Fix vignette for now

vignettes/precompile.R

@@ -7,19 +7,21 @@ old_wd <- getwd()
 setwd("vignettes/")
 # Precompile vignettes
 library(knitr)
-knit("./.source/rredlist.Rmd", "rredlist.Rmd")
+knit("./source/_rredlist.Rmd", "rredlist.Rmd")
 
 # Build vignettes
 library(devtools)
 build_vignettes()
 
-# x = vignette file name including file extension (e.g. "rredlist.Rmd")
+# x = vignette file name including file extension (e.g., "rredlist.Rmd")
 read_only <- function(x) {
   tmp <- file(x)
-  writeLines(c(
-    paste0("% Generated by vignettes/precompile.R: do not edit by hand.\n",
-           "% Please edit source in vignettes/.source/", x),
-    readLines(x)), tmp)
+  nlines <- grep("^---\\s*$", readLines(x))[2]
+  writeLines(
+    c(readLines(x)[1:(nlines + 1)],
+      paste0("<!-- Generated by vignettes/precompile.R: do not edit by hand.\n",
+             "Please edit source in vignettes/source/_", x, " -->"),
+      readLines(x)[(nlines + 2):length(readLines(x))]), tmp)
   close(tmp)
 }
 # Add read only info

vignettes/rredlist.Rmd

@@ -1,24 +1,24 @@
-% Generated by vignettes/precompile.R: do not edit by hand.
-% Please edit source in vignettes/.source/rredlist.Rmd
 ---
 title: "Introduction to rredlist"
 author: "William Gearty"
-date: "2024-09-30"
+date: "2024-10-01"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Introduction to rredlist}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
 
+<!-- Generated by vignettes/precompile.R: do not edit by hand.
+Please edit source in vignettes/source/_rredlist.Rmd -->
 
 
 `rredlist` is an R client for the IUCN Red List API (https://api.iucnredlist.org/).
 The [IUCN Red List](https://www.iucnredlist.org/) is the world’s most comprehensive information source on the global extinction risk status of animal, fungus and plant species. This package provides access via R to the various data contained within this database which span range details, population size, habitat and ecology, use and/or trade, threats, and conservation actions.
 
 Documentation for the IUCN Red List API are available at https://api.iucnredlist.org/api-docs. **Note that use of the web API, and therefore this package, [requires authentication](#authentication).**
 
-### What `rredlist` is not
+#### What `rredlist` is not:
 
 1. [`redlistr`](https://cran.r-project.org/package=redlistr) is a different package for contributors to the IUCN Red List - not working with the IUCN Red List API.
 2. `rredlist` does not include support for the spatial API, described at https://apiv3.iucnredlist.org/spatial.

vignettes/.source/rredlist.Rmd → vignettes/source/_rredlist.Rmd

@@ -49,7 +49,7 @@ The [IUCN Red List](https://www.iucnredlist.org/) is the world’s most comprehe
 
 Documentation for the IUCN Red List API are available at https://api.iucnredlist.org/api-docs. **Note that use of the web API, and therefore this package, [requires authentication](#authentication).**
 
-### What `rredlist` is not
+#### What `rredlist` is not:
 
 1. [`redlistr`](https://cran.r-project.org/package=redlistr) is a different package for contributors to the IUCN Red List - not working with the IUCN Red List API.
 2. `rredlist` does not include support for the spatial API, described at https://apiv3.iucnredlist.org/spatial.