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)
```
Related
In R Studio, my R Markdown document begins like this:
---
title: 'ST 412: Homework 3'
author: "Camden White"
documentclass: amsart
geometry: margin=1in
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## 1. Read Data Set and Define Variables
```{r, message=FALSE, warning=FALSE}
library(tidyverse)
library(magrittr)
```
When I do not include documentclass: amsart, everything works fine, but when I do include it, the library section is placed before the ## 1. Read Data Set and Define Variables header.
When there is text between the two components, the order is the same order in the code, but without it, the library section comes first. This does not happen with the default article document class, and I do not know why this occurs. How can I use the amsart document class and fix this ordering issue?
The problem seems to be that a subsection in amsart is basically what a paragraph is in normal classes: an unnumbered bold piece of text without an new paragraph after it. The text will just continue in the same line. As the grey box with the source code spans a whole line, it can't be placed there and shows up above. You can reproduce this with normal article class like this:
\documentclass{article}
\usepackage{framed}
\begin{document}
\paragraph{1. Read Data Set and Define}
\begin{framed}
test
\end{framed}
\end{document}
You can avoid the problem by making sure the source code isn't the first text in the subsection, e.g. by adding something invisible:
---
title: 'ST 412: Homework 3'
author: "Camden White"
documentclass: amsart
geometry: margin=1in
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## 1. Read Data Set and Define Variables
\mbox{}
```{r, message=FALSE, warning=FALSE}
library(tidyverse)
library(magrittr)
```
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$set(echo = TRUE)
```
Here is a reference to the plot below \ref{fig:minGraph}
```{r minGraph, echo=FALSE, fig.cap="\\label{fig:minGraph}test"}
plot(x=1)
```
Is there any way to pass parameters in an rmarkdown document outside of a code chunk? For example, I'd love to have the ability to have a parameter value be a heading.
Here is a short example .Rmd file:
---
title: "param_test"
author: "test"
date: "September 14, 2017"
output: pdf_document
params:
param_test: this_text
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## I want this heading to be the value of params$param_test
```{r cars}
params$param_test
print(params$param_test)
```
Does anyone have any ideas on this?
You just need to add results='asis' to the chunk then you can print out the header from within the code.
cat("#", params$param_test, "\n")
Another option would be to use the pander library and run
pandoc.header(params$param_test)
Often when I include r code in a rmarkdown pdf presentation, I want to use the space of the whole slide and therefore want to present the code and the output side-by-side.
In pure LaTex I would go for \begin{columns}...\end{columns} and then include the code/output manually using lstlistings or some other code-highlighting library. But that proves tedious if I exceed a couple of code examples.
Now I want to use RMarkdown for the presentations and would like to achieve a similar result.
However, the following code throws an error:
## This is slide 1
\begin{columns}[t]
\begin{column}{0.5\textwidth}
```{r, eval=F}
plot(1:10)
```
\end{column}
\begin{column}{0.5\textwidth}
```{r, echo=F}
plot(1:10)
```
\end{column}
\end{columns}
Leaving out the knitr code-chunks and replacing them with text works.
I am aware that it has something to do with the pandoc engine (see here), but wanted to ask if anybody has found a way around this issue.
Well, I may should have looked with a wider focus.
Here is a solution that works for Python, but can easily be adapted to Rmarkdown: https://stackoverflow.com/a/26069751/3048453
I ended up with this code:
in header.tex
\newcommand{\columnsbegin}{\begin{columns}}
\newcommand{\columnsend}{\end{columns}}
in presentation.Rmd
---
title: "Two-column codes in RMarkdown"
author: "My Name"
date: "February 4, 2017"
output:
beamer_presentation:
includes:
in_header: header.tex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Testslide with Columns
\columnsbegin
\column{.5\textwidth}
```{r, eval=F}
plot(mtcars[, 1:3])
```
\column{.5\textwidth}
```{r, echo=F}
plot(mtcars[, 1:3])
```
\columnsend
Which results in this
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.