15 create pkgdown website

.Rbuildignore

@@ -4,3 +4,6 @@
 ^data-raw$
 LICENSE
 ^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/.gitignore

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

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

@@ -20,7 +20,8 @@ jobs:
         config:
 #         - {os: macos-latest,   r: 'release'}
 #         - {os: windows-latest, r: 'release'}
-         - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+#         - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+         - {os: ubuntu-latest, r: 'release'}
 #         - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:

.github/workflows/pkgdown.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:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -11,3 +11,4 @@ src/*.h
 mastiff_*.tar.gz
 *.DS_Store
 ..Rcheck/
+docs

DESCRIPTION

@@ -11,7 +11,7 @@ License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
-URL: https://github.com/BDI-pathogens/mastiff
+URL: https://github.com/BDI-pathogens/mastiff, https://bdi-pathogens.github.io/mastiff/
 BugReports: https://github.com/BDI-pathogens/mastiff/issues
 Suggests: 
     knitr,

NAMESPACE

@@ -37,7 +37,6 @@ importFrom(data.table,set)
 importFrom(data.table,setnames)
 importFrom(dplyr,if_else)
 importFrom(magrittr,"%>%")
-importFrom(matrixStats,colMaxs)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)
 importFrom(rstan,sampling)

README.Rmd

@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# mastiff <img src="man/figures/mastiff_logo_2.svg" align="right" height="148" /></a>
+# mastiff <img src="man/figures/logo.svg" align="right" height="139" alt="mastiff logo" />
 
 <!-- badges: start -->
 <!-- badges: end -->

_pkgdown.yml

@@ -0,0 +1,62 @@
+url: https://bdi-pathogens.github.io/mastiff/
+template:
+  bootstrap: 5
+reference:
+- contents:
+  - check_logical
+  - check_numeric
+  - estimate_mixture_of_two_normals
+  - logistic
+  - logit
+  - plot_posterior
+  - posterior_intervals
+  - posterior_mass_in_range
+  - posterior_means
+  - rename_params_cmdstanfile_to_rstan
+  - simulate_mixture_of_two_normals
+  - stan_example_regression
+  - stanfit_to_matrix
+  - uniroot.vectorized
+- title: R6 Interface Classes
+  desc: |
+    Class definitions for an extension to R6 classes including interfaces
+  contents:
+  - R6.class
+  - R6.interface
+  - R6.interface.implements
+- title: R6 Distribution Classes
+  desc: |
+    Constructor functions for R6 distribution classes
+  contents:
+  - Mastiff-Distributions
+  - is.distribution
+  - distribution.mixture
+- subtitle: Discrete Distributions
+  contents:
+  - distribution.binomial
+  - distribution.negative_binomial
+  - distribution.point_mass
+  - distribution.poisson
+- subtitle: Continuous Distributions
+  contents:
+  - distribution.exponential
+  - distribution.gamma
+  - distribution.lognormal
+  - distribution.normal
+  - distribution.uniform
+- title: Class Definitions
+  contents:
+  - distribution.abstract.class
+  - distribution.continuous.class
+  - distribution.continuous.exponential.class
+  - distribution.continuous.gamma.class
+  - distribution.continuous.lognormal.class
+  - distribution.continuous.normal.class
+  - distribution.continuous.uniform.class
+  - distribution.discrete.binomial.class
+  - distribution.discrete.class
+  - distribution.discrete.negative_binomial.class
+  - distribution.discrete.point_mass.class
+  - distribution.discrete.poisson.class
+  - distribution.mixture.class
+