diff --git a/.gitignore b/.gitignore index 800d24e..fc42754 100644 --- a/.gitignore +++ b/.gitignore @@ -56,3 +56,4 @@ /.quarto/ +.Rproj.user diff --git a/_quarto.yml b/_quarto.yml index d85bc11..45cff5a 100644 --- a/_quarto.yml +++ b/_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: john.doe@jdct.edu + 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 diff --git a/docs/Reproducible-Publications.docx b/docs/Reproducible-Publications.docx deleted file mode 100644 index 57bf389..0000000 Binary files a/docs/Reproducible-Publications.docx and /dev/null differ diff --git a/docs/Reproducible-Publications.pdf b/docs/Reproducible-Publications.pdf index 6f4777b..b7e2453 100644 Binary files a/docs/Reproducible-Publications.pdf and b/docs/Reproducible-Publications.pdf differ diff --git a/index.qmd b/index.qmd index 5643af2..684e3ef 100644 --- a/index.qmd +++ b/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) +``` \ No newline at end of file diff --git a/qmd/03_results.qmd b/qmd/03_results.qmd index a2e9a6e..8e023fc 100644 --- a/qmd/03_results.qmd +++ b/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. \ No newline at end of file diff --git a/qmd/09_references.qmd b/qmd/09_references.qmd index dfe3366..77ea29a 100644 --- a/qmd/09_references.qmd +++ b/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} :::