Infra update

.gitignore

@@ -13,4 +13,3 @@ _freeze/
 *_files/
 /cache/
 /data/
-model-ar1

Makefile

@@ -0,0 +1,15 @@
+all: renv docs
+
+renv: renv.lock
+	Rscript -e "renv::restore()"
+
+docs: index.qmd
+	quarto render
+
+clean:
+	rm -rf *.pdf *.typ *.png *_cache/ *_files/ docs/
+
+clean-hard:
+	rm -rf *.pdf *.typ *.png *_cache/ *_files/ docs/ cache/
+
+.PHONY: all clean clean-hard

README.md

@@ -1,43 +1,32 @@
 # Introduction to latent means models in R
 
 
-Repository for our manuscript discussing an
-[R](https://cran.r-project.org/) and
-[brms](https://cran.r-project.org/web/packages/brms/) implementation of
-latent mean centering in multilevel models of longitudinal psychological
-data.
+Repository for our manuscript discussing an [R](https://cran.r-project.org/) and [brms](https://cran.r-project.org/web/packages/brms/) implementation of latent mean centering in multilevel models of longitudinal psychological data.
 
-- Repo on GitHub: <https://github.com/mvuorre/latent-mean-centering-ms>
+- Repo on GitHub: <https://github.com/mvuorre/funky-firefly>
 - Archived repo: tbd
 - Online: tbd
 - preprint: tbd
 
 ## Reproduce
 
-Everything is coded in [R](https://cran.r-project.org/) and bunched
-together as a [Quarto](https://quarto.org/) website. To reproduce, clone
-the repo and render the Quarto documents:
+To reproduce, download our materials, restore the R environment (renv) and knit `ms.Rmd`.
+
+In terminal:
 
 ``` bash
 # Download materials
-git clone https://github.com/mvuorre/latent-mean-centering-ms.git
-cd latent-mean-centering-ms
+git clone https://github.com/mvuorre/funky-firefly.git
 
-# Set up R environment
-Rscript -e 'renv::restore(prompt = FALSE)'
+# Enter directory
+cd funky-firefly
 
-# Modify environment variables in .Renviron.example & rename it to .Renviron
+# (Optional) modify .Renviron.example & rename it to .Renviron
 
-# Run code and render outputs
-quarto render
+# Run code and produce outputs
+make
 ```
 
-Once the computations are finished (this will take a long time depending
-on your computer) the rendered documents are in `docs/`.
-
 ## Contribute
 
-Contributions preferably via pull requests. You can also grab the
-rendered manuscript (Word, PDF) from the latest
-[release](https://github.com/mvuorre/latent-mean-centering-ms/releases)
-for comments & edits.
+Contributions preferably via pull requests. You can also grab the rendered manuscript (Word, PDF) from the latest [release](https://github.com/mvuorre/latent-mean-centering-ms/releases) for comments & edits.

_extensions/mvuorre/preprint/_extension.yml

@@ -0,0 +1,14 @@
+title: Preprint
+author: Matti Vuorre
+version: 0.9.0
+quarto-required: ">=1.5.47"
+contributes:
+  formats:
+    typst:
+      template-partials:
+        - typst-template.typ
+        - typst-show.typ
+      format-resources:
+        - '*.svg'
+    docx: 
+      reference-doc: preprint.docx

_extensions/mvuorre/preprint/typst-show.typ

@@ -0,0 +1,108 @@
+#show: doc => preprint(
+$if(title)$
+  title: [$title$],
+$endif$
+$if(running-head)$
+  running-head: [$running-head$],
+$endif$
+$if(by-author)$
+  authors: (
+$for(by-author)$
+$if(it.name.literal)$
+    ( name: [$it.name.literal$],
+      affiliation: [$for(it.affiliations)$$it.id$$sep$, $endfor$],
+      $if(it.orcid)$orcid: "https://orcid.org/$it.orcid$",$endif$
+      $if(it.email)$email: [$it.email$]$endif$),
+$endif$
+$endfor$
+    ),
+$endif$
+$if(affiliations)$
+  affiliations: (
+    $for(affiliations)$(
+      id: "$it.id$",
+      name: "$it.name$",
+      $if(it.department)$department: "$it.department$"$endif$
+    ),
+    $endfor$
+  ),
+$endif$
+$if(date)$
+  date: [$date$],
+$endif$
+$if(leading)$
+  leading: $leading$,
+$endif$
+$if(branding)$
+  branding: "$branding$",
+$endif$
+$if(spacing)$
+  spacing: $spacing$,
+$endif$
+$if(linkcolor)$
+  linkcolor: $linkcolor$,
+$endif$
+$if(citation)$
+  citation: (
+    type: "$citation.type$",
+    container-title: "$citation.container-title$",
+    doi: "$citation.doi$",
+    url: "$citation.url$"
+  ),
+$endif$
+$if(authornote)$
+  authornote: [$authornote$],
+$endif$
+$if(lang)$
+  lang: "$lang$",
+$endif$
+$if(region)$
+  region: "$region$",
+$endif$
+$if(abstract)$
+  abstract: [$abstract$],
+$endif$
+$if(keywords)$
+  keywords: [$for(keywords)$$it$$sep$, $endfor$],
+$endif$
+$if(margin)$
+  margin: ($for(margin/pairs)$$margin.key$: $margin.value$,$endfor$),
+$endif$
+$if(papersize)$
+  paper: "$papersize$",
+$endif$
+$if(mainfont)$
+  font: ("$mainfont$",),
+$endif$
+$if(fontsize)$
+  fontsize: $fontsize$,
+$endif$
+$if(section-numbering)$
+  section-numbering: "$section-numbering$",
+$endif$
+$if(toc)$
+  toc: $toc$,
+$endif$
+$if(toc_depth)$
+  toc_depth: $toc_depth$,
+$endif$
+$if(toc_title)$
+  toc_title: "$toc_title$",
+$endif$
+$if(toc_indent)$
+  toc_indent: "$toc_indent$",
+$endif$
+$if(columns)$
+  cols: $columns$,
+$endif$
+$if(col-gutter)$
+  col-gutter: $col-gutter$,
+$endif$
+$if(bibliography-style)$
+  bibliography-style: [$bibliography-style$],
+$endif$
+$if(bibliography-title)$
+  bibliography-title: [$bibliography-title$],
+$endif$
+  doc,
+)