Update vignette source files and precompile.R

palaeoverse · Oct 2, 2024 · 5657d1e · 5657d1e
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Showing 7 changed files with 33 additions and 10 deletions.
diff --git a/vignettes/a-getting-started.Rmd b/vignettes/a-getting-started.Rmd
@@ -1,4 +1,6 @@
 ---
+# Generated by vignettes/precompile.R: do not edit by hand.
+# Please edit source in vignettes/source/_a-getting-started.Rmd
 title: "Getting started with rphylopic"
 output: rmarkdown::html_vignette
 vignette: >
@@ -9,7 +11,7 @@ vignette: >
 
 **Authors:** Lewis A. Jones & William Gearty
 
-**Last updated:** 2024-09-03
+**Last updated:** 2024-10-02
 
 
 
@@ -53,9 +55,9 @@ citation("rphylopic")
 ```
 ## To cite rphylopic in publications, use the following citation:
 ## 
-##   Gearty, W. and Jones, L.A. 2023. rphylopic: An R package for fetching, transforming,
-##   and visualising PhyloPic silhouettes. Methods in Ecology and Evolution, 14(11),
-##   2700-2708. doi: 10.1111/2041-210X.14221.
+##   Gearty, W. and Jones, L.A. 2023. rphylopic: An R package for fetching, transforming, and visualising
+##   PhyloPic silhouettes. Methods in Ecology and Evolution, 14(11), 2700-2708. doi:
+##   10.1111/2041-210X.14221.
 ## 
 ## A BibTeX entry for LaTeX users is
 ## 
@@ -251,7 +253,7 @@ get_attribution(uuid = uuid, text = TRUE)
 ```
 
 ```
-## Organism silhouettes are from PhyloPic (https://www.phylopic.org/; T. Michael Keesey, 2023) and were added using the rphylopic R package ver. 1.4.0.9000 (Gearty & Jones, 2023). Silhouette was made by Mareike C. Janiak, 2020 (Public Domain Mark 1.0). Silhouette was contributed by Mareike Janiak.
+## Organism silhouettes are from PhyloPic (https://www.phylopic.org/; T. Michael Keesey, 2023) and were added using the rphylopic R package ver. 1.5.0 (Gearty & Jones, 2023). Silhouette was made by Mareike C. Janiak, 2020 (Public Domain Mark 1.0). Silhouette was contributed by Mareike Janiak.
 ```
 
 ## Save an image

diff --git a/vignettes/b-advanced-ggplot.Rmd b/vignettes/b-advanced-ggplot.Rmd
@@ -1,4 +1,6 @@
 ---
+# Generated by vignettes/precompile.R: do not edit by hand.
+# Please edit source in vignettes/source/_b-advanced-ggplot.Rmd
 title: "Advanced examples in ggplot"
 output: rmarkdown::html_vignette
 vignette: >
@@ -9,7 +11,7 @@ vignette: >
 
 **Authors:** William Gearty & Lewis A. Jones
 
-**Last updated:** 2024-09-03
+**Last updated:** 2024-10-02
 
 
 

diff --git a/vignettes/c-advanced-base.Rmd b/vignettes/c-advanced-base.Rmd
@@ -1,4 +1,6 @@
 ---
+# Generated by vignettes/precompile.R: do not edit by hand.
+# Please edit source in vignettes/source/_c-advanced-base.Rmd
 title: "Advanced examples in base R"
 output: rmarkdown::html_vignette
 vignette: >
@@ -9,7 +11,7 @@ vignette: >
 
 **Authors:** William Gearty & Lewis A. Jones
 
-**Last updated:** 2024-09-03
+**Last updated:** 2024-10-02
 
 
 

diff --git a/vignettes/precompile.R b/vignettes/precompile.R
@@ -4,14 +4,31 @@ old_wd <- getwd()
 setwd("vignettes/")
 
 library(knitr)
-knit("a-getting-started.Rmd.orig",
+knit("./source/_a-getting-started.Rmd",
      "a-getting-started.Rmd")
-knit("b-advanced-ggplot.Rmd.orig",
+knit("./source/_b-advanced-ggplot.Rmd",
      "b-advanced-ggplot.Rmd")
-knit("c-advanced-base.Rmd.orig",
+knit("./source/_c-advanced-base.Rmd",
      "c-advanced-base.Rmd")
 
 library(devtools)
 build_vignettes()
 
+# x = vignette file name including file extension (e.g., "a-getting-started.Rmd")
+read_only <- function(x) {
+  # Create file
+  tmp <- file(x)
+  # write lines
+  writeLines(c(c("---"),
+               c("# Generated by vignettes/precompile.R: do not edit by hand."),
+               paste0("# Please edit source in vignettes/source/_", x),
+               readLines(x)[2:length(readLines(x))]), tmp)
+  close(tmp)
+}
+# Add read only info
+read_only("a-getting-started.Rmd")
+read_only("b-advanced-ggplot.Rmd")
+read_only("c-advanced-base.Rmd")
+rm(read_only)
+
 setwd(old_wd)
diff --git a/vignettes/a-getting-started.Rmd.orig → vignettes/source/_a-getting-started.Rmd b/vignettes/a-getting-started.Rmd.orig → vignettes/source/_a-getting-started.Rmd
diff --git a/vignettes/b-advanced-ggplot.Rmd.orig → vignettes/source/_b-advanced-ggplot.Rmd b/vignettes/b-advanced-ggplot.Rmd.orig → vignettes/source/_b-advanced-ggplot.Rmd
diff --git a/vignettes/c-advanced-base.Rmd.orig → vignettes/source/_c-advanced-base.Rmd b/vignettes/c-advanced-base.Rmd.orig → vignettes/source/_c-advanced-base.Rmd