I try to reference to a single footnote in a few places in the text. However, with the code below, I've got two footnotes with the same content.
---
title: "My document"
output: html_document
---
One part of the text [^1].
Two pages later [^1].
[^1]: My footnote
Is it possible to reference more than once to a specific footnote using rmarkdown?
I had the same problem. I used html tags which worked really well. Whatever you want as superscript just put between the <\sup> like below:
<sup> text </sup>
jan 6 2023 update:
now I use quarto which is eally easy as you can just use do[^1]
[^1]footnote text
My workaround here is to just do it manually using inline latex mathmode (e.g, \(^2\) ).. Annoying, but even if they had a solution, you'd have to remember the citation number anyways...
I would suggest you to go with latex solution if you do not have many footnotes per page. By latex solution I mean:
(in Markdown, use Latex to superscript the footnote number)
First part$^1$
(and the next one)
Second part$^2$
(at the end of your text add *** to create a line across the document)
(under the line, add the text below:)
1, 2: Text for your footnote
On the other hand, there is a thread created on this specific R-Markdown bug. Maybe take a look at it, in this link.
Hope I helped somehow.
Related
I am using bookdown in R. I have some sections I only want to appear in the HTML (gitbook) version (and not the PDF version).
I know about is_html_output(), but that doesn't appear to be what I want, and doesn't work except for very simple bits of text. So this works:
`r if (knitr:::is_html_output())'
## Some text {-}
Things to say to HTML readers.
'
`
But this doesn't (does not compile) because of the tick in don't :
`r if (knitr:::is_html_output())'
## Some text {-}
Things I don't want to say to PDF readers.
'
`
And any R code I wish to place in the chunk fails too.
So while I can use is_html_output(), it very much restricts what I can do.
Is there an easy way to have some text--whole sections, and other large amounts--only visible in the HTML version?
Seems simple... but I can't find a solution. Thanks for help.
P.
You may consider using child documents, e.g.,
```{r, child = if (knitr::is_html_output()) 'child.Rmd'}
Then you can write arbitrary content in child.Rmd.
I am trying to insert a pdf image into an r markdown file. I know it is possible to insert jpg or png images. I was just wondering if it is also possible to insert a pdf image. Thanks very much!
If you are just trying to insert an image that has been exported from, for example, some R analysis into a pdf image, you can also use the standard image options from the knitr engine.
With something like:
```{r, out.width="0.3\\linewidth", include=TRUE, fig.align="center", fig.cap=c("your caption"), echo=FALSE}
knitr::include_graphics("./images/imagename.pdf")
```
Unfortunately you can't specify the initial dimensions of your image output (fig.width and fig.height), which you would need to pre-define in your initial output, but you can specify the ultimate size of the image in your document (out.width). As noted below, however, this is limited to scaling down.
You could also of course leave out the initial directory specification if your files are in the same working directory. Just be aware of operating system differences in specifying the path to the image.
An alternative method is to use Markdown syntax noted by #hermestrismegistus on this post:
{width=65%}
This can also be collected for multiple images side-by side:
{width=33%}{width=33%}{width=33%}
Edit:
After working more extensively with in-text referencing, I have found that using r chunks and the include_graphics option to be most useful. Also because of the flexibility in terms of image alignment (justification).
As an example:
```{r image-ref-for-in-text, echo = FALSE, message=FALSE, fig.align='center', fig.cap='Some cool caption', out.width='0.75\\linewidth', fig.pos='H'}
knitr::include_graphics("./folder/folder/plot_file_name.pdf")
```
The reference can later be used in-text, for example, Figure \#ref(fig:image-ref-for-in-text) illustrates blah blah.
Some important things to note using this format:
You can only expand PDF images via a code chunk up to the out.width and out.height conditions set in the original .pdf file. So I would recommend setting them slightly on the larger side in your original image (just note that any chart text will scale accordingly).
The in-text reference code (in this case image-ref-for-in-text) CANNOT contain any underscores (_) but can contain dashes (-). You will know if you get this wrong by an error message stating ! Package caption Error: \caption outside float.
To stop your plots drifting to the wrong sections of your document, but in a way that unfortunately will generate some white space, the above example includes fig.pos='H'. Where H refers to "hold" position. The same can be achieved for the former Markdown option by placing a full-stop (period .) immediately after the last curly bracket.
Example:
{width=75%}.
Unfortunately, this latter option results in some unsightly full-stops. Another reason I prefer the include_graphics option.
Sorry, I found that there is a similar post before:
Add pdf file in Rmarkdown file
Basically, I can use something like below works well for the html output:
<img src="myFirstAlignment2.pdf" alt="some text" width="4200" height="4200">
And something like below works well for the pdf output:
(1)possible solution
\begin{center} <br>
\includegraphics[width=8in]{myFirstAlignment2.pdf} <br>
\end{center}
(2)possible solution
The myFirstAlignment2.pdf should be replaced with path\myFirstAlignment2.pdf if the pdf file is not in your working directory.
In relation to the comment of the best answer, there is a way to use the second option, and the output not come out tiny.
Use the following syntax below with the height being a large number. Having text in the brackets is necessary for it to work.
{width=100% height=400}
None of the answers outlined worked well for me in terms of sizing the pdf, so adding another answer using the code chunk options for out.height and out.width to control the size:
```{r out.height = "460px", out.width='800px', echo=F}
knitr::include_graphics("./images/imagename.pdf")
```
I am using knitr to write my thesis and compiling it as a latex document. I have successfully included figures with the appropriately labeled caption; however, in addition to the caption I would like to include additional lines of text directly below the caption and associated with the figure. For example, below the caption I would like to hove: "NOTE: These data are distributed with mu=0 and sd=1" and "SOURCE: These data were randomly generated in R."
EDIT 1 to question: I also need to have a list of figures page with just the caption information included not any of the NOTE or SOURCE information. In addition the caption under the figure must be centered, while the NOTE and SOURCE are left hand justified.
I believe that many publications have figures with notes about the figure or information about the source of the data that is separate from the caption title; so, I believe this question is not just applicable to me.
EDIT 1 to code. Here is a synthesis of the code that #user29020 provided and the link they suggested, as well as the .pdf work around I have assembled from other posts. The advantage of the "pure" knitr method provided by #user29020 is that the plot is beautiful with the text scaled consistently with the body of the text. The disadvantage is a lack of control of the caption information: I would like to center the "Caption" element and left justify the and sub-caption lines and I do not know how to accomplish this; so, if anybody knows how to do this that would be great. The advantage of the pdf work around is that I have greater control over the captions. In addition to not taking full advantage of knitr's ability to create and track figures, the disadvantage is that while the font matches, by using "Ghostscript" the scaling appears a little off and needs to be adjusted in an ad-hoc fashion in the R code.
\documentclass{article}
\usepackage{caption}
\usepackage{tikz}%Draw Graphs
\begin{document}
\listoffigures
\newpage
%THIS IS A SYNTHESIS OF user29020 CODE AND THE LINK THEY PROVIDED IN THEIR COMMENTS
<<cap-setup1,include=FALSE>>=
scap="This is a Caption."
NOTE="NOTE: Here is a note with one linebreak from above."
SOURCE="SOURCE: Here is my source with an extra linebreak to separate it."
EXTRA="{\\tiny EXTRA: Here is smaller text. You could explore more text sizing in \\LaTeX.} And bigger again."
hspace="\\\\\\hspace{\\textwidth}"
cap<- paste(
scap,
hspace,
NOTE,
hspace,
SOURCE,
hspace,
EXTRA)
#
In Figure \ref {fig:fig1}, we see a scatter plot.
<<fig1, echo=FALSE,fig.cap=cap, fig.scap=scap,fig.pos="!h", >>=
r<-rnorm(100)
plot(r)
#
%THIS IS THE PDF WORK AROUND
%Loading R Packages
<<loading,include=FALSE>>=
require(extrafont)
require(graphicx)
font_install("fontcm") #this gets the cm roman family from package extrafont for pdf output in r to match latex
#
<<fig-pdf,echo=FALSE, include=FALSE,fig.cap=paste("This is a Caption"),fig.pos="!h", >>=
Sys.setenv(R_GSCMD="C:/Program Files/gs/gs9.15/bin/gswin64c.exe") #this needs to go inside every r code chunk to call GhostScript for embedding latex font "computer modern roman" (so R font in pdfs matches latex document font)
pdf("tikz-plot-pdf.pdf", family="CM Roman")
set.seed(2015)
r<-rnorm(100)
plot(r)
dev.off()
embed_fonts("tikz-plot-pdf.pdf") #this embeds the pdf font so that when graphicx calls the pdf the fonts from R to latex match
#
\newpage
In Figure \ref{fig:scatter}, we see a scatter plot.
\begin{figure}[!h]
\centering
\includegraphics[width=\textwidth]{tikz-plot-pdf}
\caption{This is also a Caption}\label{fig:scatter}
\begin{minipage}{\textwidth}
NOTE: Here is a note with one linebreak from above.\\
SOURCE: Here is my source with an extra linebreak to separate it.\\
EXTRA:{\tiny EXTRA: Here is smaller text. You could explore more text sizing in \LaTeX.} And bigger again.
\end{minipage}
\end{figure}
\end{document}
I would like to have the "NOTE" and "SOURCE" lines below the caption line, EDIT 1: only the caption included in the \listoffigures and the caption centered, while the NOTE and SOURCE are left justified (like the output from the pdf workaround):
I have not asked a question on this forum before, although I have found many answers, so any meta-feedback on my question EDIT 1: or how I am editing is also appreciated.
Thank You
This answer assumes that multiline captions are sufficient for your purposes. I used your method of passing an R variable to the Knitr fig.cap= argument. This lets us compose the caption ahead of time in other code chunks before use.
The tricks were that A) we need to find out how to add line break to caption without using caption package, and B) know how to pass literal "\" (backslash) characters to the resulting Latex document.
The reference about adding captions suggests adding \\\hspace{\textwidth} to start a new line within the caption (in the Latex file). So, we escape it in the Knitr file like this \\\\\\hspace{\\textwidth}.
Indeed, almost any Latex code you want to end up in the Latex file will have to be escaped this way. When writing your thesis, you'll want to refer to your Figures, no doubt. You can use the Latex references by putting the figure \label into the caption and then using a \ref{} elsewhere.
See the modified version of your file below for multiline captions and figure references:
\documentclass[12pt]{article}%12 Pt font, article document class
\usepackage{caption}
\usepackage{tikz}%Draw Graphs
\begin{document}
<<>>=
x <- paste(
"This is a Caption.",
"\\\\\\hspace{\\textwidth}",
"NOTE: Here is a note with one linebreak from above.",
"\\\\\\hspace{\\textwidth}",
"\\\\\\hspace{\\textwidth}",
"SOURCE: Here is my source with an extra linebreak to separate it.",
"\\\\\\hspace{\\textwidth}",
"{\\tiny EXTRA: Here is smaller text. You could explore more text sizing in \\LaTeX.} And bigger again.",
"\\label{figure:demo-of-multiline-captions}",
"\n" )
cat(x)
#
We can also show the variable "x" in the "asis" formate here:
<<results="asis">>=
cat(x)
#
This text right here (now) is a new paragraph, so it is indented.
Below, in \textbf{Figure~\ref{figure:demo-of-multiline-captions}}, we use the "x" variable in the "fig.cap=" argument to Knitr.
<<fig1, echo=FALSE,fig.cap=x,fig.pos="!h", >>=
r<-rnorm(100)
plot(r)
#
\end{document}
Results give this:
I writing a Word document with R markdown in R Studio. I can get many things, but at the moment I am not figuring out how can I get a page break. I have found solutions but only for rendered latex / pdf document that it is not my case.
Added: To insert a page break, please use \newpage for formats including LaTeX, HTML, Word, and ODT.
https://bookdown.org/yihui/rmarkdown-cookbook/pagebreaks.html
Paragraph before page break.
\newpage
First paragraph on a new page.
Previously: There is a way by using a fifth-level header block (#####) and a docx template defined in YAML.
After creating headingfive.docx in Microsoft Word, you select Modify Style of the Heading 5, and then select Page break before in the Line and Page Breaks tab and save the headingfive.docx file.
---
title: 'Making page break using fifth-level header block'
output:
word_document:
reference_docx: headingfive.docx
---
In your Rmd document, you define reference_docx in the YAML header, and now you can use the page-breaking #####.
Please see below.
https://www.r-bloggers.com/r-markdown-how-to-insert-page-breaks-in-a-ms-word-document/
With the help of John MacFarlane and others on the pandoc google group, I put together a filter that does this. Please see:
https://groups.google.com/forum/#!topic/pandoc-discuss/FzLrhk0vVbU
In short, the filter needs to look for something to replace with the openxml for pagebreak. In this case
\newpage
is being replaced with
<w:p><w:r><w:br w:type=\"page\"/></w:r></w:p>
This allows for a single latex markup to be interpreted for both pdf and word output.
Joel
What you are trying to do is force a "page break" or "new page" in a word document generated with Pandoc. I have found a way to do this in my environment but I'm not sure it will work in every environment.
My environment:
* R-studio / Pandoc / MS-WORD starting with an "*.Rmd" file and generating a DOCX file.
In my RMD file the key idea is that i've created what acts like a TEMPLATE document (MyFormattingDocument.docx) and in that word document I tweak the STYLES for things like "Heading 1" and/or "Heading 2" and or "footnote" or whatever other predefined styles I want to tweak.
(SEE THIS: http://rmarkdown.rstudio.com/word_document_format.html#style-reference ) for explanation of style reference and how to set the header information in your RMD file to specify a reference document.
SOOOO in my case... i tweak the "Heading 1" style in WORD to include a forced "Page Break Before" in the Paragraph formatting for "Heading 1". Exactly how you force every "Heading 1" to always "Page Break" is different in different versions of Microsoft WORD but if you follow the WORD documentation and modify the "Heading 1" style THEN every "Heading 1" will always have a pagebreak before it.
THEN... you save this template file in the some directory you're working from with the RMD file... and it is USED AS a template. THE CONTENTS of the file are ignored.... so don't worry... you can put sample text in this file and test that the formatting all works.... THE CONTENTS ARE IGNORED but the STYLES are USED in the new word document which will be built by the RMD file so.... then every "Heading 1" will have a break before it.
NOTE: You could obviously do the same with ANY style that has a one-to-one mapping from PANDOC MARKUP so you could instead just make all "Heading 3" or whatever.... just look at see in your RMD created DOCX what "STYLE" is being applied and then tweak that style even if you need to insert some "fake" lines with essentially blank content just for the purpose of forcing a style to appear in the DOCX
Here is an R script that can be used as a pandoc filter to replace LaTeX breaks (\pagebreak) with word breaks, per #JAllen's answer above. With this you don't need to compile a pandoc script. Since you are working in R Markdown I assume one has R available in the system.
#!/usr/bin/env Rscript
json_in <- file('stdin', 'r')
lat_newp <- '{"t":"RawBlock","c":["latex","\\\\newpage"]}'
doc_newp <- '{"t":"RawBlock","c":["openxml","<w:p><w:r><w:br w:type=\\"page\\"/></w:r></w:p>"]}'
ast <- paste(readLines(json_in, warn=FALSE), collapse="\n")
ast <- gsub(lat_newp, doc_newp, ast, fixed=TRUE)
write(ast, "")
Save this as page-break-filter.R or something like that and make it executable by running chmod +x page-break-filter.R in the terminal.
Then include this filter the R Markdown YAML like so:
---
title: "Title
author: "Author"
output:
word_document:
pandoc_args: [
"--filter", "/path/to/page-break-filter.R"
]
---
You can use the R package worded. This avoids the need for a template word file. See https://github.com/davidgohel/worded.
The output parameter needs to be set to worded::rdocx_document and you need to call library(worded).
---
date: "2018-03-27"
author: "David Gohel"
title: "Document title"
output:
worded::rdocx_document
---
```{r setup, include=FALSE}
library(worded)
```
You can then add <!---CHUNK_PAGEBREAK---> to your document whenever you want a page break.
The package allows various word formatting options using a similar mechanism.
When updating to R 4.0.0, the <!---CHUNK_PAGEBREAK---> solution was not working any more for me.
Instead I could use the run_pagebreak() function from the officer package, still in combination with the officedown package:
---
output: word_document
---
```{r settings}
library(officedown)
library(officer)
```
Hello world on page 1
`r run_pagebreak()`
Hello world on page 2
R Markdown 1.16 introduced a new feature which allows to insert a page break by adding a paragraph that contains only the commands \pagebreak or \newpage:
Paragraph before page break.
\pagebreak
First paragraph on a new page.
See also the pagebreaks section in the R Markdown cookbook.
It is not an automated solution. But I have been adding the text '#####page break' to my markdown document. Then in MS Word using find-replace to replace the text "page break" with "^m" (manual page break).
Sungpil's article was close, but didn't quite work. This was the best solution I found for this:
https://scriptsandstatistics.wordpress.com/2015/12/18/rmarkdown-how-to-inserts-page-breaks-in-a-ms-word-document/
Even better, the author included the Word template to make this work. The R-blogger's link to his template is broken, and the header is formatted wrong. Some notes I took:
1) You might need to include the whole path to the word template in your Rmd header, like so:
output:
word_document:
reference_docx: C:/workspace/myproject/mystyles.docx
2) The template at the link above changed some of the default style settings so you'll need to change them back
My solution is not very robust but can work for some of us.
Assuming you need a page break before each level 1 title in your word document, I defined this in the format template used in the yaml field reference_docx: .
In this document you modify the Heading 1 format (or equivalent) to insert a page break before the Title. Do not forget to start your template with the first docx rendered with knitr (pandoc) in RStudio.
Ok, I found this in the markdown docs.
Horizontal Rule / Page Break
Three or more asterisks *** or dashes ---.
I want to center an image and/or text using R Markdown and knit a PDF report out of it.
I have tried using:
->Text<-
-><-
That does not do the trick! Any other way of getting this done?
I had the same question. I have tried all solutions provided above and none of them worked... But I have found a solution that works for me, and hopefully for others too.
<center>
</center>
This code will center both the image and the caption. It is essential that you leave lines between <center>, the image code, and </center>, otherwise the image will be centered but the caption will disappear.
If you want your image to have a clickable link, you can embed things like
[](www.link_to_image.com)
However, the caption will no longer appear.
So if you want a clickable caption you will have to do it in two steps:
<center>
[your image caption](www.link_to_image.com)
</center>
Same here, make sure there are empty lines in between each command ones. If you want both the image and the caption to be clickable, then combine the middle and the last codes above. I hope this helps a bit.
If you are centering the output of an R code chunk, e.g., a plot, then you can use the fig.align option in knitr.
```{r fig.align="center"}
plot(mtcars)
```
You can use raw LaTeX in R Markdown. Try this:
\begin{center}
Text
\end{center}
There is, of course, a catch: everything between begin{...} and \end{...} is interpreted as raw LaTeX by Pandoc, so you can't use this technique to center the output of R code chunks, or Markdown content.
You can set the center (or other) alignment for the whole document as a Knitr option, using:
knitr::opts_chunk$set(echo = TRUE, fig.align="center")
None of the answers work for all output types the same way and others focus on figures plottet within the code chunk and not external images.
The include_graphics() function provides an easy solution. The only argument is the name of the file (with the relative path if it's in a subfolder). By setting echo to FALSE and fig.align=center you get the wished result.
```{r, echo=FALSE, fig.align='center'}
include_graphics("image.jpg")
```
I used the answer from Jonathan to google inserting images into LaTeX and if you would like to insert an image named image1.jpg and have it centered, your code might look like this in Rmarkdown
\begin{center}
\includegraphics{image1}
\end{center}
Keep in mind that LaTex is not asking for the file exention (.jpg). This question helped me get my answer. Thanks.
The simple solution given by Jonathan works with a modification to cheat Pandoc. Instead of direct Latex commands such as
\begin{center}
Text
\end{center}
you can define your own commands in the YAML header:
header-includes:
- \newcommand{\bcenter}{\begin{center}}
- \newcommand{\ecenter}{\end{center}}
And then you use:
\bcenter
Text and more
\ecenter
This works for me for centering a whole document with many code chunks and markdown commands in between.
I'm using beamer to knit pdf from Rmarkdown and what worked for me is:
\centering
If you know your format is PDF, then I don't see how the HTML tag
can be useful... It definitely does not seem to work for me. The other pure LaTeX solutions obviously work just fine. But the whole point of Markdown is not to do LaTeX but to allow for multiple format compilation I believe, including HTML.
Therefore, with this in mind, what works for me is a variation of Nicolas Hamilton's answer to Color Text Stackoverflow question:
#############
## CENTER TXT
ctrFmt = function(x){
if(out_type == 'latex' || out_type == 'beamer')
paste0("\\begin{center}\n", x, "\n\\end{center}")
else if(out_type == 'html')
paste0("<center>\n", x, "\n</center>")
else
x
}
I put this inside my initial setup chunk.
Then I use it very easily in my .rmd file:
`r ctrFmt("Centered text in html and pdf!")`
There is now a much better solution, a lot more elegant, based on fenced div, which have been implemented in pandoc, as explained here:
::: {.center data-latex=""}
Some text here...
:::
All you need to do is to change your css file accordingly. The following chunk for instance does the job:
```{cat, engine.opts = list(file = "style.css")}
.center {
text-align: center;
}
```
(Obviously, you can also directly type the content of the chunk into your .css file...).
The tex file includes the proper centering commands.
The crucial advantage of this method is that it allows writing markdown code inside the block.
In my previous answer, r ctrFmt("Centered **text** in html and pdf!") does not bold for the word "text", but it would if inside a fenced div.
For images, etc... the lua filter is available here
Just to update the question. To do this some easy way, you can add fig.align="center" to the chunk with the chuck knitr options:
knitr::opts_chunk$set(echo = TRUE,
fig.align="center" #align all the figures in the center
)
none of the answers worked but this
\newcommand{\bcenter}{\begin{center}}
\newcommand{\ecenter}{\end{center}}
but then the following problem is that it works for only one figure and then will not for any other figures.
I just started learning R I knew it was going to be difficult but what's worst is that there is little to no info that I can refer to.
None of these solutions worked for me when inserting a pdf figure in the text. After intensive trial and error, what made the trick for me (for a pdf output) was:
\hfil  \hfil
Since the question asks for both text and image alignment and I had a hard time finding an option for text that worked, with non of the ones above working withing a code chunk (for me). I wanted to share this: it seem to do the trick to the best of it's abilities (meaning it's not perfectly centered but close)
centerText <- function() {
width <- getOption("width")
out <- "your text"
ws <- rep(" ", floor((width - nchar(out))/2))
cat(ws, out, sep = "")
}
centerText()
Original code comes from here