Merge pull request #3 from kapsner/main

.gitignore

@@ -56,3 +56,4 @@
 
 
 /.quarto/
+.Rproj.user

_quarto.yml

@@ -1,45 +1,57 @@
 project:
-  type: book
+  type: default
   output-dir: docs
-
-book:
-  title: "Reproducible Publications"
-
-  # https://quarto.org/docs/journals/authors.html#author-metadata
-  author:
-    - name: Jonathan M. Mang
-      orcid: 0000-0003-0518-4710
-      corresponding: true
-      affiliations:
-        - id: diz
-          name: Medical Center for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany.
-    - name: Lorenz A. Kapsner
-      orcid: 0000-0003-1866-860X
-      affiliations:
-        - ref: diz
-        - id: dr
-          name: Institute of Radiology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany.
-
-  chapters:
+  execute-dir: project
+  render:
     - index.qmd
+output-file: Reproducible-Publications
+
+title: "Reproducible Publications"
+
+# https://quarto.org/docs/journals/authors.html#author-metadata
+author:
+  - John Doe:
+      affiliations: [jdct]
+      correspondence: true
+      email: [email protected]
+      orcid: 0000-1111-2222-3333
+  - Jane Roe:
+      affiliations: [jdct, iot]
+      orcid: 0000-2222-1111-3333
+
+affiliations:
+  - id: jdct
+    name: John Doe Center for Technology, John Doe University, Doetown, Germany.
+  - id: iot
+    name: Institute of Technology, John Doe University, Doetown, Germany.
 
 bibliography: meta/references.bib
 csl: meta/ios-press-books.csl
+
+filters:
+  # watch https://github.com/pandoc/lua-filters/issues/226 for updates on
+  # quarto adjustments of these filters
+  - scholarly-metadata-quarto.lua
+  - author-info-blocks-quarto.lua
 
 format:
- docx:
-  toc: true
- pdf:
-  toc: true
-  latex-engine: xelatex
+  #docx: default
+  pdf:
+    documentclass: article
+    latex-engine: xelatex
+    geometry:
+      - left=25mm
+      - right=25mm
+      - top=25mm
+      - bottom=25mm
 
 
-## https://quarto.org/docs/reference/formats/opml.html#execution
+# https://quarto.org/docs/reference/formats/opml.html#execution
 execute:
+  include: false
   echo: false
   message: false
   warning: false
-  include: false
   error: true
 
 

index.qmd

@@ -1,15 +1,67 @@
-# Manuscript {.unnumbered}
+---
+output: html_document
+editor_options: 
+  chunk_output_type: console
+---
 
 ```{r}
-#| include: false
-
 library(magrittr)
+
+# download lua filters
+download.file(
+  url = "https://raw.githubusercontent.com/kapsner/lua-filters/affiliations_quarto_compatibility/author-info-blocks/author-info-blocks-quarto.lua",
+  destfile = "author-info-blocks-quarto.lua"
+)
+download.file(
+  url = "https://raw.githubusercontent.com/kapsner/lua-filters/affiliations_quarto_compatibility/scholarly-metadata/scholarly-metadata-quarto.lua",
+  destfile = "scholarly-metadata-quarto.lua"
+)
 ```
 
+\newpage
 
 {{< include qmd/00_abstract.qmd >}}
+\newpage
 {{< include qmd/01_introduction.qmd >}}
+\newpage
 {{< include qmd/02_methods.qmd >}}
+\newpage
 {{< include qmd/03_results.qmd >}}
+\newpage
 {{< include qmd/04_discussion.qmd >}}
+\newpage
 {{< include qmd/09_references.qmd >}}
+
+\newpage
+# Tables {.unnumbered}
+
+
+```{r}
+#| tbl-cap: "Data"
+#| label: tbl-data
+#| include: true
+#| column: body-outset
+#| echo: false
+#| warning: false
+iris |>
+  summary() |> 
+  knitr::kable()
+```
+
+\newpage
+# Figures {.unnumbered}
+
+```{r}
+#| layout-ncol: 2
+#| fig-cap: "Data plots."
+#| fig-subcap:
+#|   - "Sepal.Length vs. Sepal.Width."
+#|   - "Petal.Length vs. Petal.Width"
+#| out.width: "98%"
+#| label: fig-data
+#| include: true
+#| column: body-outset
+
+plot(iris$Sepal.Length, iris$Sepal.Width)
+plot(iris$Petal.Length, iris$Petal.Width)
+```

qmd/03_results.qmd

@@ -1,3 +1,7 @@
 # Results
 
 Here it is: A template for reproducible research.
+
+@tbl-data shows a summary of the data.
+
+A dotplot of Sepal.Lentgh and Sepal.Width is shown in @fig-data.

qmd/09_references.qmd

@@ -1,8 +1,6 @@
 # References {.unnumbered}
 
-Quarto will include the references here. 
-The position of the reference-list can therefore be adjusted by moving the
-inclusion of this file within `index.qmd`.
+>Quarto will include the references here. The position of the reference-list can therefore be adjusted by moving the inclusion of this file within `index.qmd`.
 
 ::: {#refs}
 :::