# coarseDataTools 0.4 
+
+* added functions for simulation precision of estimated percentiles from coarse incubation period datasets.
+
+# coarseDataTools 0.3  
+
+* added documentation for datafiles.
+
+# coarseDataTools 0.2 
+
+* added functions (with documentation) for estimating a univariate distribution with an arbitrary mixture of doubly interval-censored, single interval-censored and exact observations using a maximum likelihood approach.  
+
+# coarseDataTools 0.1 
+
+* added functions (with documentation) for estimating the relative case fatality ratio.  Currently only tested on situations with two groups of interest, i.e. two levels of covariate J.
+
+

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: http://nickreich.github.io/coarseDataTools/
+template:
+  bootstrap: 5
+