Correct CMD builds & CMD checks errors

.Rbuildignore

@@ -2,3 +2,4 @@
 ^cran-comments.md$
 ^\.travis\.yml$
 ^CRAN-RELEASE$
+^\.github$

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

@@ -0,0 +1,51 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+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
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/render-vignette-yaml.yml

@@ -0,0 +1,25 @@
+on:
+  push:
+    branches:
+      - main
+name: vignettes
+jobs:
+  vignette:
+    name: Render-Vignette
+    runs-on: ubuntu-latest
+    container:
+      image: rocker/tidyverse
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install R dependencies
+        run: Rscript -e 'install.packages(c("DEoptimR","mathjaxr"))'
+      - name: Render Vignette
+        run: Rscript -e 'rmarkdown::render("vignette/guide.Rmd", output_dir = "vignette_output")'
+      - name: Deploy to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages
+          FOLDER: vignette_output
+          CLEAN: true
+

R/functions.R

@@ -5,6 +5,7 @@
 #--------------------------------------------------------------------------------------------	
 # global variables
 # if(getRversion() >= "2.15.1")  utils::globalVariables(c())
+utils::globalVariables("intcal20")
 #--------------------------------------------------------------------------------------------
 getTruncatedModelChoices <- function(){
 	# Required in several functions, so avoids duplication if others are added to the package

README.md

@@ -3,11 +3,11 @@
 <a href="https://www.shh.mpg.de"><img src="tools/logos/logo_MPI.png" alt="Max Planck Institute for the Science of Human History" height="70"/></a>
 <a href="https://www.shh.mpg.de/1143811/pan-ev"><img src="tools/logos/logo_PanEv.png" alt="Pan African Evolution ResearchGroup" height="70"/></a>
 
-[![Build Status](https://app.travis-ci.com/AdrianTimpson/ADMUR.svg?branch=master)](https://app.travis-ci.com/AdrianTimpson/ADMUR)
-
 # ADMUR
 ## Ancient Demographic Modelling Using Radiocarbon
 
+[![R-CMD-check](https://github.com/simoncarrignon/ADMUR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/simoncarrignon/ADMUR/actions/workflows/R-CMD-check.yaml)
+
 Statistical tools to directly model underlying population dynamics using date datasets (radiocarbon and other). 
 
 ### Population modelling
@@ -74,4 +74,4 @@ Also thanks to the following who have reported bugs, requested additional functi
 - Ricardo Fernandes
 - Mark G. Thomas
 - Robert Staniuk
----
+---

man/SPDsimulationTest.Rd

@@ -68,7 +68,7 @@
 	The default N = 20000 can be increased if greater precision is required, however this can be very time costly.
 	}
 \examples{
-\donttest{
+\dontrun{
 # trivial example showing a single date can never be rejected under a uniform model:
 data <- data.frame(age=6500, sd=50, phase=1, datingType='14C')
 x <- SPDsimulationTest(data, 

man/getPhaseModelChoices.Rd

@@ -4,7 +4,7 @@
 \description{
 	Lists currently available models for the PDF of an archaeological phase, the number of parameters, and a brief description
 	\loadmathjax }
-\usage{getTruncatedModelChoices()}
+\usage{getPhaseModelChoices()}
 
 \details{
 

man/intcal20.Rd

@@ -1,5 +1,5 @@
-\name{intcal20} 
 \docType{data}
+\name{intcal20} 
 \alias{intcal20} 
 \title{Northern hemisphere 2020 calibration curve} 
 \description{
@@ -17,3 +17,4 @@
 	}
 \references{Reimer P, Austin WEN, Bard E, Bayliss A, Blackwell PG, Bronk Ramsey C, Butzin M, Cheng H, Edwards RL, Friedrich M, Grootes PM, Guilderson TP, Hajdas I, Heaton TJ, Hogg AG, Hughen KA, Kromer B, Manning SW, Muscheler R, Palmer JG, Pearson C, van der Plicht J, Reimer RW, Richards DA, Scott EM, Southon JR, Turney CSM, Wacker L, Adolphi F, Büntgen U, Capano M, Fahrni S, Fogtmann-Schulz A, Friedrich R, Köhler P, Kudsk S, Miyake F, Olsen J, Reinig F, Sakamoto M, Sookdeo A, Talamo S. 2020. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0-55 cal kBP). Radiocarbon 62. doi: 10.1017/RDC.2020.41.}
 
+\keyword{datasets}

man/mcmc.Rd

@@ -57,7 +57,7 @@ cal <- simulateCalendarDates(toy, N)
 age <- uncalibrateCalendarDates(cal, shcal20)
 data <- data.frame(age = age, sd = 50, phase = 1:N, datingType = '14C')
 
-\donttest{
+\dontrun{
 # Calibrate each phase, taking care to restrict to the modelled date range
 CalArray <- makeCalArray(shcal20, calrange = range(toy$year), inc = 5)
 PD <- phaseCalibrator(data, CalArray, remove.external = TRUE)

man/phaseModel.Rd

@@ -38,9 +38,18 @@
 	# specify the prior probabilities of the parameter values of a gaussian model in a matrix
 	mu.range <- c(5500,7000)
 	sigma.range <- c(5,700)
-	prior.matrix <- matrix(1,150,150); prior.matrix <- prior.matrix/sum(prior.matrix)
-	row.names(prior.matrix) <- seq(min(mu.range),max(mu.range),length.out=nrow(prior.matrix))
-	colnames(prior.matrix) <- seq(min(sigma.range),max(sigma.range),length.out=ncol(prior.matrix))
+	prior.matrix <- matrix(1,150,150)
+    prior.matrix <- prior.matrix/sum(prior.matrix)
+    row.names(prior.matrix) <- seq(
+       from = min(mu.range),
+       to = max(mu.range),
+       length.out = nrow(prior.matrix)
+    )
+	colnames(prior.matrix) <- seq(
+           from = min(sigma.range),
+           to = max(sigma.range),
+           length.out=ncol(prior.matrix)
+        )
 
 	# generate the posterior parameter probabilities
 	pm <- phaseModel(data, calcurve, prior.matrix, model='norm', plot=TRUE)

man/plotCalArray.Rd

@@ -16,6 +16,7 @@
 \examples{
 \donttest{
 	# generate a CalArray of the intcal20 curve covering 5500 calBP to 6000 calBP
+    data(intcal20)
 	x <- makeCalArray( calcurve = intcal20, calrange = c(5500,6000), inc = 1 )
 	plotCalArray(x)
 	}

man/plotSimulationSummary.Rd

@@ -21,7 +21,7 @@
 	Default NULL for legend.x and legend.y will automatically add a legend, which may not be ideally placed to avoid overlapping other components of the plot. To remove the legend, simply place well outside the boundary.
 	}
 \examples{
-	\donttest{
+	\dontrun{
 	summary <- SPDsimulationTest(data=SAAD, 
 		calcurve=shcal20, 
 		calrange=c(2500,14000), 

vignettes/guide.Rmd

@@ -11,13 +11,18 @@ output:
   logo: logo.jpg
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteIndexEntry{Guide to using ADMUR}
+  %\VignetteIndexEntry{ADMUR: Ancient Demographic Modelling Using Radiocarbon }
   %\usepackage[utf8]{inputenc}
 ---
+
 <style>
 p.caption {font-size: 0.7em;}
 </style>
 
+```{r setup, include=FALSE}
+options(rmarkdown.html_vignette.check_title = FALSE)
+```
+
 **********
 
 # 1. Overview
@@ -93,7 +98,7 @@ data6[1:10,]
 
 **********
 
-# 2. radiocarbon date calibration and SPDs
+# 2. Radiocarbon date calibration and SPDs
 
 Generating a single calibrated date distribution, or a Summed Probability Distribution (SPD) of several calibrated dates, requires either a two-step process to give the user full control of the date range and temporal resolution, or a simpler one step process using a wrapper function that automatically estimates a sensible date range and resolution from the dataset.
 
@@ -124,6 +129,7 @@ Generating the SPD without the wrapper gives you more control, and requires a tw
 This is useful for improving computational times if generating many SPDs, for example in a simulation framework, since the CalArray needs generating only once. 
 
 ```{r, eval = TRUE, fig.height = 3, fig.width=7, fig.align = "center", dev='jpeg', quality=100, warning=FALSE}
+data(intcal20)
 data <- data.frame( age = c(9144), sd=c(151) )
 CalArray <- makeCalArray( calcurve=intcal20, calrange=c(8000,13000) )
 cal <- summedCalibrator(data, CalArray)
@@ -563,7 +569,7 @@ plotPD(spd)
 lines(mod.combo, col=cols[1], lwd=5)
 legend(x=4000, y=max(spd)*1.2,  lwd=5, col=cols[1], bty='n', legend=c('combo.sine.logistic'))
 ```
-![Example of a combination model](combination_model.png){width=680px}  
+![Example of a combination model](combo_models.png){width=680px}  
 
 **********