I'm having a lot of trouble getting basic references to work in R Markdown. To reduce complexity from my original project, I've decided to use the bookdown example code, but I'm experiencing the same problem. Here's a link to the intro exmample code: https://github.com/rstudio/bookdown-demo/blob/master/01-intro.Rmd
When I use Knitr to HTML or PDF the file is being generated fine but the references are not working, instead the file will just containt "#ref(example)". Here is an image to show better the output (my emphasis added in red):
Direct link to image: https://i.imgur.com/2yxB5h3.png
Here is a minimal example:
---
title: "Minimal"
output:
pdf_document:
fig_caption: yes
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Here is a reference to the plot below \#ref(fig:minGraph)
```{r minGraph, echo=FALSE, fig.cap="\\label{fig:minGraph}test"}
plot(x=1)
```
With the output appearing as such:
https://i.imgur.com/J3UECqn.png
If you want make use of the bookdown extensions in a normal rmarkdown document you can use bookdown::html_document2 and bookdown::pdf_document2 instead of rmarkdown::html_document and rmarkdown::pdf_document. Example:
---
title: "Minimal"
output:
bookdown::html_document2:
fig_caption: yes
bookdown::pdf_document2:
fig_caption: yes
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Here is a reference to the plot below \#ref(fig:minGraph)
```{r minGraph, echo=FALSE, fig.cap="test"}
plot(x=1)
```
Looks like I was getting my syntax confused by reading the bookdown guide while using just R markdown. Thanks to Ralf for pointing me in the this direction. The correct minimal code would be like so:
---
title: "Minimal"
output:
pdf_document:
fig_caption: yes
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Here is a reference to the plot below \ref{fig:minGraph}
```{r minGraph, echo=FALSE, fig.cap="\\label{fig:minGraph}test"}
plot(x=1)
```
Related
I'm need to generate a "bunch" of tables in R that must be included in a Latex document.
I can create very nice tables using flextable... but I am not able to generate ANY format that can then be inserted in (multiple places) in a latex document.
The problem is that any method that I try will add extra "margins" (like in pdf... prints a table to a full page) or has some limitation (like png).
Does any ne has a solution, either using directly an RScript or trough knitting R-Markdown?
(Note: The solution of producing the whole latex doc in RMarkdown is Not feasible.)
Just to present an example. I would like this would produce a Full-Page (with dimensions of the table... not A4) of the table.
Thank you very much for your Help :).
---
title: "Untitled"
output:
pdf_document:
latex_engine: xelatex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(flextable)
```
```{r}
ft <- flextable(head(airquality))
ft <- autofit(ft)
theme_vader(ft)
```
You could use the standalone class (a bit of extra space is still there, but much less than a full page):
---
documentclass: standalone
classoption: varwidth
output:
pdf_document:
latex_engine: xelatex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(flextable)
```
```{r}
ft <- flextable(head(airquality))
ft <- autofit(ft)
theme_vader(ft)
```
I was able to figure out how to include a multi-page PDF document in my RMarkdown output using "\includepdf", but I need to be able to change the path to different PDFs based on conditions in the data. I'd like to be able to call the PDF file path based on an object I set in a chunk beforehand (e.g. "test"). Any ideas?
Thanks!
---
title: "Personnel Reports"
output:
pdf_document
header-includes:
- \usepackage{pdfpages}
---
This works:
\includepdf[pages=-,pagecommand={}]{Person1_report.pdf}
```{r global_options, include=FALSE}
test <- "Person2_report.pdf"
```'
This doesn't work:
\includepdf[pages=-,pagecommand={}]{test}
---
title: "Personnel Reports"
output:
pdf_document:
keep_tex: true
header-includes:
- \usepackage{pdfpages}
---
```{r global_options, include=FALSE}
test <- "example-image-duck.pdf"
```
\includepdf[pages=-,pagecommand={}]{`r test`}
I would like my pdf output to satisfy 3 conditions:
Title page on page 1
Table of contents on page 2
Cross reference figures and tables.
I am able to do 1 and 2 with pdf_document but as explained here, pdf_document2 is required for 3.
How can I build a pdf document that can satisfy these 3 conditions? I would like to avoid setting my document class to a report if possible.
This answer is the closest I have found.
Sample code:
---
title: "Untitled"
output:
pdf_document:
number_sections: true
---
\newpage
\tableofcontents
\listoffigures
\listoftables
\newpage
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
Figure (...) below is a
```{r pressure}
plot(pressure)
```
You just need to add \ref{}
## R Markdown
Figure (\ref{fig:pressure}) below is a ...
```{r pressure}
plot(pressure)
```
I have the following Rmarkdown (.Rmd) document where I call existing .png images and create a .pdf with captions. By default, pandoc? is automatically adding "Figure #." before the caption for each picture. I can see how this would be the normal thing to do, but in my case I would like to define this. I have found variations on this topic but don't seem to find a solution. Below is an example of how my .Rmd file looks:
---
title: "TITLE"
author: "ME"
date: "`r Sys.Date()`"
output:
pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\newpage
You could use the caption-package
Create a .tex-file that you specify the following in, this below remove the entire label and you are free to hardcode the labels.
\usepackage{caption}
\captionsetup[figure]{labelformat=empty}
Then your .rmd should look like this:
---
title: "TITLE"
author: "ME"
date: "`r Sys.Date()`"
output:
pdf_document:
includes:
in_header: YourName.tex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\newpage
Simplified: As suggested in the comments, we can achieve this within our .Rmd file, as shown below.
---
title: "TITLE"
author: "ME"
date: "`r Sys.Date()`"
output:
pdf_document:
header-includes:
- \usepackage{caption}
- \captionsetup[figure]{labelformat=empty}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\newpage
I have a R markdown file that I want to output rmarkdown from the script itself. For example, I would have the following simple code in an Rmd file.
---
title: "test"
author: "johndoe"
date: "September 5, 2015"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r cars}
paste("## This is a Heading in Code")
summary(cars)
```
I want "This is a Heading in Code" to render in rmarkdown. There is a solution in an R script to generate markdown as per http://rmarkdown.rstudio.com/r_notebook_format.html. But I am trying to figure out how to do this in a Rmarkdown file. Any help appreciated. Thanks.
Why build the header markup (either in markdown or HTML) manually? Try inline R expressions or some helper functions in pander (to generate markdown programatically):
---
title: "test"
author: "johndoe"
date: "September 5, 2015"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## `r 'This is a Heading in Code'`
```{r title, results='asis'}
library(pander)
pandoc.header("This is a Heading in Code", level = 2)
```
```{r cars, results='asis'}
summary(cars)
```
I searched for a good answer for this for some time after using cat("## Heading") inside results='asis' code chucks. I have seen many people dissatisfied by the results='asis' setting in the code chunk because it sets all results of the code chunk to not be wrapped in a code markup block. We have many cases when we want to output the heading along with results that should be wrapped in markup (e.g. a kable table that renders to a html table).
Here is the solution I found by simply specifying the "asis" attribute to the text object with knitr::asis_output and keeping the code chunk in the default 'markup' setting.
---
title: "test"
author: "johndoe"
date: "September 5, 2015"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r cars}
knitr::asis_output("## This is a Heading in Code")
summary(cars)
knitr::kable(summary(cars))
```
Unfortunately, at the current time knitr::asis_output only works in top-level R expressions, and it will not work when it is called inside another expression, such as a for-loop.