I am using RMarkdown to create a set of 6,000 letters. I am using parameters to create custom inputs into the document. I am using a loop to render the PDFs and calling it as follows:
for (i in 1:6000) {
rmarkdown::render(
input = "/template/letter.Rmd",
output_dir = "/output/",
output_file = paste0("report", i)
)
}
Now, this creates a 6,000 separate PDFs, but I would like to have it in one long document. Does anyone have any suggestions for how to use rmarkdown::render() and have it append the current PDF it generates onto the existing one? If I set output_file = report, for example, it will simply overwrite the existing PDF in the loop.
You can merge the outputs using a toolkit for pdf files. For instance, you can use the staplr package:
library(staplr)
ofiles <- c()
for (i in 1:6000) {
ofile <- rmarkdown::render(
input = "/template/letter.Rmd",
output_dir = "/output/",
output_file = paste0("report", i)
)
ofiles <- c(ofiles, ofile)
}
staple_pdf(input_files = ofiles, output_filepath = "/output/all-in-one.pdf")
In Linux, you can also merge the pdf files using pdftk:
cd /output/
pdftk report*.pdf cat output all-in-one.pdf
Related
I write a package, which will be used to create automated reports.
There is one function createPdfReport which basically looks as follows (I use RStudio):
createPdfReport <- function(dataset, save_path) {
rmdName <- strsplit(x = basename(dataset, split = ".", fixed = TRUE)[[1]][1]
# some code here which uses "dataset"
relPath <- dirname(rstudioapi::getSourceEditorContext()$path)
rmarkdown::render(input = paste0(relPath, "/myRMDfile.Rmd"),
output_dir = save_path,
output_file = paste0(rmdName , ".html"),
encoding = "UTF-8", quiet = TRUE)
}
Most likely, R will finally run on a server and it is not clear, which operating system or editor is used there.
Therefore, I would like to get rid of rstudioapi::getSourceEditorContext().
But how? I could not find anything.
createPdfReport is part of a typical package with the following structure:
DESCRIPTION
NAMESPACE
/man
/R
createPdfReport.R --> Contains the function createPdfReport() above
myRMDfile.Rmd
/tests
You could store myRMDfile.Rmd in inst/extdata, see package raw data.
This allows to get the file path and use it after package installation with:
system.file("extdata", "myRMDfile.Rmd", package = "myPackage")
So I'm trying to write an html R markdown document with interactive shiny bits that allow the user to edit a graph and then download the results to a pdf. However, there is something catastrophically wrong with the way that I'm trying to do this because as soon as the html starts, it overwrites the original markdown file with the contents of the pdf - turning it into complete gibberish right in the editor.
I doubt that I've found a completely new way to fail at R but I haven't been able to find where anybody else has had this issue. Additionally, I've looked over the shiny reference material and I'm just going in circles at this point, so any help would be greatly appreciated.
I'm using Rstudio 1.0.44, rmarkdown 1.2 and shiny 0.14.2. A small (not)working example:
---
title: "Minimum Failing Example"
author: "wittyalias"
date: "December 5, 2016"
output: html_document
runtime: shiny
---
```{r echo = FALSE}
library(ggplot2)
today <- Sys.Date()
inputPanel(downloadButton("dnld", label = "Download pdf"))
renderPlot({
# Example code from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/
p1 <<- ggplot(ChickWeight, aes(x=Time, y=weight, colour=Diet, group=Chick)) +
geom_line() +
ggtitle("Growth curve for individual chicks")
p1
})
reactive({
fname <- paste0("Chick Weight - ", today, ".pdf")
output$dnld <- downloadHandler(filename = fname,
content = makethepdf(file))
makethepdf <- function(fname) {
pdf(fname,
width = 14,
height = 8.5)
p1
dev.off()
}
})
```
EDIT: To be clear: I want the user to be able to download multiple pages of graphs, some of which will have different formatting. The user won't be downloading just a pdf version of the markdown document.
This happens because reasons I weren't able to identify makethepdf runs with the file = [name of the file]. Insert a print(fname) to see. The download handler isn't supposed to be inside an observer though. You need to have it outside on its own. I also failed to make pdf() dev.off() combination work for some reason so here's a working version below.
output$dnld = downloadHandler(filename = paste0("Chick Weight - ", today, ".pdf"),
content = function(file){
ggsave(file, plot = p1, width = 14, height = 8.5)
})
Use tempfile() and tempdir() to create a temporary file:
output$downloadReport = downloadHandler(
filename = function() {
normalizePath(tempfile("report_", fileext = ".docx"), winslash = "/")
},
content = function(file) {
out = rmarkdown::render("./report.Rmd",
output_file = file,
output_dir = tempdir(),
output_format = "pdf_document",
intermediates_dir = tempdir(),
envir = new.env(),
params = list( fontSize = 10)
)
})
I usually use a separate .Rmd template for my downloaded reports as the layout and text are usually similar but not identical to what works in an app.
I also find using parameters is a convenient way to pass input settings from my app to my report. See this RStudio post for details
Alright, so there are a number of problems with my code, but using some of the suggestions in the other answers I've been able to work it out.
The primary problem with this little document is that content in the downloadHandler is a function, but in my code I set content equal to the result of a function call. It looks like when the shiny app is first run it compiles content, thinking that it is a function, but actually ends up calling the function. It sends file as an arguement, which doesn't seem to exist except as a base function. Calling makethepdf with just file throws an error when I use it in the console, but for whatever reason in this app it just goes with the call, apparently with file = [name of the .Rmd] (just as OganM said).
To fix, change this:
output$dnld <- downloadHandler(filename = fname,
content = makethepdf(file))
to
output$dnld <- downloadHandler(filename = fname,
content = makethepdf)
To be clear: this code does not overwrite the .Rmd file if content calls makethepdf with any argument other than file. For instance, content = makethepdf(fnm)) causes the download button to display an object not found error and content = makethepdf(fname)) causes the download button to throw an attempt to apply non-function error when pressed.
In this following MWE on a Windows 7 machine running R 3.12
I am trying to create an md file from an Rmd. It creates the md file in my working directory, not int he specified path. The HTML file is created in the specified path instead. How can I make the md get created in deleteMe/my.md?
## Create a minimal Rmd:
dir.create("deleteMe")
cat("\nminimal", file = "deleteMe/my.Rmd")
## knit it to md
knitr::knit2html(input = "deleteMe/my.Rmd", output = "deleteMe/my.md")
## If I set the working directory to deleteME it is correct but I'm don't like to use setwd in functions
setwd("deleteMe")
knitr::knit2html(input = "deleteMe/my.Rmd", output = "deleteMe/my.md")
I realize it's a knit2html, not knit2md, but it creates an md as well. I'm open to other functions/packages/methods if this is the wrong approach. I do not want a yaml though as this is for a README.md creation that I don't want the yaml to appear in.
Looking at the source of knit2html(), you can see that when it calls knit(), it doesn't specify output=. That means that knit() is assuming you want the .md created in the working directory (hence why it works when you change working directory).
Creating a new version of knit2html() makes it work:
knit2html2 <- function (input, output = NULL, ..., envir = parent.frame(),
text = NULL, quiet = FALSE, encoding = getOption("encoding"))
{
#Specify output path in knit()
out = knit(input, output, text = text, envir = envir, encoding = encoding,
quiet = quiet)
if (is.null(text)) {
output = knitr:::sub_ext(if (is.null(output) || is.na(output))
out
else output, "html")
markdown::markdownToHTML(out, output, encoding = encoding,
...)
invisible(output)
}
else markdown::markdownToHTML(text = out, ...)
}
It seems reasonable that output= be passed on to knit() - maybe a pull request is in order
I would like to include at the end of the R markdown documention the help page about the mtcars dataset.
In my file I included the following:
```{r}
?mtcars
```
When I compile the markdown (output is to PDF - knitr), upon processing this instruction the help page comes up in my browser but the resulting pdf lacks this section.
Is there a way I could acheive this other then copying from one place to the other?
Thank you.
We can adapt Yihui Xie's static_help function to get the html source for a given help file
static_help <- function(pkg, topic, out, links = tools::findHTMLlinks()) {
pkgRdDB = tools:::fetchRdDB(file.path(find.package(pkg), 'help', pkg))
force(links)
tools::Rd2HTML(pkgRdDB[[topic]], out, package = pkg,
Links = links, no_links = is.null(links))
}
If we write the source to a temporary file we can then read it back in and strip off the header and footer, giving you the body of the help file to include in your markdown document
```{r, echo = FALSE, results = "asis"}
static_help <- function(pkg, topic, out, links = tools::findHTMLlinks()) {
pkgRdDB = tools:::fetchRdDB(file.path(find.package(pkg), 'help', pkg))
force(links)
tools::Rd2HTML(pkgRdDB[[topic]], out, package = pkg,
Links = links, no_links = is.null(links))
}
tmp <- tempfile()
static_help("datasets", "mtcars", tmp)
out <- readLines(tmp)
headfoot <- grep("body", out)
cat(out[(headfoot[1] + 1):(headfoot[2] - 1)], sep = "\n")
```
EDIT
The above solution produced HTML output, whereas the question actually asked for PDF output. We can adapt the above to return latex output instead; this time the only-post-editing required is to switch % for \n
```{r, echo = FALSE, results = "asis"}
static_help <- function(pkg, topic, out, links = tools::findHTMLlinks()) {
pkgRdDB = tools:::fetchRdDB(file.path(find.package(pkg), 'help', pkg))
force(links)
tools::Rd2latex(pkgRdDB[[topic]], out, package = pkg,
Links = links, no_links = is.null(links))
}
tmp <- tempfile()
static_help("datasets", "mtcars", tmp)
out <- readLines(tmp)
out <- gsub("%", "\n", out, fixed = TRUE)
cat(out, sep = "\n")
```
However the .Rd files depend on Rd.sty. The simplest way to get LaTeX to find Rd.sty is to put a copy in the same directory as your .Rmd file. Then you need to define a custom template to replace the default pandoc LaTeX template. Again, the simplest solution is to put a copy of the default template in the same directory as your .Rmd file, then modify it by replacing everything between the \documentclass command and the \begin{document} command (lines 2 - 145) with the command
\usepackage{Rd}
Finally modify the metadata of your .Rmd file to use the new template
---
output:
pdf_document:
template: template.tex
---
I would like to know if there is any function which makes it easy to visualize an html object in the RStudio's viewer pane. For instance, I would like to know if it would be possible to view an html table in the viewer pane.
library("Quandl")
library("knitr")
df <- Quandl("FBI_UCR/USCRIME_TYPE_VIOLENTCRIMERATE")
kable(head(df[,1:9]), format = 'html', table.attr = "class=nofluid")
I have a solution that works for kable tables.
kable(iris) %>% kableExtra::kable_styling()
This is automatically displayed in the viewer pane. No need for tempfile.
I have this functionality in my htmlTable package and the function is rather simple:
print.htmlTable<- function(x, useViewer = TRUE, ...){
# Don't use viewer if in knitr
if (useViewer &&
!"package:knitr" %in% search()){
htmlFile <- tempfile(fileext=".html")
htmlPage <- paste("<html>",
"<head>",
"<meta http-equiv=\"Content-type\" content=\"text/html;charset=UTF-8\">",
"</head>",
"<body>",
"<div style=\"margin: 0 auto; display: table; margin-top: 1em;\">",
x,
"</div>",
"</body>",
"</html>", sep="\n")
cat(htmlPage, file=htmlFile)
viewer <- getOption("viewer")
if (!is.null(viewer) &&
is.function(viewer)){
# (code to write some content to the file)
viewer(htmlFile)
}else{
utils::browseURL(htmlFile)
}
}else{
cat(x)
}
}
RStudio recommends that you use the getOption("viewer") instead of #Ramnath's suggestion, the raw RStudio::viewer(). My solution also adds the utils::browserURL() in case you are not using RStudio. I got the idea from this blog post.
Here is a quick way to do this in RStudio
view_kable <- function(x, ...){
tab <- paste(capture.output(kable(x, ...)), collapse = '\n')
tf <- tempfile(fileext = ".html")
writeLines(tab, tf)
rstudio::viewer(tf)
}
view_kable(head(df[,1:9]), format = 'html', table.attr = "class=nofluid")
If the kable function can return an object of class kable, then one could rename view_kable as print.kable in which case merely calling the kable function would open the table in the viewer. If you think this is useful, please go ahead and file a feature request on the knitr github page.
As was explained on this RStudio Support page, the key is to use tempfile() :
Note that the Viewer pane can only be used for local web content. This
content can either be static HTML files written to the session
temporary directory (i.e. files with paths generated by the tempfile
function) or a locally run web application.
See my answer to this question for a bare-bones example.
For kable objects, we can use print.kableExtra
library(knitr)
x <- kable(head(iris), format = "html")
library(kableExtra)
class(x) <- c("kableExtra", class(x))
print(x)