I'm trying to produce an automated report using Rmarkdown. In this report I have sections with tables. The sections are produced using the following Rmarkdown. However, it refuses to produce any tables(tried using kable and pander) when I hit knit. Knit will just produce the headings, without any tables. When I use the immediate mode, I get the appropriate markdown. So what might I be doing wrong.
```{r, results='asis'}
for(p in names(presentations)) {
deats <- presentations[p][[1]]
cat('#', p, '\n')
pander(deats)
str(deats)
cat('\n')
}
```
If using pander, disable the auto asis results:
```{r, results='asis'}
library(pander)
panderOptions('knitr.auto.asis', FALSE)
for(p in names(mtcars)) {
cat('#', p, '\n')
pander(table(mtcars[, p]))
}
```
For more details, see the related Using pander with knitr vignette
When knitr::kable() or pander::pander() is not top-level R expression, you have to explicitly print it. You may see this post for more background information.
Related
I want to generate an rMarkdown pdf that for each of several variables has a summary table followed by a graph, and to put the table and graph for each variable on its own page. If I use asis then the table formatting is lost. If I omit asis, the way I insert the page break has no effect. Since this is only for data exploration, I’m too lazy to do any post-processing ;-). Is there a simple way to have my cake and eat it too?
---
output: pdf_document
---
some markdown text
```{r UglyTable, results = 'asis'}
for (n.var in 1:2) {
cat("\n\\pagebreak\n")
print(summary(iris[ , n.var]))
hist(iris[ , n.var])
}
```
more text
```{r NoPageBreaks}
for (n.var in 1:2) {
cat("\n\\pagebreak\n")
print(summary(iris[ , n.var]))
hist(iris[ , n.var])
}
```
These questions describe the use of pagebreaks with asis: In Markdown PDF, how to add page break after each iteration of for loop?, rmarkdown: page break within a chunk?
I have the following code in R
{r echo=F }
listA <- list(knitr::kable(mtcars[1:4,1:4]),knitr::kable(mtcars[1:4,1:4]),knitr::kable(mtcars[1:4,1:4]))
listA[[1]]
listA[[2]]
listA[[3]]
¿How can I increase the blank space between the three resulting tables without putting them in different chunks and considering that they are supposed to be part of an html document using bookdown and prettydoc?
For normal RMarkdown docs this workaround is ok:
{r echo=F, results='asis'}
listA <- list(knitr::kable(mtcars[1:4,1:4]),knitr::kable(mtcars[1:4,1:4]),knitr::kable(mtcars[1:4,1:4]))
listA[[1]]
cat("\n")
cat("#####\n")
cat("\n")
listA[[2]]
listA[[3]]
For anything more complicated, like using bookdown + prettydocs, this solution won't work.
I want my html file to show the code, but not the output of this chunk:
```{r echo=True, include=FALSE}
fun <- function(b)
{
for(a in b)
{print(a)
return(a * a)}
}
y <- fun(b)
```
When I run the code, i need the print to see the progress (it is quite a long function in reality).
But in the knitr file, I use the output in a further chunk, so I do not want to see it in this one (and there's no notion of progress, since the code has already been run).
This echo=True, include=FALSE here does not work: the whole thing is hidden (which is the normal behavior of include=FALSE).
What are the parameters I could use to hide the prints, but show my code?
As # J_F answered in the comments, using {r echo = T, results = 'hide'}.
I wanted to expand on their answer - there are great resources you can access to determine all possible options for your chunk and output display - I keep a printed copy at my desk!
You can find them either on the RStudio Website under Cheatsheets (look for the R Markdown cheatsheet and R Markdown Reference Guide) or, in RStudio, navigate to the "Help" tab, choose "Cheatsheets", and look for the same documents there.
Finally to set default chunk options, you can run (in your first chunk) something like the following code if you want most chunks to have the same behavior:
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T,
results = "hide")
```
Later, you can modify the behavior of individual chunks like this, which will replace the default value for just the results option.
```{r analysis, results="markup"}
# code here
```
The results = 'hide' option doesn't prevent other messages to be printed.
To hide them, the following options are useful:
{r, error=FALSE}
{r, warning=FALSE}
{r, message=FALSE}
In every case, the corresponding warning, error or message will be printed to the console instead.
```{r eval=FALSE}
The document will display the code by default but will prevent the code block from being executed, and thus will also not display any results.
For muting library("name_of_library") codes, meanly just showing the codes, {r loadlib, echo=T, results='hide', message=F, warning=F} is great. And imho a better way than library(package, warn.conflicts=F, quietly=T)
For completely silencing the output, here what works for me
```{r error=FALSE, warning=FALSE, message=FALSE}
invisible({capture.output({
# Your code here
2 * 2
# etc etc
})})
```
The 5 measures used above are
error = FALSE
warning = FALSE
message = FALSE
invisible()
capture.output()
To hide warnings, you can also do
{r, warning=FALSE}
I'm writing in R Markdown and have a contingency table that is quite wide. I am converting the R markdown document to a PDF using pandoc.
Is it possible to rotate or shrink the table? Ideally this would be done without having to switch to LaTeX formatting.
My Attempts:
I've been abusing the figure options in knitr to attempt this, but whether I use kable or xtable, I haven't had any luck. Some permutations I have tried include:
```{r out.extra='angle=90', results='asis'}
library(knitr)
kable(iris[1:5,])
```
``{r size='footnotesize', results='asis'}
library(knitr)
kable(iris[1:5,])
```
```{r out.extra='angle=90', results='asis'}
library(xtable)
xtable(iris[1:5,])
```
```{r size='footnotesize', results='asis'}
library(xtable)
xtable(iris[1:5,])
```
All of these show the table nicely, but do not rotate it.
The code I'm using to knit is:
Rscript -e "library(knitr); knit('table.Rmd', 'table.md')"
And to convert to pdf:
pandoc table.md -o table.pdf
The out.extra='angle=90' only works on Figures, and unfortunately not tables. Here are several potential approaches:
KableExtra (Rotate Page)
You can easily rotate tables using the useful addon package kableExtra. Specifically, the landscape() function will put the table on an single landscape page. It’s useful for wide tables that can’t
be printed on a portrait page.
library(kableExtra)
kable(iris[1:5,],
format = "latex", booktabs = TRUE) %>%
kableExtra::landscape()
The limitation of these function is that it does force a new page, so depending on the size of your table it could leave a bit of blank space.
KableExtra (Scale Width)
You can scale the width of the table using the function kable_styling(latex_options = "scale_down"). This will force the table to the width of the page.
kable(iris[1:5,],
format = "latex", booktabs = TRUE) %>%
kable_styling(latex_options = "scale_down")
For more examples of the kableExtra package, check out the package here: https://haozhu233.github.io/kableExtra/awesome_table_in_pdf.pdf
Stargazer (Rotate Table)
Other options are available, but these largely require the installation of additional LaTeX packages. For example, the stargazer package can print tables in landscape using the float.env argument:
```{r, results="asis"}
stargazer(iris[1:5,],
float.env = "sidewaystable")
```
This requires \usepackage{dcolumn} in LaTeX preamble
Read more about customising your LaTex preamble here: https://tex.stackexchange.com/questions/171711/how-to-include-latex-package-in-r-markdown
You can add some LATEX code in your Rmd file :
\usepackage{lscape}
\usepackage{pdfpages}
Some text on a portrait page.
\newpage
\blandscape
## Title, lorem ipsum
```{r, results = "asis"}
kable(iris[1:5,], caption = "Lorem again")
```
Lorem ipsum...
\elandscape
Some other text on a portrait page.
Can you just use t()?
library(xtable)
xtable(t(iris[1:5,]))
If your table is still to long, split it up into multiple tables. e.g.:
splits = floor(seq(1, ncol(iris), length=5))
for(i in 2:length(splits)){
mini.tab = iris[ , splits[i-1]:splits[i]]
xtable(mini.tab)
}
I am sorry, I am new to using knitr to make slides. I generally use the latex() function in Hmisc package to generate my tables based on R objects. I would like to produce a slide that shows the r code and then below it displays the properly formatted table. Something like:
``` {r}
latex(tabdat,file="tables/tabdat.tex",ctable=TRUE,caption="A basic table",caption.loc="bottom",label="tab:dat1",row.names=NULL,rowlabel="")
```
So that the finished slide displays the exact r code and the formatted table looking exactly as if I had run latex using \input{tabdat}
I would appreciate any advice on how to accomplish this.
Thanks!
I am a bit puzzled because you talk about PDF/LaTeX output but you are using R markdown tags.
Here are small examples for both cases, R Sweave, i.e. LaTeX output, and R markdown, i.e. HTML output. For creating the LaTeX code there are several packages available (xtable, Hmisc etc.) for HTML AFAIK only xtable.
The main point of how to include the raw output just like it appears in the console is the same for both output types and was already explained by Tyler Rinker above, i.e. by adding results="asis" to the chunk options.
PDF/LaTeX / Rnw-file
\documentclass{article}
\begin{document}
<<echo=FALSE, message=FALSE>>=
library(Hmisc)
library(xtable)
#
<<results='asis'>>=
latex(head(iris), file = '')
#
<<results='asis'>>=
xtable(head(iris))
#
\end{document}
HTML, Rmd-file
```{r echo=FALSE}
library(xtable)
```
```{r results='asis'}
tbl <- xtable(head(iris))
print(tbl, type="html")
```
Look here for more examples and options: http://www.stat.iastate.edu/centers/CCGS/slides/slides-Rtables.pdf