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HTML output formats for RMarkdown documents

R 20.16% HTML 16.47% CSS 51.22% JavaScript 12.15%
rmarkdown rstudio r html-theme html cran material docco

rmdformats's Introduction

rmdformats

CRAN_Status_Badge CRAN Downloads R build status

Note for quarto users: these templates are only suitable for RMarkdown documents. I published one quarto custom format called bookup which is a porting of the robobook template.

This R package provides ready-to-use HTML output formats and templates for RMarkdown documents. The goal is to produce clean documents "out of the box", with or without the RStudio IDE.

Formats gallery

The package provides several HTML output formats. Click on any image to see an HTML output sample.

downcute

Taken from the docute project theme and its adaptation by John Coene. Responsive, with a dynamic table of contents and a dark theme switcher.

downcute example

downcute chaos is a variation created by Zac Garland. It has a slightly different color theme, and defaults to dark mode. To use it, add a downcute_theme: "chaos" option in your YAML preamble.

downcute chaos example

robobook

Adapted from the bookdown theme, with Roboto family fonts. Fully responsive with dynamic table of contents and collapsible navigation.

robobook example

material

Format taken from the Material design theme for Bootstrap 3. Document is split into pages at each <h1> header, and the table of contents allows an animated navigation between these pages (you can use the cards: false preamble parameter to disable the splitting and display all the cards at once).

material example

readthedown

Adapted from the corresponding readtheorg theme of the org-html-themes project, fully responsive with dynamic table of contents and collapsible navigation.

readthedown example

html_clean

Simple and clean template with dynamic table of contents, very similar to the one from the great knitrBootstrap package by Jim Hester.

html_clean example

html_docco

Simple template, no table of contents. CSS heavily inspired from the default one of the docco project.

html_docco example

lockdown

lockdown is an exact copy of the default RMarkdown html_document template, with an added functionality : each time you click on a link to get out, you'll see a friendly reminder to wash your hands and wear a mask. Yes, it is a (bad) attempt at a (bad) joke, sorry !

lockdown example

Features and helpers

Features matrix

Responsive Dynamic TOC Dark mode Thumbnails / Lightbox Code folding Tabsets Bad joke
html_docco x x x x
html_clean x x x x x
readthedown x x x x
material x x x
robobook x x x x x
downcute x x x x x x
lockdown x

Helpers

The package also provides RStudio document templates to easily generate an empty and ready to use rmarkdown file with several configuration directives.

It also provides the pilltabs() helper function, which allows to display a crosstab dynamically. See one of the output samples for a live example.

Installation

You can install the latest stable release from CRAN :

install.packages("rmdformats")

Or the latest development snapshot from GitHub :

install.packages(remotes)  # if necessary
remotes::install_github("juba/rmdformats")

Creating a new document

Just create a new Rmd file and add the following in your YAML preamble :

---
output: rmdformats::<template name>
---

Within RStudio , you can also choose File > New File... > R Markdown..., then select From Template. You should then be able to create a new document from one of the package templates.

Options

Depending on the features provided by the template, you can add the following options to your YAML preamble. Look at the template function help page for a valid list :

  • fig_width : figures width, in inches
  • fig_height : figures height, in inches
  • fig_caption : toggle figure caption rendering
  • highlight : syntax highlighting
  • thumbnails : if TRUE, display content images as thumbnails
  • lightbox : if TRUE, add lightbox effect to content images
  • gallery : if TRUE, add navigation between images when displayed in lightbox
  • use_bookdown : if TRUE, will use bookdown instead of rmarkdown for HTML rendering, thus providing section numbering and cross references.
  • embed_fonts : if TRUE (default), use local files for fonts used in the template instead of links to Google Web fonts. This leads to bigger files but ensures that the fonts are available
  • additional aguments are passed to the base html_document RMarkdown template

Example preamble :

---
title: "My document"
date: "`r Sys.Date()`"
author: John Doe
output:
  rmdformats::downcute:
    self_contained: true
    thumbnails: true
    lightbox: true
    gallery: false
    highlight: tango
---

Credits

  • Magnific popup lightbox plugin
  • The CSS for the html_docco format is heavily inspired from the default one of the docco project.
  • The CSS and JavaScript for readthedown is adapted from the corresponding readtheorg theme of the org-html-themes project, which is itself inspired by the Read the docs Sphinx theme.
  • The CSS and JavaScript for material has been taken from the Material design theme for Bootstrap 3 project and its presentation page.
  • The CSS for robobook is directly derived from the bookdown project template.
  • The CSS for downcute is directly derived from the default theme of the docute project and its adaptation by John Coene for some of its projects documentation.
  • The downcute chaos theme has been created by Zac Garland.
  • JavaScript and HTML code for code folding and tabbed sections are taken from the RStudio's default rmarkdown HTML template.
  • The html_clean styling and features are very similar to the ones from the knitrBootstrap package by Jim Hester.

rmdformats's People

Contributors

gungormetehan avatar juba avatar lovetoken avatar marveluck avatar sciatro avatar thatchersj avatar

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rmdformats's Issues

Compatibility with embedded Shiny applications?

Can I embed a Shiny app in a readthedown template html document? I tried changing the document preamble to resemble what I typically see on an HTML document with Shiny content:

Usual Preamble Chunk-

output: html_document
runtime: shiny

Tried this for readthedown (added the runtime line)-

output:
  rmdformats::readthedown:
    highlight: haddock
runtime: shiny

I get the following error:

Error: formal argument "extra_dependencies" matched by multiple actual arguments

Is there a fundamental incompatibility with the readthedown template and embedding Shiny content, or is there something incorrect about my attempt to enable Shiny content using this template?

Lightbox scales too large for browser window

I would have expected, based on experiences with other (generic) image galleries and lightboxes, that the lightbox of an Rmarkdown plot would be scaled to fully fit my browser window. That is, unfortunately, not the case (see screenshot below), unless I maximize or full-screen the browser window (which I prefer not to do).

It's never been different from the situation below (even after a fresh install of everything; recently got a new company laptop and had to install everything fresh and it still happened), so it must be something very local to my setup or is it perhaps by design (or otherwise unavoidable).

Can I (locally) fix this by including additional CSS or is this a true bug?

image

Using pilltabs with standard htmldocument

When I try to use pilltabs with a standard htmldocument or bookdown, it works, but initially there is no selected tab. I do not want to use one of your special templates, because these do bad things with small inserted png images in tables, stretching to fill the column, That's probably another issue to report separately.

rmdformats::pilltabs(table(iris$Species, cut(iris$Petal.Length, 3)))

material table of content

Hi,

It looks like each card is treated separately now. I used the material example on the repo and I had to click on each item on table of content to move into the next section.

I am using pandoc 2.5 since the 1.19.2.1 gave me problem when knitting.

Thanks!

Check and install package `ProjectTemplate` in your rmarkdown skeleton files?

Hello, when I was trying to organize some rmd templates on CRAN, I came across this package. I like the theme included in this package. Good job!

Also, for all the projecttemplate templates, do you want to write a check & install step for package ProjectTemplate? This package is not declared in the DESCRIPTION (and I also see why you didn't). For people without that package, it will throw an error message on their first attempt.

Width left and right panel readthedown

Hello,
I'm trying to change the width of the right and left pannel using readthedown.
I tried to add a .css file with the following:

But it didn't do the trick.

.main-container { max-width: 1500px !important; }
Is it possible? and if yes, how should I do it?

Many thanks !

Warning about templates

Dear Maintainer,

When I load rmdformats package, I found some warnings about HTML templates.

> library(rmdformats)
Warning messages:
1: In readLines(con) :
  读'/home/wsx/R/x86_64-pc-linux-gnu-library/3.5/rmdformats/rmarkdown/templates/readthedown/template.yaml'时最后一行未遂
2: In readLines(con) :
  读'/home/wsx/R/x86_64-pc-linux-gnu-library/3.5/rmdformats/rmarkdown/templates/html_clean/template.yaml'时最后一行未遂
3: In readLines(con) :
  读'/home/wsx/R/x86_64-pc-linux-gnu-library/3.5/rmdformats/rmarkdown/templates/material/template.yaml'时最后一行未遂
4: In readLines(con) :
  读'/home/wsx/R/x86_64-pc-linux-gnu-library/3.5/rmdformats/rmarkdown/templates/html_docco/template.yaml'时最后一行未遂

The warnings all say readLines functions cannot read the last line of templates. A new line is suggested to insert into these files.

Thanks to your package.

Best,
Shixiang


> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Deepin 15

Matrix products: default
BLAS: /opt/microsoft/ropen/3.5.1/lib64/R/lib/libRblas.so
LAPACK: /opt/microsoft/ropen/3.5.1/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8       
 [4] LC_COLLATE=zh_CN.UTF-8     LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rmdformats_0.3.4     RevoUtils_11.0.1     RevoUtilsMath_11.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       bookdown_0.9     later_0.8.0      digest_0.6.18    mime_0.6        
 [6] R6_2.3.0         xtable_1.8-3     magrittr_1.5     evaluate_0.13    highr_0.7       
[11] rstudioapi_0.9.0 promises_1.0.1   miniUI_0.1.1.1   rmarkdown_1.11   tools_3.5.1     
[16] questionr_0.7.0  shiny_1.2.0      httpuv_1.4.5.1   xfun_0.4         yaml_2.2.0      
[21] compiler_3.5.1   htmltools_0.3.6  knitr_1.21     

Fluid images

Thank you for the great templates! Is there a way to make the figures fluid - resize with the window? I am setting fig_width: 9, which causes the image to "bleed" off the column when the browser is resized.

Add some demo contents to your templates?

Hello, as I said in the last issue, I like the styles of this package. I'm also wondering if you can add some functionality demonstration contents to those skeleton files (like what they have done in the rstudio/tufte package)?

Add Github icon

Please add functionality for a Github icon to link to the Github repository for the code just like in readthedocs

YAML templates missing blank lines at end of file?

It appears as though the YAML templates are missing a blank line at the end of the file. So R Studio users are getting the following: incomplete final line found on '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmdformats/rmarkdown/templates/readthedown/template.yaml

It looks like this happens with html_docco, material and html_clean's template.yaml files as well.

Error in template.yaml files

rmdformats template.yaml issue

The material and readthedown formats were throwing the following error:

Error in (function (file, template, package = NULL, create_dir = "default",  : 
  template.yaml must contain name and description fields

The fix

Navigate to the template.yaml file found here (on my Mac): Macintosh HD⁩/Library⁩/Frameworks⁩/R.framework⁩/Versions⁩/3.5⁩/Resources⁩/library⁩/rmdformats⁩/rmarkdown⁩/templates⁩/material⁩/template.yaml

And add the following text:

name: HTML material template
description: HTML material template

After selecting R Markdown > From Template > HTML Material or HTML readthedown, name the file, and select the location.

This produces the following yaml header (for material format)

---
title: "html_material"
date: "`r Sys.Date()`"
output:
  rmdformats::material:
    highlight: kate
---

incomplete final line with CRAN version - works with GitHub

Hi

I am getting the following warnings when having the CRAN version installed, but it works with the GitHub version.

Thanks,

Rainer

Warning messages:
1: In readLines(con) :
  incomplete final line found on '/usr/local/lib/R/3.5/site-library/rmdformats/rmarkdown/templates/readthedown/template.yaml'
2: In readLines(con) :
  incomplete final line found on '/usr/local/lib/R/3.5/site-library/rmdformats/rmarkdown/templates/html_docco/template.yaml'
3: In readLines(con) :
  incomplete final line found on '/usr/local/lib/R/3.5/site-library/rmdformats/rmarkdown/templates/material/template.yaml'
4: In readLines(con) :
  incomplete final line found on '/usr/local/lib/R/3.5/site-library/rmdformats/rmarkdown/templates/html_clean/template.yaml'

Enable MathJax Functionality

Custom R Markdown templates (like rmdformats) do not work with MathJax when self_contained: true. A workaround making it possible to enable MathJax is described in rstudio/rmarkdown#727.

I already implemented in another custom R Markdown project but did not look closer in your source code. Thoughts?

Do not split into pages in material

Is it possible to add an option in the material format so pages are not split at each <h1> and all cards appear in one page like in html_clean?

Bad xtable formatting in material

Issue reported by @holtzy :

---
title: "test table"
output:
  rmdformats::readthedown:
    highlight: kate
  html_document:
    toc: yes
---

# Partie 1
here is some code

```{r}
data=head(iris)
```

```{r my_table1, results='asis' , echo=FALSE}
library(xtable)
print(xtable(data), type = "html", include.rownames = F , comment=FALSE)
```

readthedown width: Auto-expand for wide content?

I really like the readthedown template, but I'm running into the issue where DT::datatables keep overflowing to the right. I tried digging into the HTML/CSS, but I have basically no idea what I'm doing or what I should even be looking for, but essentially I'm looking for a way to make the content-areay wider.
Besides the table issue, I feel that the current width is a little narrow anyway.

Would it be possible to make the width of the content area be adjustable through the YAML front matter? Or make it "smart" about its width, to accommodate any wide tables?

Lightbox text unusable with smaller images

When you click on the image in #26, the text looks bad in the lightbox. Maybe give lightbox caption a minimal width? I see the point that captions are probably never useful with such small images

material design error

When I create a new Rmarkdown from template (HTML material design template), I get an error when I press knit. The YAML is this:

---
title: ""
date: "`r Sys.Date()`"
output:
  rmdformats::material:
    highlight: kate
---

The error:

pandoc.exe: Could not fetch https://fonts.googleapis.com/css?family=Roboto:300,400,500,700
TlsExceptionHostPort (HandshakeFailed (Error_Misc "user error (unexpected type received. expecting handshake and got: Alert [(AlertLevel_Fatal,HandshakeFailure)])")) "fonts.googleapis.com" 443
Error: pandoc document conversion failed with error 67

My sessionInfo():

R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252   
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19     rstudioapi_0.8   bindr_0.1.1      knitr_1.20      
 [5] magrittr_1.5     tidyselect_0.2.4 xtable_1.8-3     R6_2.3.0        
 [9] rlang_0.2.2      stringr_1.3.1    highr_0.7        dplyr_0.7.6     
[13] tools_3.5.0      xfun_0.3         miniUI_0.1.1.1   htmltools_0.3.6 
[17] assertthat_0.2.0 yaml_2.2.0       rprojroot_1.3-2  digest_0.6.17   
[21] tibble_1.4.2     crayon_1.3.4     bookdown_0.7     bindrcpp_0.2.2  
[25] shiny_1.1.0      purrr_0.2.5      questionr_0.6.3  later_0.7.5     
[29] promises_1.0.1   glue_1.3.0       evaluate_0.11    mime_0.6        
[33] rmarkdown_1.8    stringi_1.1.7    pillar_1.3.0     compiler_3.5.0  
[37] rmdformats_0.3.3 backports_1.1.2  httpuv_1.4.5     pkgconfig_2.0.2 

readthedown: dropdown don't work

A dropdown menu {.tabset .tabset-dropdown}

Code to reproduce

```{r, result = 'asis'}
for(i in 1:10){
cat("\n \n")
  cat(paste("##", "test", i))
  cat("\n \n")
  plot(i:10)
  cat("\n \n")
}

caption position of pilltabs in readthedown

When I use

data(airquality)
tab <- table(airquality$Month, airquality$Ozone > 25)
pilltabs(tab)

in a fresh readthedown document, I get an ugly positioning of the caption:

2016-03-21 21_05_43-mozilla firefox

Version:
2016-02-26

Add rstudio's code_folding: hide

Would be very usefulo to have code_folding as a generic argument (like here), be it with rstudio's templates or with yours.
In particular, I feel like it would really fit well with readthedown for a tutorial.

Pandoc can't find tabsets.js

Hey,

I'm having an issue with the rmdformats templates where pandoc can't find all the related files if self_contained: yes. self_contained: no stops the problem, but I want my files to be self-contained, so it's not very helpful. The issue also doesn't affect my colleagues, so it's probably something I've configured incorrectly (it turned out my colleague was still on rmdformats 0.2 and I had 0.3. With 0.3 or the master branch from github, it was broken for both of us, see below), but I can't work out what so I was hoping that perhaps someone here can help. This is the full error message just trying to knit the default material template:

  |................................                                 |  50%
   inline R code fragments

  |.................................................................| 100%
label: knitr_init (with options) 
List of 2
 $ echo : logi FALSE
 $ cache: logi FALSE



processing file: testing.rmd

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS testing.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output testing.html --smart --email-obfuscation none --self-contained --mathjax --variable "mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:false" --standalone --section-divs --table-of-contents --toc-depth 1 --template "C:\Users\mstanley\Documents\R\win-library\3.3\rmdformats\templates\material\material.html" --highlight-style kate --variable "theme:bootstrap" --include-in-header "C:\Users\mstanley\AppData\Local\Temp\RtmpeeCmZv\rmarkdown-str1bdc103554f2.html" 
output file: testing.knit.md

pandoc.exe: Could not fetch /tabsets.js
/tabsets.js: openBinaryFile: does not exist (No such file or directory)
Error: pandoc document conversion failed with error 67
In addition: Warning messages:
1: MathJax doesn't work with self_contained when not using the rmarkdown "default" template. 
2: running command '"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS testing.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output testing.html --smart --email-obfuscation none --self-contained --mathjax --variable "mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:false" --standalone --section-divs --table-of-contents --toc-depth 1 --template "C:\Users\mstanley\Documents\R\win-library\3.3\rmdformats\templates\material\material.html" --highlight-style kate --variable "theme:bootstrap" --include-in-header "C:\Users\mstanley\AppData\Local\Temp\RtmpeeCmZv\rmarkdown-str1bdc103554f2.html"' had status 67 
Execution halted

I should add that I'm behind a proxy that requires custom Certificate Authorities to be added to the certificate store of anything that's connecting to the internet. I haven't identified where pandoc keeps its CA certs yet so when pandoc is trying to get https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML, it will fail. I tried explicitly setting mathjax: "http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" as an option under rmdformats::material: in the yaml header of my rmd file and that didn't solve the issue, so this might be a red herring, and the error message refers to tabsets.js anyway.

---
title: ""
date: "`r Sys.Date()`"
output:
  rmdformats::material:
    highlight: kate
    mathjax: "http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
---

Hide code in readthedown

I really like the readthedown template and thank the author for this nice library.
However, it looks like the option allowing to hide code by default does not work.

This piece of code works with base rmd:

---
title: "test hide code"
output:
  html_document:
    code_folding: hide
---
here is some code
```{r }
1+1
```

But the code is not hidden anymore if we use the template:

---
title: "test hide code"
output:
  rmdformats::readthedown:
    highlight: kate
  html_document:
    code_folding: hide
---

here is some code

```{r }
1+1
```

Thanks for your help!

pandoc: Could not determine mime type Error

Hi,

The following test Rmd is causing an error in pandoc on my linux box (pandoc version 1.12 knitr 1.14 rmarkdown 1.0 rmdformats 0.3).


---
title: "Test Report"
output:
  rmdformats::html_docco:
    self_contained: true

---

This is a Test

pandoc: Could not determine mime type for `/usr/lib64/R/library/rmdformats/templates/bootstrap-3.3.6/css/../fonts/glyphicons-halflings-regular.woff2'

however, if I turned self_contained to false, pandoc renders ok, but it lose the purpose of embedding object in rmd file.

Thanks.

[Question] How do I plug in an unevaluated header string in a loop?

Hi, I was trying to utilize the readthedown theme to layout my report.
However, the h1() tag, which should be equivalent to # after evaluation, was not pick up by the theme to generate tab on the TOC menu. Is there any workaround here? My minimal example below, I was expecting 'p1' 'p2' to show up on the TOC menu.


---
title: "Untitled"
output: 
  rmdformats::readthedown:
    self_contained: true
    highlight: tango  

---

{r message=FALSE,echo=FALSE,warning=FALSE}
library(plotly)
library(htmltools)

d <- diamonds[sample(nrow(diamonds), 1000), ]
p1 <- plot_ly(d, x = ~carat, y = ~price, mode = "markers", color = ~carat)
p2 <- plot_ly(d, x = ~price,y = ~carat,  mode = "markers", color = ~carat)
ls <- list(list(comment = 'p1',viz = p1),
           list(comment = 'p2',viz = p2)
)

b <- lapply(ls,function(obj){
  tags$div(h1(paste0('Header: ',obj$comment)),
           obj$viz,
           hr()
  )
})
htmltools::tagList(b)

Compatibility with Rmd-websites

I was playing around with the Rmarkdown websites format, and I was hoping to use readthedown as a page layout, but unfortunately this goes wrong in all sorts of ways.

Of course I didn't expect this to work out of the box, but I think it would be a very nice addition.

My simple experimental site can be viewed here

Is there a way to turn off the extra js codes?

I have only used docco. There are extra javascript codes added after the content. One is to add class and behavior to img. Another is for MathJax. I am wondering can this be turned off? Rightnow I just manually remove them after the HTML files are generated.

Thanks!

Makefile generated by create.doc() overrides html settings inside Rmd document

Hi,

I have the following preamble in an Rmarkdown document:

---
title: "Heavy Metal Exposure of Muskrats"
author: "Gabriel A. Devenyi"
date: "`r Sys.Date()`"
output:
  rmdformats::html_clean:
    fig_width: 6.5
    fig_height: 4.875
    highlight: kate
    thumbnails: true
    lightbox: true
    gallery: true
---

I get a properly themed html_clean document with lightbox popups and thumbnails, however the lightbox popups do not have the "gallery" navigation interface.

# headers with . not behaving properly

In the material theme, any <h1> header (# in markdown) with a period in the title doesn't display. Having a period in the title of the # headers has a different symptom in the readthedown template: Anchors don't form properly.

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