I'm actually using xaringan, but it uses reveal.js, so it should be the same.
I have a slide which prints bibliography using RefManageR, and I'd like to use as many slides as needed:
---
```
{r results = "asis", echo = FALSE}
PrintBibliography(bib, .opts = list(check.entries = FALSE, sorting = "ynt"))
```
---
I guess I'm looking for some type of allowframebreaks, but I couldn't manage to find one.
Xaringan uses remark.js, not reveal.
Related
In Quarto, I'd like to change the default behavior of a single callout block type so that it will
always automatically have the same caption (e.g. "Additional Resources")
always be folded (collapse="true")
Let's say I want this for the tip callout block type while the others (note, warning, caution, and important) should not be affected.
In other words, I want the behavior/output of this:
:::{.callout-tip collapse="true"}
## Additional Resources
- Resource 1
- Resource 2
:::
by only having to write this:
:::{.callout-tip}
- Resource 1
- Resource 2
:::
Update:
I have actually converted the following lua filter into a quarto filter extension collapse-callout, which allows specifying default options for specific callout blocks more easily. See the github readme for detailed instructions on installation and usage.
As #stefan mentioned, you can use pandoc Lua filter to do this more neatly.
quarto_doc.qmd
---
title: "Callout Tip"
format: html
filters:
- custom-callout.lua
---
## Resources
:::{.custom-callout-tip}
- Resource 1
- Resource 2
:::
## More Resources
:::{.custom-callout-tip}
- Resource 3
- Resource 4
:::
custom-callout.lua
local h2 = pandoc.Header(2, "Additional Resources")
function Div(el)
if quarto.doc.isFormat("html") then
if el.classes:includes('custom-callout-tip') then
local content = el.content
table.insert(content, 1, h2)
return pandoc.Div(
content,
{class="callout-tip", collapse='true'}
)
end
end
end
Just make sure that quarto_doc.qmd and custom-callout.lua files are in the same directory (i.e. folder).
After a look at the docs and based on my experience with customizing Rmarkdown I would guess that this requires to create a custom template and/or the use of pandoc Lua filters.
A more lightweight approach I used in the past would be to use a small custom function to add the code for your custom callout block to your Rmd or Qmd. One drawback is that this requires a code chunk. However, to make your life a bit easier you could e.g. create a RStudio snippet to add a code chunk template to your document.
---
title: "Custom Callout"
format: html
---
```{r}
my_call_out <- function(...) {
cat(":::{.callout-tip collapse='true'}\n")
cat("## Additional Resources\n")
cat(paste0("- ", ..., collapse = "\n\n"))
cat("\n:::\n")
}
```
```{r results="asis"}
my_call_out(paste("Resource", 1:2))
```
Blah blah
```{r results="asis"}
my_call_out("Resource 3", "Resource 4")
```
Blah blah
I try to generate multiple reports (1 per group) with rmarkdown::render(), but it produces no section numbers.
I use the following file-structure for this in case you want to reproduce the sample (I tried to simplify each file and use only necessary code to reproduce the error):
*) groups.R: defines groups and subgroups in a nested list (all groups stored in a list and each group is a list itself)
groups <- list(
list(c("subgroup1","subgroup2"),"maingroup1"),
list(c("subgroup3","subgroup4"),"maingroup2")
)
*) main.Rmd: template for the reports
---
output:
pdf_document:
number_sections: true
classoption: a4paper
geometry: left=2cm,right=1cm,top=1.5cm,bottom=1cm,includeheadfoot
fontfamily: helvet
fontsize: 11pt
lang: en
header-includes:
- \usepackage{lastpage}
- \usepackage{fancyhdr}
- \pagestyle{fancy}
- \fancyhf{}
- \fancyhead[R]{\fontsize{9}{11} \selectfont \leftmark}
- \fancyhead[L]{\fontsize{9}{11} \selectfont Special report xxx}
- \fancyfoot[R]{\fontsize{9}{0} \selectfont Page \thepage\ of
\pageref{LastPage}}
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(echo =
FALSE,comment=NA,warning=FALSE,message=FALSE)
```
\thispagestyle{empty}
\tableofcontents
\newpage
\setcounter{page}{1}
# Introduction
Some text...
```{r results="asis"}
source("graphics.R")
```
*) graphics.R: generates graphics for each subgroup (sections/section numbers are produced with cat() for each subgroup)
load("actgroup.RData")
source("template_graphics.R")
for (g in 1:length(act.group[[1]][[1]])) {
subgroup.name <- act.group[[1]][[1]][g]
cat("\\clearpage")
cat("\n# ",subgroup.name, "\n")
template_graphics(cars)
cat("\n\n")
cat("\\clearpage")
template_graphics(iris)
cat("\n\n")
cat("\\clearpage")
template_graphics(airquality)
cat("\n\n")
cat("\\clearpage")
cat("\n")
}
*) template_graphics.R: template for plotting
template_graphics <- function(data) {
plot(data)
}
*) loop.R: used for generating all reports as PDF - 1 per group
setwd("YOUR DIRECTORY HERE")
library(rmarkdown)
source("groups.R")
for(i in 1:length(groups)) {
act.group = list(groups[[i]])
save(act.group,file="actgroup.RData")
rmarkdown::render("main.Rmd",
output_format=pdf_document(),
output_file=paste0("Special Report ",act.group[[1]][[2]],".pdf"),
output_dir="~/Reports")
}
The problem is, that the final documents do not show the section numbers. When I knit manually in main.Rmd (pressing knit-Button), the section numbers are printed.
Version rmarkdown::render
Version knit-Button
I thought that pressing the knit-Button also starts the rendering-process with rmarkdown::render()? So it's surprising that the reports are not identical?
In advance I installed tinytex::install_tinytex(). The used latex-packages in main.Rmd were automatically installed during the first time rendering.
I am not sure what the problem is. I use R 4.1.0 and RStudio 2022.02.2.
Thanks for your help!!
The behaviour of pdf_document() as the output-format in rmarkdown::render caused the missing section-numbers.
In my YAML-header in main.Rmd I chose to keep the section numbers with number_sections: true. If this should also be rendered when using rmarkdown::render, it has to be an argument in the function:
pdf_document(number_sections=TRUE)
The code of loop.R produces now pdfs with section numbers:
library(rmarkdown)
source("groups.R")
for(i in 1:length(groups)) {
act.group = list(groups[[i]])
save(act.group,file="actgroup.RData")
rmarkdown::render("main.Rmd",
output_format=pdf_document(number_sections=TRUE),
output_file=paste0("Special Report ",act.group[[1]][[2]],".pdf"),
output_dir="~/Reports")
}
More information on pdf_document() can be found here:
https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html
Alternatively, fill in just a text-reference as output-format: output_format="pdf_document". When set like this, the options of the YAML-Header are not overwritten and the numbers are also included.
When I knit the following RMarkdown document:
title: "Reprex"
author: "Jeremy Colman"
date: "17/07/2018"
output:
html_document: default
pdf_document: default
word_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{stan, output.var='priors', eval = FALSE, tidy = FALSE}
parameters {
real<lower = 0> qtilde1;
}
model {
qtilde1 ~ gamma(38.9, 0.67);
}
```
The Stan code chunk is rendered as ordinary text, including the three reverse single quotes and word stan from the chunk header. I cannot show that in this post because stackoverflow tells me, correctly but unhelpfully, "Your post appears to contain code that is not properly formatted as code". That sums up my problem!
Code chunks in R are rendered correctly.
Your
```{stan output.var='priors', eval = FALSE, tidy = FALSE}
needs to be flush-left, but you have a leading space before the ```
I have a bookdown document that cites other documents using a bibtex bibliography file. It appears to no process at all, since the output (both gitbook format and pdf) don't translate the actual citation to a reference. The output always copies the plain text of the citation, not the actual reference, like this:
Here's a minimal reproducing example, which I build using:
Rscript -e 'bookdown::render_book("index.Rmd", "bookdown::gitbook")'
index.Rmd:
---
title: "test"
site: "bookdown::bookdown_site"
documentclass: book
bibliography: test.bib
biblio-style: apalike
link-citations: true
# toc: yes
# toc_depth: 2
---
# Introduction {#ch:intro}
Conference publication takes the lead role in describing innovative research,
while journals are often delegated to archival purposes [#vrettas15:conferences].
```{r echo=FALSE}
sessionInfo()
```
test:bib:
#article{vrettas15:conferences,
title = {Conferences versus journals in computer science},
author = {Vrettas, George and Sanderson, Mark},
journal = {Journal of the Association for Information Science and Technology},
volume = 66,
number = 12,
pages = {2674--2684},
year = 2015,
publisher = {Wiley Online Library}
}
_bookdown.yml:
rmd_files: [
"index.Rmd",
]
new_session: no
bookdown::gitbook:
split_bib: no
It turns out to be due to the too low version of Pandoc. A version 1.19.x or higher should fix the problem.
I am writing a Rmarkdown document about a package called SparseTSCGM and have trouble suppressing messages generated by functions in this package. The messages I'm referring to can be generated by the following code:
if(!require(SparseTSCGM)) install.packages('SparseTSCGM')
library(SparseTSCGM)
datas <- sim.data(model="ar1", time=10,n.obs=10, n.var=5, prob0=0.35,
network="random")
res.tscgm <- sparse.tscgm(data=datas$data, lam1=NULL, lam2=NULL,nlambda=NULL, model="ar1", penalty="scad",optimality="bic_mod", control=list(maxit.out = 5, maxit.in = 5))
I have tried using the functions invisible() and suppressMessages() but these do not help in either Rmarkdown or the R console. I also tried adding the option message = FALSE as follows:
```{r message=FALSE}
library(SparseTSCGM)
datas <- sim.data(model="ar1", time=10, n.obs=10, n.var=7, prob0=0.35, network="random")
res.tscgm <- sparse.tscgm(data = data.fit, lam1 = NULL, lam2 = NULL, nlambda = NULL, model = "ar1", penalty = "lasso", optimality = "bic", control = list(maxit.out = 10, maxit.in = 100))
```
but this does not help.
I have found that I can suppress output in the R console using sink('NUL') (I'm working on a Windows system), but this approach does not work in Rmarkdown. When I try this approach the message I tried to suppress is still there but the Rmarkdown console gives a warning: "Warning message: In sink() : no sink to remove".
Does sink() not work with Rmarkdown, is there another way do to this? If there is no solution I can always manually remove the section from the HTML file but that's a last resort.