Build the crosstalk vignette on installation.

This renames the vignette file, gives it a clearer title and sets it up so that it gets rendered when the package in installed.
R-Lum · Feb 10, 2025 · 5cdffe2 · 5cdffe2 · RLumSK · Feb 10, 2025
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Showing 5 changed files with 16 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -65,13 +65,14 @@ Suggests:
     rstudioapi (>= 0.16.0),
     rjags (>= 4-15),
     coda (>= 0.19-4),
+    knitr,
     pander (>= 0.6.5),
     testthat (>= 3.2.1),
     vdiffr (>= 1.0.0),
     tiff (>= 0.1-12),
     devtools (>= 2.4.5),
     R.rsp (>= 0.46.0)
-VignetteBuilder: R.rsp
+VignetteBuilder: R.rsp, knitr
 Encoding: UTF-8
 Language: en-US
 RoxygenNote: 7.3.2

diff --git a/NEWS.Rmd b/NEWS.Rmd
@@ -12,7 +12,8 @@ header-includes:
 
 * `apply_Crosstalk()`, `calc_MoransI()`, `plot_SingleGrainDisc()` and
 `plot_MoranScatterplot()` were contributed by Anna-Maartje de Boer and Luc
-Steinbuch (#560).
+Steinbuch (#560). An introductory example on how to use these functions
+is available by executing `vignette("crosstalk")`.
 
 * `calc_EED_Model()` models incomplete and heterogeneous bleaching of
 mobile grains after Guibert et al. (2017). Along with the function, the

diff --git a/NEWS.md b/NEWS.md
@@ -5,13 +5,14 @@
 
 <!-- NEWS.md was auto-generated by NEWS.Rmd. Please DO NOT edit by hand!-->
 
-# Changes in version 0.9.26.9000-110 (2025-02-07)
+# Changes in version 0.9.26.9000-110 (2025-02-10)
 
 ## New functions
 
 - `apply_Crosstalk()`, `calc_MoransI()`, `plot_SingleGrainDisc()` and
   `plot_MoranScatterplot()` were contributed by Anna-Maartje de Boer and
-  Luc Steinbuch (#560).
+  Luc Steinbuch (#560). An introductory example on how to use these
+  functions is available by executing `vignette("crosstalk")`.
 
 - `calc_EED_Model()` models incomplete and heterogeneous bleaching of
   mobile grains after Guibert et al. (2017). Along with the function,

diff --git a/vignettes/.gitignore b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/crosstalk_vignette.Rmd → vignettes/crosstalk.Rmd b/vignettes/crosstalk_vignette.Rmd → vignettes/crosstalk.Rmd
@@ -1,10 +1,10 @@
 ---
-title: "crosstalk_vignette"
+title: "Assessing crosstalk in single-grain luminescence detection"
 output: 
     rmarkdown::html_vignette:
      toc: true
-author: "Luc Steinbuch, Anna-Maartje de Boer, Wageningen University & Research, 2025"
-date: "`r Sys.Date()`"
+author: "Luc Steinbuch, Anna-Maartje de Boer, Wageningen University & Research"
+date: "February 2025"
 vignette: >
   %\VignetteIndexEntry{crosstalk_vignette}
   %\VignetteEngine{knitr::rmarkdown}
@@ -20,7 +20,10 @@ knitr::opts_chunk$set(
 
 # Crosstalk
 
-This vignette explores the crosstalk related functions in the "luminescence" package, related to  research paper "A novel tool to assess crosstalk in single-grain luminescence detection", by Anna-Maartje de Boer, Luc Steinbuch, Gerard Heuvelink and Jakob Wallinga.
+This vignette explores the crosstalk-related functions in the "Luminescence"
+package, related to  research paper "A novel tool to assess crosstalk in
+single-grain luminescence detection", by Anna-Maartje de Boer, Luc Steinbuch,
+Gerard Heuvelink and Jakob Wallinga.
 Crosstalk in single-grain luminescence imaging (EMCCD) is the overlapping of luminescence signals from adjacent grains on a single-grain disc. The actual signal on one grain location influences the observed signal on a neighboring grain location which happens to be on the same measurement disc (one "position" in the reader). In this research and the shown functions, we define "neighboring" as rook-wise (horizontally and vertically) only, and we assume that all measurement discs have a regular grid of 10x10 grain locations.