update

Author: larry-leon

_pkgdown.yml

@@ -26,7 +26,7 @@ articles:
       Technical details on the statistical methods implemented in
       weightedsurv.
     contents:
-      - weightedcox_methodology
+      - articles/weightedcox_methodology
 
 reference:
   - title: "Data Preparation"

dev/weightedsurv_devtools-helpers.R

@@ -79,10 +79,8 @@ cat(readLines("NAMESPACE"), sep = "\n")
 dir.create("vignettes/articles", recursive = TRUE, showWarnings = FALSE)
 usethis::use_build_ignore("vignettes/articles")
 
-
 pkgdown::check_pkgdown()
 
-
 # Build the full site (renders all vignettes and articles)
 pkgdown::build_site()
 
@@ -91,12 +89,23 @@ pkgdown::build_home()              # README → index.html
 pkgdown::build_reference()         # Function reference pages
 pkgdown::build_articles()          # All vignettes and articles
 pkgdown::build_article("weightedsurv_examples")      # Just the main vignette
-pkgdown::build_article("weightedcox_methodology")     # Just the methodology article
+pkgdown::build_article("articles/weightedcox_methodology")     # Just the methodology article
 
 # Preview locally
 pkgdown::preview_site()
 
+# What files are in vignettes/articles/?
+list.files("vignettes/articles", recursive = TRUE)
+
+# What does pkgdown detect as articles?
+pkg <- pkgdown::as_pkgdown()
+pkg$vignettes
 
 
+# Keys referenced in the document
+doc <- readLines("vignettes/articles/weightedcox_methodology.Rmd")
+regmatches(doc, gregexpr("@[A-Za-z0-9_]+", doc)) |> unlist() |> unique()
 
+# Keys defined in the bib file
+grep("^@", readLines("vignettes/articles/weightedcox.bib"), value = TRUE)
 

…tes/articles/weightedcox_methodology.qmd …tes/articles/weightedcox_methodology.Rmdvignettes/articles/weightedcox_methodology.qmd renamed to vignettes/articles/weightedcox_methodology.Rmd vignettes/articles/weightedcox_methodology.qmd renamed to vignettes/articles/weightedcox_methodology.Rmd

@@ -5,10 +5,10 @@ output:
          code_folding: hide
          toc: true
          toc_depth: 3
-bibliography: ../references.bib
+bibliography: ../weightedsurv_references.bib
 vignette: >
   %\VignetteIndexEntry{Weighted Cox Model Estimation Methodology}
-  %\VignetteEngine{quarto::html}
+  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
 

vignettes/references.bib

@@ -3,7 +3,7 @@ title: "Weighted Survival Analysis Examples"
 output: 
   html_document:
          code_folding: hide
-bibliography: references.bib
+bibliography: weightedsurv_references.bib
 vignette: >
   %\VignetteIndexEntry{Weighted Survival Analysis Examples}
   %\VignetteEngine{knitr::rmarkdown}