In certe-medical-epidemiology/certestyle: A Certe R Package for Applying Certe Organisational Style
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
The letters of the name [TeX] are meant to represent the capital Greek letters tau, epsilon, and chi, as TeX is an abbreviation of τέχνη (ΤΕΧΝΗ technē), Greek for both "art" and "craft", which is also the root word of technical. English speakers often pronounce it /tɛk/, like the first syllable of technical.
Wikipedia about the pronounciation of TeX
This certestyle package comes with a robust and flexible TeX template designed for a variety of documentation needs. This template is an essential tool for creating our departments' high-quality documents. The template has a variety of options that can be set to alter the look and feel.
Initialisation
The YAML header of a Quarto file (.qmd) or R Markdown file (.Rmd) should at least contain the formatting output to be PDF, the PDF engine, and the path to the TeX file:
```{yaml, eval = FALSE}
for Quarto
format:
pdf:
pdf-engine: "xelatex"
template: "/path/to/library/certestyle/rmarkdown/latextemplate/certe.tex"
lang: "nl"
for R Markdown
output:
pdf_document:
latex_engine: "xelatex"
template: "/path/to/library/certestyle/rmarkdown/latextemplate/certe.tex"
lang: "nl"
Note that this snippet is not required on Quarto if [making use of `_quarto.yaml` in a parent folder](https://quarto.org/docs/projects/quarto-projects.html#metadata-merging).
Setting `lang` will make sure that all automated TeX texts are translated, such as "Table of Contents", "List of Figures", "Table", "Figure", etc. This setting accepts an [ISO-639-1 code](https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes) such as `"nl"` for Dutch and `"de"` for German.
## Title Page
The following so-called 'keys' can be set for the title page.
### `title`
The title for the document. If left blank or omitted, there will be **no title page**, thus ignoring `subtitle`, `subtitle2`, `author`, `date` and other title page related fields.
```{yaml, eval = FALSE}
title: "My title" # will add a title page
title: "" # will omit a title page
# will also omit a title page
subtitle / subtitle2
The subtitle(s) for the document. They will appear directly below the title. subtitle2 will appear smaller than subtitle. Either can be used without the other.
```{yaml, eval = FALSE}
subtitle: "My subtitle"
subtitle2: "My smaller extra subtitle"
### `author`
The author name of the document. Can be omitted to leave blank. To automate, this can be `rmarkdown_author()` to read the key `user.{username}.fullname` from [the secrets file](certetoolbox::read_secret()). Be sure to add `certestyle::`, since no packages are loaded yet at the moment the YAML is being processed.
```{yaml, eval = FALSE}
author: "`r certestyle::rmarkdown_author()`"
date
The date of the document. Can be omitted to leave blank. For R Markdown, this can be any text, so use e.g. format2() to format the date into the right format. But for Quarto, this must be in YYYY-MM-DD. You can then set the format using the date-format key. See this Quarto page for date formats.
```{yaml, eval = FALSE}
for Quarto
date: "r Sys.Date()" # R prints Date objects as YYYY-MM-DD, so that's safe
date-format: "D MMMM YYYY"
for R Markdown
date: "r certestyle::format2(Sys.Date(), 'd mmmm yyyy')"
### `identifier`
This will be printed on the bottom left of the title page as a small string. For Certe projects, this should always be `certeprojects::project_identifier()`, which generates the project identifier automatically based on the file name or path:
```{yaml, eval = FALSE}
identifier: "`r certeprojects::project_identifier()`"
titlepage-logo
The title page can contain a logo at the top of 16x7 cm, by setting titlepage-logo to an image or (preferably) a PDF file.
Currently included logos for the title page are:
url <- "https://github.com/certe-medical-epidemiology/certestyle/blob/main/inst/rmarkdown/latextemplate/"
logos <- list.files(file.path(find.package("certestyle"), "rmarkdown", "latextemplate"),
pattern = "[.]pdf$",
include.dirs = TRUE,
recursive = FALSE,
full.names = FALSE)
logos <- sort(logos[!grepl("footer", logos)])
r paste0("* [\u0060", logos, "\u0060](", url, logos, ")", collapse = "\n")
Using rmarkdown_logo(), they can be set without the need to specify the library path.
``{yaml, eval = FALSE}
titlepage-logo: "r certestyle::rmarkdown_logo('certe')`"
or a custom path
titlepage-logo: "/path/to/library/certestyle/rmarkdown/latextemplate/certe.pdf"
For backwards compatibility, `logofront` can also be used instead of `titlepage-logo`.
### Alignment
The alignment of the title page items can be set to `right`, `left`, or `center`. These are the default values:
```{yaml, eval = FALSE}
align-title: "right"
align-subtitle: "right"
align-subtitle2: "right"
align-author-date: "right"
align-identifier: "left"
Figures, Tables, and Table of Contents
Setting the initial height and width of figures, and the table of contents (toc), is dependent on whether you use the TeX template for R Markdown or Quarto.
```{yaml, eval = FALSE}
for Quarto
title: "Some title"
fig-width: 6.5
fig-height: 3.5
toc: true
toc-depth: 2
for R Markdown
title: "Some title"
output:
pdf_document:
# notice the underscore (_), instead of a hyphen (-)
# and placement below output > pdf_document
fig_width: 6.5
fig_height: 3.5
toc: true
toc_depth: 2
Values have to be set in inch, so remember that $cm = inch * 2.54$. The default figure width of 6.5 inch (16.5 cm) is approximately page-wide for A4 portrait.
Additionally, in Quarto, a List of Tables (`lot`) and a List of Figures (`lof`) can be printed. They are similar to a Table of Contents and will print just after the title page, by setting these keys to `true`. Their default is `false`.
```{yaml, eval = FALSE}
# Quarto
title: "Some title"
lot: true # List of Tables
lof: true # List of Figures
Colours
All colours can be set separately, greatly influencing the look and feel of the resulting document. All colours must be set in HTML-codes, with or without #, such as #000000 or 000000 for black. Colour names (such as "black") do not work, unless certestyle::colourpicker() is used.
These are the defaults and what they mean:
``{yaml, eval = FALSE}
colour-titlepage-titlebanner: "#4A647D" # horizontal background banner colour for the title
colour-titlepage-full: "#FFFFFF" # full page colour for title page
colour-verticalbars: "#4A647D" # 1 cm wide vertical bar to left (odd) and right (even) page edges
colour-title: "#FFFFFF" # colour of title
colour-subtitle: "#4A647D" # colour of subtitle
colour-subtitle2:colour-subtitle# exception - this is the same ascolour-subtitle` at default
colour-author-date: "#4A647D" # colour of author name and date on title page
colour-identifier: "#CBCBCB" # colour of project identifier on title page
colour-heading1: "#4A647D" # colour of heading 1
colour-heading2: "#B4527F" # colour of heading 2
colour-heading3: "#4A647D" # colour of heading 3
colour-url: "#B4527F" # colour of for URL's and href, so text and
You can set these using a function as well:
```{yaml, eval = FALSE}
colour-titlepage-full: "`r certestyle::colourpicker('certeroze3')`"
Using colour-main
Furthermore, colour-main can be set as a default for the following fields:
colour-titlepage-titlebannercolour-verticalbarscolour-subtitlecolour-subtitle2colour-author-datecolour-heading1
This means that you can quickly change the primary colours of the template. You can set colour-main and then override some of the colours it sets.
```{yaml, eval = FALSE}
set main colours to certeroze, but set heading 1 to red:
colour-main: "r certestyle::colourpicker('certeroze')"
colour-heading1: "#FF0000" # red
### Colour of Callout Blocks
In Quarto, the so-called [callout blocks](https://quarto.org/docs/authoring/callouts.html) will take colours from headings as follows:
* `callout-note`: same colour as `colour-heading1`
* `callout-caution`: same colour as `colour-heading2`
* `callout-important`: same colour as `colour-heading2`
* `callout-warning`: same colour as `colour-heading2`
* `callout-tip`: same colour as `colour-heading3`
## Fonts
Use `mainfont` for the general font, and `monofont` for syntaxes. The default values are:
```{yaml, eval = FALSE}
mainfont: "Source Sans Pro"
monofont: "Fira Code"
They have to be installed on the system level. Examples of cross-platform fonts (that are available on Windows, macOS, and Linux, without installation) are e.g. 'Verdana' and 'Arial' for mainfont, and 'Courier New' for monofont.
Footer
At the bottom of each page after the title page, you can remove the page numbers:
```{yaml, eval = FALSE}
remove-footer-page-numbers: true
The page numbers will be print in the format `"x of y"` Note that the text `" of "` is language-specific. This text is set in the TeX template and only supports `lang: nl` (which prints `"x van y"`) and `lang: de` (which prints `"x von y"`). It will assume Dutch if `lang` is not set. It will print `"x of y"` in all other cases.
Below the footer text, a PDF file can be placed, e.g. with a small organisational logo. It must be 16x0.7 cm.
```{yaml, eval = FALSE}
footer-logo: "`r certestyle::rmarkdown_logo('footer')`"
To remove the logo:
```{yaml, eval = FALSE}
footer-logo: ""
For backwards compatibility, `logofooter` can also be used instead of `footer-logo`.
## Examples
These examples work in both R Markdown and Quarto. For each example, this was set:
```{yaml, eval = FALSE}
title: "Titel analyse"
subtitle: "Dit is een ondertitel"
subtitle2: "En dit is een nog kleinere ondertitel"
author: "Certe Medische Epidemiologie"
date: "`r Sys.Date()`"
date-format: "D MMMM YYYY"
identifier: "abc123456"
# logo's
titlepage-logo: "`r certestyle::rmarkdown_logo('certe')`"
footer-logo: "`r certestyle::rmarkdown_logo('footer')`"
Example 1: Default
This is the default; no additional formatting has been defined:
knitr::include_graphics("example1-p1.jpg")
knitr::include_graphics("example1-p2.jpg")
Example 2: Colour change
This example sets colour-main to directly influence different elements such as the title page elements, and heading 1:
``{yaml, eval = FALSE}
colour-main: "r certestyle::colourpicker('certeroze')`"
```r
knitr::include_graphics("example2-p1.jpg")
knitr::include_graphics("example2-p2.jpg")
Example 3: Full page colour
This example adds another logo (white Certe letters, aligned to the left) and uses colour-titlepage-full to give the title page a completely new look:
```{yaml, eval = FALSE}
certeroze for main elements
colour-main: "r certestyle::colourpicker('certeroze')"
certeroze2, somewhat lighter than certeroze
colour-titlepage-titlebanner: "r certestyle::colourpicker('certeroze2')"
certeroze3, lighter than certeroze2
colour-titlepage-full: "r certestyle::colourpicker('certeroze3')"
colour-subtitle: "r certestyle::colourpicker('certeroze3')" # this effectively makes text invisible
colour-subtitle2: "r certestyle::colourpicker('certeroze3')" # this effectively makes text invisible
colour-verticalbars: "r certestyle::colourpicker('certeroze3')"
certeroze5, a very bright certeroze variant
colour-author-date: "r certestyle::colourpicker('certeroze5')"
colour-identifier: "r certestyle::colourpicker('certeroze5')"
```r
knitr::include_graphics("example3-p1.jpg")
knitr::include_graphics("example3-p2.jpg")
certe-medical-epidemiology/certestyle documentation built on July 12, 2024, 2:45 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
The letters of the name [TeX] are meant to represent the capital Greek letters tau, epsilon, and chi, as TeX is an abbreviation of τέχνη (ΤΕΧΝΗ technē), Greek for both "art" and "craft", which is also the root word of technical. English speakers often pronounce it /tɛk/, like the first syllable of technical.
Wikipedia about the pronounciation of TeX
This certestyle package comes with a robust and flexible TeX template designed for a variety of documentation needs. This template is an essential tool for creating our departments' high-quality documents. The template has a variety of options that can be set to alter the look and feel.
Initialisation
The YAML header of a Quarto file (.qmd) or R Markdown file (.Rmd) should at least contain the formatting output to be PDF, the PDF engine, and the path to the TeX file:
```{yaml, eval = FALSE}
for Quarto
format: pdf: pdf-engine: "xelatex" template: "/path/to/library/certestyle/rmarkdown/latextemplate/certe.tex" lang: "nl"
for R Markdown
output: pdf_document: latex_engine: "xelatex" template: "/path/to/library/certestyle/rmarkdown/latextemplate/certe.tex" lang: "nl"
Note that this snippet is not required on Quarto if [making use of `_quarto.yaml` in a parent folder](https://quarto.org/docs/projects/quarto-projects.html#metadata-merging).
Setting `lang` will make sure that all automated TeX texts are translated, such as "Table of Contents", "List of Figures", "Table", "Figure", etc. This setting accepts an [ISO-639-1 code](https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes) such as `"nl"` for Dutch and `"de"` for German.
## Title Page
The following so-called 'keys' can be set for the title page.
### `title`
The title for the document. If left blank or omitted, there will be **no title page**, thus ignoring `subtitle`, `subtitle2`, `author`, `date` and other title page related fields.
```{yaml, eval = FALSE}
title: "My title" # will add a title page
title: "" # will omit a title page
# will also omit a title page
subtitle / subtitle2
The subtitle(s) for the document. They will appear directly below the title. subtitle2 will appear smaller than subtitle. Either can be used without the other.
```{yaml, eval = FALSE} subtitle: "My subtitle" subtitle2: "My smaller extra subtitle"
### `author`
The author name of the document. Can be omitted to leave blank. To automate, this can be `rmarkdown_author()` to read the key `user.{username}.fullname` from [the secrets file](certetoolbox::read_secret()). Be sure to add `certestyle::`, since no packages are loaded yet at the moment the YAML is being processed.
```{yaml, eval = FALSE}
author: "`r certestyle::rmarkdown_author()`"
date
The date of the document. Can be omitted to leave blank. For R Markdown, this can be any text, so use e.g. format2() to format the date into the right format. But for Quarto, this must be in YYYY-MM-DD. You can then set the format using the date-format key. See this Quarto page for date formats.
```{yaml, eval = FALSE}
for Quarto
date: "r Sys.Date()" # R prints Date objects as YYYY-MM-DD, so that's safe
date-format: "D MMMM YYYY"
for R Markdown
date: "r certestyle::format2(Sys.Date(), 'd mmmm yyyy')"
### `identifier`
This will be printed on the bottom left of the title page as a small string. For Certe projects, this should always be `certeprojects::project_identifier()`, which generates the project identifier automatically based on the file name or path:
```{yaml, eval = FALSE}
identifier: "`r certeprojects::project_identifier()`"
titlepage-logo
The title page can contain a logo at the top of 16x7 cm, by setting titlepage-logo to an image or (preferably) a PDF file.
Currently included logos for the title page are:
url <- "https://github.com/certe-medical-epidemiology/certestyle/blob/main/inst/rmarkdown/latextemplate/" logos <- list.files(file.path(find.package("certestyle"), "rmarkdown", "latextemplate"), pattern = "[.]pdf$", include.dirs = TRUE, recursive = FALSE, full.names = FALSE) logos <- sort(logos[!grepl("footer", logos)])
r paste0("* [\u0060", logos, "\u0060](", url, logos, ")", collapse = "\n")
Using rmarkdown_logo(), they can be set without the need to specify the library path.
``{yaml, eval = FALSE}
titlepage-logo: "r certestyle::rmarkdown_logo('certe')`"
or a custom path
titlepage-logo: "/path/to/library/certestyle/rmarkdown/latextemplate/certe.pdf"
For backwards compatibility, `logofront` can also be used instead of `titlepage-logo`.
### Alignment
The alignment of the title page items can be set to `right`, `left`, or `center`. These are the default values:
```{yaml, eval = FALSE}
align-title: "right"
align-subtitle: "right"
align-subtitle2: "right"
align-author-date: "right"
align-identifier: "left"
Figures, Tables, and Table of Contents
Setting the initial height and width of figures, and the table of contents (toc), is dependent on whether you use the TeX template for R Markdown or Quarto.
```{yaml, eval = FALSE}
for Quarto
title: "Some title" fig-width: 6.5 fig-height: 3.5 toc: true toc-depth: 2
for R Markdown
title: "Some title" output: pdf_document: # notice the underscore (_), instead of a hyphen (-) # and placement below output > pdf_document fig_width: 6.5 fig_height: 3.5 toc: true toc_depth: 2
Values have to be set in inch, so remember that $cm = inch * 2.54$. The default figure width of 6.5 inch (16.5 cm) is approximately page-wide for A4 portrait.
Additionally, in Quarto, a List of Tables (`lot`) and a List of Figures (`lof`) can be printed. They are similar to a Table of Contents and will print just after the title page, by setting these keys to `true`. Their default is `false`.
```{yaml, eval = FALSE}
# Quarto
title: "Some title"
lot: true # List of Tables
lof: true # List of Figures
Colours
All colours can be set separately, greatly influencing the look and feel of the resulting document. All colours must be set in HTML-codes, with or without #, such as #000000 or 000000 for black. Colour names (such as "black") do not work, unless certestyle::colourpicker() is used.
These are the defaults and what they mean:
``{yaml, eval = FALSE}
colour-titlepage-titlebanner: "#4A647D" # horizontal background banner colour for the title
colour-titlepage-full: "#FFFFFF" # full page colour for title page
colour-verticalbars: "#4A647D" # 1 cm wide vertical bar to left (odd) and right (even) page edges
colour-title: "#FFFFFF" # colour of title
colour-subtitle: "#4A647D" # colour of subtitle
colour-subtitle2:colour-subtitle# exception - this is the same ascolour-subtitle` at default
colour-author-date: "#4A647D" # colour of author name and date on title page
colour-identifier: "#CBCBCB" # colour of project identifier on title page
colour-heading1: "#4A647D" # colour of heading 1
colour-heading2: "#B4527F" # colour of heading 2
colour-heading3: "#4A647D" # colour of heading 3
colour-url: "#B4527F" # colour of for URL's and href, so text and
You can set these using a function as well:
```{yaml, eval = FALSE}
colour-titlepage-full: "`r certestyle::colourpicker('certeroze3')`"
Using colour-main
Furthermore, colour-main can be set as a default for the following fields:
colour-titlepage-titlebannercolour-verticalbarscolour-subtitlecolour-subtitle2colour-author-datecolour-heading1
This means that you can quickly change the primary colours of the template. You can set colour-main and then override some of the colours it sets.
```{yaml, eval = FALSE}
set main colours to certeroze, but set heading 1 to red:
colour-main: "r certestyle::colourpicker('certeroze')"
colour-heading1: "#FF0000" # red
### Colour of Callout Blocks In Quarto, the so-called [callout blocks](https://quarto.org/docs/authoring/callouts.html) will take colours from headings as follows: * `callout-note`: same colour as `colour-heading1` * `callout-caution`: same colour as `colour-heading2` * `callout-important`: same colour as `colour-heading2` * `callout-warning`: same colour as `colour-heading2` * `callout-tip`: same colour as `colour-heading3` ## Fonts Use `mainfont` for the general font, and `monofont` for syntaxes. The default values are: ```{yaml, eval = FALSE} mainfont: "Source Sans Pro" monofont: "Fira Code"
They have to be installed on the system level. Examples of cross-platform fonts (that are available on Windows, macOS, and Linux, without installation) are e.g. 'Verdana' and 'Arial' for mainfont, and 'Courier New' for monofont.
Footer
At the bottom of each page after the title page, you can remove the page numbers:
```{yaml, eval = FALSE} remove-footer-page-numbers: true
The page numbers will be print in the format `"x of y"` Note that the text `" of "` is language-specific. This text is set in the TeX template and only supports `lang: nl` (which prints `"x van y"`) and `lang: de` (which prints `"x von y"`). It will assume Dutch if `lang` is not set. It will print `"x of y"` in all other cases.
Below the footer text, a PDF file can be placed, e.g. with a small organisational logo. It must be 16x0.7 cm.
```{yaml, eval = FALSE}
footer-logo: "`r certestyle::rmarkdown_logo('footer')`"
To remove the logo:
```{yaml, eval = FALSE} footer-logo: ""
For backwards compatibility, `logofooter` can also be used instead of `footer-logo`.
## Examples
These examples work in both R Markdown and Quarto. For each example, this was set:
```{yaml, eval = FALSE}
title: "Titel analyse"
subtitle: "Dit is een ondertitel"
subtitle2: "En dit is een nog kleinere ondertitel"
author: "Certe Medische Epidemiologie"
date: "`r Sys.Date()`"
date-format: "D MMMM YYYY"
identifier: "abc123456"
# logo's
titlepage-logo: "`r certestyle::rmarkdown_logo('certe')`"
footer-logo: "`r certestyle::rmarkdown_logo('footer')`"
Example 1: Default
This is the default; no additional formatting has been defined:
knitr::include_graphics("example1-p1.jpg") knitr::include_graphics("example1-p2.jpg")
Example 2: Colour change
This example sets colour-main to directly influence different elements such as the title page elements, and heading 1:
``{yaml, eval = FALSE}
colour-main: "r certestyle::colourpicker('certeroze')`"
```r
knitr::include_graphics("example2-p1.jpg")
knitr::include_graphics("example2-p2.jpg")
Example 3: Full page colour
This example adds another logo (white Certe letters, aligned to the left) and uses colour-titlepage-full to give the title page a completely new look:
```{yaml, eval = FALSE}
certeroze for main elements
colour-main: "r certestyle::colourpicker('certeroze')"
certeroze2, somewhat lighter than certeroze
colour-titlepage-titlebanner: "r certestyle::colourpicker('certeroze2')"
certeroze3, lighter than certeroze2
colour-titlepage-full: "r certestyle::colourpicker('certeroze3')"
colour-subtitle: "r certestyle::colourpicker('certeroze3')" # this effectively makes text invisible
colour-subtitle2: "r certestyle::colourpicker('certeroze3')" # this effectively makes text invisible
colour-verticalbars: "r certestyle::colourpicker('certeroze3')"
certeroze5, a very bright certeroze variant
colour-author-date: "r certestyle::colourpicker('certeroze5')"
colour-identifier: "r certestyle::colourpicker('certeroze5')"
```r
knitr::include_graphics("example3-p1.jpg")
knitr::include_graphics("example3-p2.jpg")
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