Merge pull request #402 from bcgov/joss-paper

Author: joethorley

DESCRIPTION

@@ -88,7 +88,6 @@ Suggests:
     magrittr,
     mle.tools,
     patchwork,
-    R.rsp,
     readr,
     reshape2,
     rmarkdown,
@@ -102,11 +101,10 @@ LinkingTo:
     RcppEigen,
     TMB
 VignetteBuilder: 
-    knitr,
-    R.rsp
+    knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.2.9000

_pkgdown.yml

@@ -127,9 +127,10 @@ reference:
 articles:
 - title: All vignettes
   contents:
-  - model-averaging
-  - distributions
+  - articles/model-averaging
+  - articles/distributions
   - articles/confidence-intervals
-  - customising-plots
-  - additional-technical-details
+  - articles/customising-plots
+  - articles/small-sample-bias
+  - articles/additional-technical-details
   - faqs

cran-comments.md

@@ -2,10 +2,9 @@
 
 0 errors | 0 warnings | 1 note
 
-> checking installed package size ... NOTE
->    installed size is 21.2Mb
->    sub-directories of 1Mb or more:
->      doc    3.6Mb
->      libs  16.9Mb
+> ❯ checking installed package size ... NOTE
+>    installed size is 18.0Mb
+>     sub-directories of 1Mb or more:
+>       libs  16.9Mb
 
-The large size of these sub-directories is necessary.
+The large size of this sub-directory is necessary as it contains a .dll for the TMB model fitting functions.

paper/paper.md

@@ -12,6 +12,7 @@ authors:
   orcid: 0000-0002-3178-7243
   affiliation: "4, 5"
 - name: Carl Schwarz
+  orcid: 0000-0002-8525-862X
   affiliation: 6
 affiliations:
 - index: 1

ssdtools.Rproj

@@ -16,4 +16,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette

vignettes/articles/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

vignettes/additional-technical-details.Rmd renamed to vignettes/articles/additional-technical-details.Rmd

@@ -2,7 +2,7 @@
 title: "Additional Technical Details"
 author: "ssdtools Team"
 date: '`r format(Sys.time(), "%Y-%m-%d", tz = "UTC")`'
-bibliography: references.bib
+bibliography: ../references.bib
 mathfont: Courier
 latex_engine: MathJax
 output: rmarkdown::html_vignette

vignettes/customising-plots.Rmd renamed to vignettes/articles/customising-plots.Rmd

@@ -2,7 +2,7 @@
 title: "Customising Plots"
 author: "ssdtools Team"
 date: '`r format(Sys.time(), "%Y-%m-%d", tz = "UTC")`'
-bibliography: references.bib
+bibliography: ../references.bib
 mathfont: Courier
 latex_engine: MathJax
 output: rmarkdown::html_vignette

vignettes/distributions.Rmd renamed to vignettes/articles/distributions.Rmd

@@ -2,7 +2,7 @@
 title: "Distributions in ssdtools"
 author: "ssdtools Team"
 date: '`r format(Sys.time(), "%Y-%m-%d", tz = "UTC")`'
-bibliography: references.bib
+bibliography: ../references.bib
 mathfont: Courier
 latex_engine: MathJax
 output: rmarkdown::html_vignette

vignettes/images/Figure1.jpg renamed to vignettes/articles/images/Figure1.jpg

@@ -2,7 +2,7 @@
 title: "Model Averaging SSDs"
 author: "ssdtools Team"
 date: '`r format(Sys.time(), "%Y-%m-%d", tz = "UTC")`'
-bibliography: references.bib
+bibliography: ../references.bib
 mathfont: Courier
 latex_engine: MathJax
 output: rmarkdown::html_vignette

vignettes/images/Figure2.jpg renamed to vignettes/articles/images/Figure2.jpg

@@ -0,0 +1,19 @@
+---
+title: "Small Sample Bias in Estimates"
+mathfont: Courier
+latex_engine: MathJax
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Small Sample Bias in Estimates}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+Link to [small-sample-bias.pdf](https://github.com/bcgov/ssdtools/tree/main/vignettes/articles/small-sample-bias.pdf)