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.
Related
do you have any solutions to producing a blank line within an Rchunk in Rmd? I want to put it out as a word document.
Currently I am doing this:
flextable(table1)
cat(" \n")
flextable(table2)
But this doesn't produce a line between the tables. If I do this instead:...
flextable(table1)
cat("Some Text")
flextable(table2)
... I get a line between the tables, but it's with a grey background and leading "## ".
I don't want to use seperate Rchunks, because I want to write a function that allows me to print multiple tables at once seperated by a blank space.
Do you have any ideas?
Kind regards
One way is to set the chunk option results='asis' such that
text output is written “as-is”, e.g., you can write out raw Markdown
text from R code
Xie, Yihui, Joseph J. Allaire, and Garrett Grolemund. R markdown: The definitive guide. Chapman and Hall/CRC, 2018.
and also make sure the output from cat is not in conflict with flextable output. Adding \n on each side of \\newline seems to work. We then have the chunk
```{r, echo=FALSE, results='asis'}
flextable(mtcars[1:4, ])
cat("\n \\newline \n")
flextable(mtcars[1:4, ])
```
results='asis' might come in conflict with some other stuff. If this is the case, you can omit this option and use knitr::asis_output() only at the desired output
```{r, echo=FALSE}
flextable(mtcars[1:4, ])
knitr::asis_output("\n \\newline \n")
flextable(mtcars[1:4, ])
```
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.
I'm working on my first R notebook which works pretty well, except for one issue.
I'd like to be the numbers that I output inline with
`r realbignumber`
to have commas as separator and max 2 decimal points: 123,456,789.12
In order to achieve this, I added a chunk at the beginning of my document, which contains...
```{r setup}
knitr::opts_chunk$set(echo = FALSE, warning=FALSE, cache = TRUE, message = FALSE)
knitr::opts_chunk$set(inline = function(x){if(!is.numeric(x)){x}else{prettyNum(round(x,1), big.mark = ",")}})
options(scipen=999)
```
The suppression of scientific numbers works like a charm, so the chunk is definitely executed. However, formatting of the inline output of numbers does not work.
Any ideas why that could be?
Do these kinds of settings generally not work with R notebooks?
Edit:
The solution suggested here also has no effect on the output format of numbers.
Here is an example illustrating two ways to print a large number in an R Markdown document. First, code to use the prettyNum() function in an inline R chunk.
Sample document where we test printing a large number. First set the number in an R chunk.
```{r initializeData}
theNum <- 1234567891011.03
options(scipen=999,digits=16)
```
The R code we'll use to format the number is: `prettyNum(theNum,width=23,big.mark=",")`.
Next, print the large number. `r prettyNum(theNum,width=23,big.mark=",")`.
The alternative of using chunk options works as follows.
Now, try an alternative using knitr chunks.
```{r prettyNumHook }
knitr::knit_hooks$set(inline = function(x) { if(!is.numeric(x)){ x }else{ prettyNum(x, big.mark=",",width=23) } })
```
Next, print the large number by simply referencing the number in an inline chunk as `theNum`: `r theNum`.
When both chunks of code are embedded in an Rmd file and knit, the output is as follows, showing that both techniques produce the same result.
regards,
Len
I am making some slides inside Rstudio following instructions here:
http://rmarkdown.rstudio.com/beamer_presentation_format.html
How do I define text size, colors, and "flow" following numbers into two columns?
```{r,results='asis', echo=FALSE}
rd <- sample(x=1e6:1e7, size = 10, replace = FALSE)
cat(rd, sep = "\n")
```
Output is either HTML (ioslides) or PDF (Beamer)
Update:
Currently the code above will only give something like the following
6683209
1268680
8412827
9688104
6958695
9655315
3255629
8754025
3775265
2810182
I can't do anything to change text size, color or put them into a table. The output of R codechunk is just plain text. Maybe it is possible to put them in a table indeed, as mentioned at this post:
http://tex.aspcode.net/view/635399273629833626273734/dynamically-format-labelscolumns-of-a-latex-table-generated-in-rknitrxtable
But I don't know about text size and color.
Update 2:
The idea weaving native HTML code to R output is very useful. I haven't thought of that. This however only works if I want to output HTML. For PDF output, I have to weave the native Latex code with R output. For example, the code following works using "knitr PDF" output:
```{r,results='asis', echo=FALSE}
cat("\\textcolor{blue}{")
rd <- sample(x=1e6:1e7, size = 10, replace = FALSE)
for (n in rd) {
cat(paste0(n, '\\newline \n')) }
cat("}")
```
You are using results='asis', hence, you can simply use print() and formatting markup. If you want your text to be red, simply do:
```{r,results='asis', echo=FALSE}
print("<div class='red2'>")
rd <- sample(x=1e6:1e7, size = 10, replace = FALSE)
cat(rd, sep = "\n")
print("</div>")
```
Hope it helps.
It sounds as if you want the output to be either PDF or HTML.
One possibility is the xtable package. It produces tables either in PDF or HTML format. There's no (output-independent) way to specify colour, however. Here's an example.
xt <- xtable(data.frame(a=1:10))
print(xt, type="html")
print(xt) # Latex default
Another option is the pandoc.table function from the pander package. You need the pandoc binary installed. If you have RStudio, you have this already. The function spits out some markdown which then can be converted to HTML or PDF by pandoc.
Here's how you could use this from RStudio. Create an RMarkdown document like this:
---
title: "Untitled"
author: "You"
date: "20 November 2014"
output: html_document
---
```{r, results='asis'}
library(pander)
tmp <- data.frame(a=1:10,b=1:10)
pandoc.table(tmp)
```
When you click "knit HTML", it will spit out a nice HTML document. If you change output to pdf_document, it will spit out a nice PDF. You can edit the options to change output - e.g.
pandoc.table(tmp, emphasize.strong.rows=c(2,4,6,8,10))
and this will work both in PDF or HTML. (Still no options to change colour though. Homework task: fix pandoc.table to allow arbitrary colours.)
Under the hood, knitr is writing markdown, and pandoc is converting the markdown to whatever you like.
I'm writing an Rmd file, to be processed by knitr into HTML. It contains some R chunks that generate figures, which get stored as data URIs in HTML.
1) How do I add a caption to such an image? I'd like to have a caption that says something like "Figure 3: blah blah blah", where the "3" is automatically generated.
2) How do I later on reference this image, i.e., "as you can see in Figure 3, blah blah".
I'm late to the party, but I wanted to mention a small package I recently built to do figure captioning and cross-referencing with knitr. It is called kfigr and you can install it using devtools::install_github('mkoohafkan/kfigr'). It is still in active development but the main functionality is there. Be sure to check out the vignette, it shows some usage examples and defines some hooks for figure captions and anchors (I may later choose to have the package import knitr and define those hooks on load).
EDIT: kfigr is now available on CRAN!
You can create the figure numbers with a simple counter in R; see one example here. The problem is whether the markdown renderer will render the figure caption for you: R Markdown v1 won't, but v2 (based on Pandoc) will.
I do not know. There is no direct way to insert a label as an identifier for figures, so it is probably not possible to cross reference figures with pure Markdown. Once you've got issues like this, think (1) do I really need it? (2) if it is intended to be a document with a complicated structure, I think it is better to use LaTeX directly (Rnw documents).
Also very late to the party I changed Yihuis suggestion here that he also linked above to do referencing.
```{r functions, include=FALSE}
# A function for captioning and referencing images
fig <- local({
i <- 0
ref <- list()
list(
cap=function(refName, text) {
i <<- i + 1
ref[[refName]] <<- i
paste("Figure ", i, ": ", text, sep="")
},
ref=function(refName) {
ref[[refName]]
})
})
```
```{r cars, echo=FALSE, fig.cap=fig$cap("cars", "Here you see some interesting stuff about cars and such.")}
plot(cars)
```
What you always wanted to know about cars is shown in figure `r fig$ref("cars")`
One way to do both of these is described here: http://rmflight.github.io/posts/2012/10/papersinRmd.html
Another is described here (but I don't know if it does your #2). http://gforge.se/2014/01/fast-track-publishing-using-knitr-part-iii/
Another solution:
https://github.com/adletaw/captioner
From the README:
captioner() returns a captioner function for each set of figures, tables, etc. that you want to create. See the help files for more details.
For example:
> fig_nums <- captioner()
> fig_nums("my_pretty_figure", "my pretty figure's caption")
"Figure 1: my pretty figure's caption"
> fig_nums("my_pretty_figure", cite = TRUE)
I did both (figure numbers + references) with bookdown. I added in output section in the header of the file:
output:
bookdown::html_document2:
fig_caption : TRUE
Then I created a figure in a R code chunk like follows:
{r, my-fig-label,echo=F, eval=T, fig.align = 'center', fig.cap="This is my caption"}
knitr::include_graphics(here::here("images", "my_image.png"))
This produces an automatic number under your figure. You can refer to it with \#ref(fig:my-fig-label).
Using the official bookdown documentation 4.10 Numbered figure captions:
---
output: bookdown::html_document2
---
```{r cars, fig.cap = "An amazing plot"}
plot(cars)
```
```{r mtcars, fig.cap = "Another amazing plot"}
plot(mpg ~ hp, mtcars)
```