I want to change the output of Rmarkdown filename based on what the parameter value using the Knit with parameter option.
Here's an example:
---
title: "Output Filename by Parameter"
author: "myself"
date: "`r Sys.Date()`"
output: html_document
params:
exp:
label: "Experiment: "
value: draft
input: select
choices: [draft, review, final]
knit: >
(function(input, ...) {
metadata <- rmarkdown::yaml_front_matter(input)
output_file <- paste0('exp_', metadata$params$exp$value, '.html')
rmarkdown::render( input, output_file = output_file )
})
---
Some texts...
When I executed this with 'Knit with Parameters' option, I can see the selection for exp parameter, but it does not save the output HTML filename according to the input value. It saves with the default value (exp_draft.html).
How can I change the output filename according the user selection? Is it something related with Shiny's reactive expression that I should write in the knit's parameter? If yes, then how should I put reactive experession in YAML?
Thanks.
Related
I try to generate multiple reports (1 per group) with rmarkdown::render(), but it produces no section numbers.
I use the following file-structure for this in case you want to reproduce the sample (I tried to simplify each file and use only necessary code to reproduce the error):
*) groups.R: defines groups and subgroups in a nested list (all groups stored in a list and each group is a list itself)
groups <- list(
list(c("subgroup1","subgroup2"),"maingroup1"),
list(c("subgroup3","subgroup4"),"maingroup2")
)
*) main.Rmd: template for the reports
---
output:
pdf_document:
number_sections: true
classoption: a4paper
geometry: left=2cm,right=1cm,top=1.5cm,bottom=1cm,includeheadfoot
fontfamily: helvet
fontsize: 11pt
lang: en
header-includes:
- \usepackage{lastpage}
- \usepackage{fancyhdr}
- \pagestyle{fancy}
- \fancyhf{}
- \fancyhead[R]{\fontsize{9}{11} \selectfont \leftmark}
- \fancyhead[L]{\fontsize{9}{11} \selectfont Special report xxx}
- \fancyfoot[R]{\fontsize{9}{0} \selectfont Page \thepage\ of
\pageref{LastPage}}
---
```{r setup, include = FALSE}
knitr::opts_chunk$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.
I think that you can pass variables to a YAML element, something like
---
output: html_document
params:
set_title: "My Title!"
title: "`r params$set_title`"
---
(as suggested here). This, however, works for output: html_document but not for bookdown::word_document2. Also, I would like to change the template of my bookdown::word_document2 output, depending on a switch, which I can set in the YAML itself, something like
---
title: ""
params:
include_signature: false
include_footer: true
file: !r if(params$include_footer){system.file("assets/template_footer.docx")}else{system.file("assets/template.docx")}
output:
bookdown::word_document2:
reference_docx: "`r params$file`"
number_sections: false
---
This, however, fails with the error message
Error in yaml::yaml.load(..., eval.expr = TRUE) :
Parser error: while parsing a block mapping at line 8, column 5 did not find expected key at line 8, column 61
Calls: <Anonymous> ... parse_yaml_front_matter -> yaml_load -> <Anonymous>
In addition: Warning message:
In yaml::yaml.load(yaml, handlers = knit_params_handlers(evaluate = evaluate), :
an error occurred when handling type 'r'; using default handler
Execution halted
I have tried other possible versions, eg
params:
include_footer: true
output:
bookdown::word_document2:
reference_docx: !expr ifelse(params$include_footer,system.file("assets/template_footer.docx"),system.file("assets/template.docx"))
(or even other variations, where !expr is replaced by r or !r but nothing seems to have made a difference.
Am I missing something obvious (eg that this is only possible in html_document output), or is this particular trick impossible?
Thanks
Gianluca
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$set(echo = TRUE)
```
```{stan, output.var='priors', eval = FALSE, tidy = FALSE}
parameters {
real<lower = 0> qtilde1;
}
model {
qtilde1 ~ gamma(38.9, 0.67);
}
```
The Stan code chunk is rendered as ordinary text, including the three reverse single quotes and word stan from the chunk header. I cannot show that in this post because stackoverflow tells me, correctly but unhelpfully, "Your post appears to contain code that is not properly formatted as code". That sums up my problem!
Code chunks in R are rendered correctly.
Your
```{stan output.var='priors', eval = FALSE, tidy = FALSE}
needs to be flush-left, but you have a leading space before the ```
Thanks to parameterized reports support by Rmarkdown, it is easy to make an .Rmd file rendered with parameters as follows (this example is from here):
---
title: "`r params$dynamictitle`"
params:
dynamictitle: My report
reportdate: !r Sys.Date()
date: "`r params$reportdate`"
---
This would be fine to knit to a .html file, but cannot be rendered in blogdown, with the following error:
Quitting from lines 2-5 ()
<simpleError in eval(parse_only(code), envir = envir): object 'params' not found>
I want to know whether there is a workaround way to make an .Rmd file parameterized?
I use bookdown to generate a document in both html and pdf. How could I insert a reference to a section of the document in the caption of a table?
Using \\ref{sec:FirstSection} works fine with pdf_book (but not gitbook):
---
title: "Test"
output: bookdown::pdf_book
---
# A section {#sec:FirstSection}
The dataset in Table \#ref(tab:aTable) contains some data.
# Another section
```{r, aTable, echo = FALSE}
knitr::kable(
cars[1:5, ],
caption = "See Section \\ref{sec:FirstSection}."
)
```
whilst using \\#ref(sec:FirstSection) works fine with gitbook (but not pdf_book)
---
title: "Test"
output: bookdown::gitbook
---
# A section {#sec:FirstSection}
The dataset in Table \#ref(tab:aTable) contains some data.
# Another section
```{r, aTable, echo = FALSE}
knitr::kable(
cars[1:5, ],
caption = "See Section \\#ref(sec:FirstSection)."
)
```
You can use text references, a Markdown extension provided by bookdown.
---
title: "Test"
output: bookdown::gitbook
---
# A section {#sec:FirstSection}
The dataset in Table \#ref(tab:aTable) contains some data.
# Another section
(ref:aTable-caption) See Section \#ref(sec:FirstSection).
```{r, aTable, echo = FALSE}
knitr::kable(
cars[1:5, ],
caption = "(ref:aTable-caption)"
)
```
This works for both pdf and html but there might be an easier way.
---
title: "Test"
output: bookdown::gitbook
---
# A section {#sec:FirstSection}
The dataset in Table \#ref(tab:aTable) contains some data.
# Another section
```{r, aTable, echo = FALSE}
txt <- ifelse(knitr:::is_latex_output(), "\\ref{sec:FirstSection}",
"\\#ref(sec:FirstSection)")
knitr::kable(
cars[1:5, ],
caption = paste0("See Section ", txt, ".")
)
```