Reproducable example:
I am knitting a .rmd document which should show a table of the airquality data frame to a beamer pdf document in RStudio.
.rmd file:
---
title: "Test"
author: "Author"
output:
beamer_presentation:
includes:
in_header: mystyle.sty
---
## Page 1
```{r echo=FALSE, results='asis'}
library(xtable)
print(xtable(airquality), comment=F, tabular.environment='longtable',floating=FALSE)
```
As the data frame is quite long I am using the tabular.environment='long table' option as described here. I am importing in the the .rmd header via mystyle.sty the longtable package, so that the LaTex compilation is prepared.
mystyle.sty:
\usepackage{longtable}
Problem:
The .pdf output is generated without error, but unfortunately the longtable does not work. There's just one page and the table has not been wrapped.
Question:
The target was to get multiple frames (pages) automatically generated fitting the data frame. Any solution to achieve this target?
You can add the latex package to your preamble in the YAML front matter:
header-includes:
- \usepackage{longtable}
This is the only thing I am doing differently and it does work for me.
Also, you might want to add the following options:
,include.colnames=TRUE, include.rownames=FALSE
The first option will repeat the header on each page, the second option will not show the row numbers in the first row.
The problem I'm still having is that it seems to render a { before my table and a } after it.
Related
I am writing a Rmarkdown document using bookdown::pdf_document2 for which I have a table that needs to do several very specific things, but I simply cannot find the solution to get all of them to work at the same time:
The table needs to float to the end of the document as it would with the latex endfloat package.
The table elements have Markdown bold and italics formatting that should appear correctly in the final PDF document
One of the columns of the table has a lot of text that I would like to wrap within the table cell.
I have tried to get these three options to work with all sorts of combinations of knitr::kable, kableExtra::column_spec and pander, but I cannot find a way to get them all going at once. Below I am pasting an example Rmarkdown document with various tests, none of which fully works.
Is there a simple way to get the table to do what I want? Even a good workaround would be acceptable...
Thanks,
David
---
title: "Test table formatting"
author: "David M. Kaplan"
date: "5/24/2020"
output: bookdown::pdf_document2
header-includes:
- \usepackage[tablesfirst]{endfloat}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
```
# Data
```{r}
df.long = data.frame(
char = c('*this is some very long text with lots of words that will cause problems with word wrap if it is not properly handled with something like kableExtra*','**b**','~~c~~'),
num = c(1,2,3))
```
# Kable with format=pandoc
```{r}
knitr::kable(df.long,caption="test1",format="pandoc")
```
**Result:** Handles formatting, but table does not float and no wordwrap.
# Kable with booktab
```{r}
knitr::kable(df.long,caption="test2",booktab=TRUE)
```
**Result:** Floats, but does not handle formatting or do wordwrap.
# kableExtra for wordwrap
```{r}
knitr::kable(df.long,caption="test3",booktab=TRUE) %>%
kableExtra::column_spec(1,width="30em")
```
**Result:** Table floats and has wordwrap, but does not handle formatting.
# Pander
```{r}
pander::panderOptions("table.alignment.default","left")
pander::pander(df.long,caption="test4")
```
**Result:** Wordwrap and formatting, but does not float.
I found a solution to this problem. It basically consists of:
In the YAML header, add a header-includes entry declaring longtable to be a float flavor using some LaTeX magic I found here.
Use pander to format the table to get wordwrap
Specifically, I have the following in the YAML header:
header-includes:
- \usepackage[tablesfirst]{endfloat}
- \DeclareDelayedFloatFlavour*{longtable}{table}
and then the table can be generated with pander:
pander::panderOptions("table.alignment.default","left")
pander::pander(df.long,caption="test pander",split.cell=50)
I think the question is quite self-explanatory but for avoidance of doubt I'll explain with more detail below:
I have an R Markdown document that works well if converted to HTML or uploaded to GitHub. When converting to PDF (using Latex), the results are not so pretty. I find that the biggest problem in a Latex PDF document are line breaks. I can fix the line breaks issue on the PDF document by adding "\ " characters, but that throws my HTML document out of whack too.
Is there a way to manually add line breaks (or "space before/after paragraphs") for the PDF output only?
Thank you!
You can redefine the relevant spacings in the YAML header. \parskip controls the paragraph spacing. Code blocks are shaded using a snugshade environment from the framed package. We can also redefine the shaded environment for code blocks to have some vertical space at the start. Here's a reproducible example. Note: I also added the keep_tex parameter so you can see exactly what the generated tex file looks like, in case this is useful:
title: "test"
author: "A.N. Other"
header-includes:
- \setlength{\parskip}{\baselineskip}
- \renewenvironment{Shaded}{\vspace{\parskip}\begin{snugshade}}{\end{snugshade}}
output:
pdf_document:
keep_tex: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
Once you output to HTML, you can just print the HTML webpage as PDF. that might be an easy way keep the original format
I am creating a .pdf using R Markdown. I would like to have a section of text in two column format, and then follow that with a graph (or table, photo, etc.) that takes up the entire width of the page, and then return to two column text. I am new at Markdown / LaTex / Pandoc and I cannot figure out how to do it.
This answer by #AlisonShelton appears to be what I want, but when I run it I get this error in the RStudo R Markdown console:
! Undefined control sequence.
l.87 \btwocol
pandoc.exe: Error producing PDF
Error: pandoc document conversion failed with error 43
I have successfully used this method by #scoa to make a two column .pdf, but I don't know how go back and forth between one and two columns using this.
Here is some sample code for testing purposes
---
title: "Test"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Two columns of text
This seciton should be in two column format.
Here are a bunch of ? to make it longer: ???????????????????????????????????????????????????????????????????????????????
????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????
## Once column section.
This part should be the whole page width
```{r plot}
plot(rnorm(20),rnorm(20))
```
## Now 2 columns again
This section should go back to two columns !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
What you can do is first, to add -- as you stated -- pandoc_args: ... into your YAML header. Second, there are a few LaTeX solutions around (like this or this one) which won't work for RMarkdown. The only way I found so far is to use \onyecolumn / \twocolumn -- just with the drawback of the page breaks. But perhaps you can live with it until there's a better solution.
---
title: "Test"
output:
pdf_document:
pandoc_args: [
"-V", "classoption=twocolumn"
]
html_document: default
header-includes:
- \usepackage{lipsum} # just used for producing example text in document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Two columns of text
\lipsum[1-7]
\onecolumn
## Once column section.
This part should be the whole page width
```{r plot}
plot(rnorm(20),rnorm(20))
```
\lipsum[1]
\twocolumn
## Now 2 columns again
This section should go back to two columns
\lipsum
\begin{table*}
This is nice, but won't work with R chunks or headers. And you'll have to format with LaTeX code (e.g. \textbf{Foo blaah}).
\lipsum[1]
\end{table*}
\lipsum
I am trying to pass pandoc arguments through rmarkdown YAML as it is linked here: http://rmarkdown.rstudio.com/html_document_format.html#advanced-customization
and the option I am trying to add is code line numbering:
--indented-code-classes=CLASSES
Specify classes to use for indented code blocks–for example, perl,numberLines or haskell. Multiple classes may be separated by spaces or commas.
My .Rmd file is below but after the rendering the output do no look like to be numbered. Does anyone know how to pass this argument correctly? I've tried many various possibilities but none of them worked.
---
title: "Untitled"
author: "Marcin Kosinski"
date: "28.12.2015"
output:
html_document:
theme: united
highlight: espresso
md_extensions: +fenced_code_attributes+fenced_code_blocks
pandoc_args: [
"--indented-code-classes","numberLines"
]
---
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r, results='hide'}
summary(cars)
iris
summary(iris)
```
I have been reading about R Markdown (here, here, and here) and using it to create solid reports. I would like to try to use what little code I am running to do some ad hoc analyses and turn them into more scalable data reports.
My question is rather broad: Is there a proper way to organize your code around an R Markdown project? Say, have one script that generates all of the data structures?
For example: Let's say that I have the cars data set and I have brought in commercial data on the manufacturer. What if I wanted to attach the manufacturer to the current cars data set, and then produce a separate summary table for each company using a manipulated data set cars.by.name as well as plot a certain sample using cars.import?
EDIT: Right now I have two files open. One is an R Script file that has all of the data manipulation: subsetting and re-categorizing values. And the other is the R Markdown file where I am building out text to accompany the various tables and plots of interest. When I call an object from the R Script file--like:
```{r}
table(cars.by.name$make)
```
I get an error saying Error in summary(cars.by.name$make) : object 'cars.by.name' not found
EDIT 2: I found this older thread to be helpful. Link
---
title: "Untitled"
author: "Jeb"
date: "August 4, 2015"
output: html_document
---
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r}
table(cars.by.name$make)
```
```{r}
summary(cars)
summary(cars.by.name)
```
```{r}
table(cars.by.name)
```
You can also embed plots, for example:
```{r, echo=FALSE}
plot(cars)
plot(cars.import)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
There is a solution for this sort of problem, explained here.
Basically, if you have an .R file containing your code, there is no need to repeat the code in the .Rmd file, but you can include the code from .R file. For this to work, the chunks of code should be named in the .R file, and then can be included by name in the .Rmd file.
test.R:
## ---- chunk-1 ----
table(cars.by.name$make)
test.Rmd
Just once on top of the .Rmd file:
```{r echo=FALSE, cache= F}
knitr::read_chunk('test.R')
```
For every chunk you're including (replace chunk-1 with the label of that specific chunk in your .R file):
```{r chunk-1}
```
Note that it should be left empty (as is) and in run-time your code from .R will be brought over here and run.
Often times, I have many reports that need to run the same code with slightly different parameters. Calling all my "stats" functions separately, generating the results and then just referencing is what I typically do. The way to do this is as follows:
---
title: "Untitled"
author: "Author"
date: "August 4, 2015"
output: html_document
---
```{r, echo=FALSE, message=FALSE}
directoryPath <- "rawPath" ##Something like /Users/userid/RDataFile
fullPath <- file.path(directoryPath,"myROutputFile.RData")
load(fullPath)
```
Some Text, headers whatever
```{r}
summary(myStructure$value1) #Where myStructure was saved to the .RData file
```
You can save an RData file by using the save.image() command.
Hope that helps!