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Short pdf report extension for quarto (#11)
* Test to see push to which branch * Test to see push to which branch * Add in the pdf short report format * Table float option and move all include-in-head to template * Add in the blah ref * Add in the float option for figure * Move the yaml block config into extension * Fix my typo * Turn on the makefile for short report * Change the format to match with the extension * Rename to pdf-report to match with Makefile * Change the "-" in the format to "+" to enable quarto to render * Move to the correct location * Update the file path name
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -3,52 +3,19 @@ | |
| title: "`r paste('Progress report for project', params[['project-number']])`" | ||
| subtitle: "Subtitle here" | ||
| params: | ||
| uni: CU | ||
| pri_bio: Your.Name | ||
| project-number: ABC1234-567XYZ | ||
| author: | ||
| - Author 1 | ||
| - Author 2 | ||
| date: "`r format(Sys.time(), '%d %B, %Y')`" | ||
| email: [email protected] | ||
| version-number: 1.0.0 | ||
|
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| # Style options (Page/font size, Table of Contents, Section numbers, ..) | ||
| fontsize: 12pt | ||
| papersize: a4 | ||
| toc: no | ||
| number-sections: no | ||
| sans-serif: yes | ||
| links-as-footnotes: no | ||
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| # Bibliography options | ||
| bibliography: references.bib | ||
| csl: assets/biometrics.csl | ||
| link-citations: true | ||
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| # LaTeX pdflatex options | ||
| header-includes: | ||
| - \usepackage{lipsum} | ||
| output: | ||
| bookdown::pdf_document2: | ||
| keep_tex: yes | ||
| latex_engine: pdflatex | ||
| template: assets/AAGI_markdown.tex | ||
| format: | ||
| aagi-pdf+short+report: default | ||
| --- | ||
|
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||
| ```{r} | ||
| #| include: false | ||
| library(rmarkdown) | ||
| knitr::opts_chunk$set( | ||
| fig.path = "figure/Rplots-", | ||
| fig.align = "center", | ||
| fig.show = "hold", | ||
| comment = NA, | ||
| background = "white", | ||
| highlight = FALSE, | ||
| size = "small", | ||
| prompt = TRUE | ||
| ) | ||
| # library(rmarkdown) | ||
| # This is probably necessary on Linux (with Proxima Nova and Cairo | ||
| # installed). We may need something else on Mac. | ||
|
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@@ -85,6 +52,30 @@ library(AAGIThemes) | |
| library(AAGIPalettes) | ||
| ``` | ||
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| ```{r} | ||
| #| include: false | ||
| #| label: config-for-title | ||
| if(params$uni == "CU"){ | ||
| project_lead = "Curtin University -- Prof Mark Gibberd, Dr Julia Easton, Prof Adam Sparks" | ||
| email = "[email protected]" | ||
| } else if(params$uni == "UA"){ | ||
| project_lead = "University of Adelaide -- Dr Julian Taylor, Dr Olena Kravchuck" | ||
| email = paste(params$pri_bio, "adelaide.edu.au", sep = "") | ||
| } else { | ||
| project_lead = "University of Queensland -- Prof Scott Chapman, Emertius Prof Kaye Basford" | ||
| email = paste(params$pri_bio, "@uq.edu.au", sep = "") | ||
| } | ||
| ``` | ||
|
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| --- | ||
| author: | ||
| - "`r params$pri_bio`" | ||
| - Author 2 | ||
| - "Project Lead: `r project_lead`" | ||
| email: "`r email`" | ||
| --- | ||
|
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| # Section 1 | ||
|
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| Report text goes here. This template is designed for smaller ("one-page") AAGI | ||
|
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@@ -93,11 +84,10 @@ reports. The AAGI logo and partners footer appear only on this first page. | |
| You can colour text/tables/etc using the various AAGI palette colours. Use | ||
| `\textcolor{aagiteal}{...}` for \textcolor{aagiteal}{AAGI Teal}, or | ||
| `\textcolor{aagibrightgreen}{...}` for | ||
| \textcolor{aagibrightgreen}{AAGI Bright Green}, for instance. Table | ||
| \@ref(tab:aagipalette) shows the standard palette colours available for use. | ||
| \textcolor{aagibrightgreen}{AAGI Bright Green}, for instance. @tbl-aagipalette shows the standard palette colours available for use. | ||
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| \begin{table}[h] | ||
| \caption{\label{tab:aagipalette}The AAGI palette colours.} | ||
| ::: {#tbl-aagipalette} | ||
| ```{=tex} | ||
| \centering | ||
| \begin{tabular}{|c | c | c | c |} | ||
| \hline | ||
|
|
@@ -111,8 +101,13 @@ You can colour text/tables/etc using the various AAGI palette colours. Use | |
| \cellcolor{aagiblack}\color{white}\texttt{aagiblack} & % | ||
| \cellcolor{aagigrey}\texttt{aagigrey} \\ | ||
| \hline | ||
| \end{tabular} | ||
| \end{table} | ||
| \end{tabular} | ||
| ``` | ||
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| The AAGI palette colours. | ||
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| ::: | ||
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| ## This is a subsection heading | ||
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@@ -128,7 +123,10 @@ this .Rmd file (but feel free to change the title to whatever you like). | |
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| Example R code, using the `AAGIThemes` package to produce | ||
| Figure \@ref(fig:example1). | ||
| ```{r example1, fig.cap="Here is a plot.", fig.pos="h", fig.height=3} | ||
| ```{r} | ||
| #| label: fig-example1 | ||
| #| fig-cap: "Here is a plot." | ||
| #| fig-height: 3 | ||
| plot_aagi(pressure) | ||
| ``` | ||
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