I need to get Quarto to put figure captions above the figure, rather than the default (below).
Following the documentation I used this:
---
title: "Test title"
format: docx
fig-cap-location: top
---
```{r}
#| label: fig-test
#| fig-cap: This caption should be above the figure
plot(cars)
'``
However, this renders like so:
I see that some people have resorted to LaTeX customisations or knit hooks, however I'm also failing at those (and I don't understand why the simple YAML marker I used, that is recommended in the documentation, isn't working).
Edit: as Mael pointed out, fig-cap-location is not an option for docx outputs. The Quarto documentation has since been amended to clarify this.
If you check the list of MS Word options, fig-cap-location is not actually one of them (compared to e.g., PDF options), so this option is just not available with a docx output.
Related
Have tried styling MS Word document from the markdown but I don't seem to get it write. What could I not be doing right? Below is the code
---
title: "Test Document"
author: "Moses Otieno"
date: "05/04/2021"
output:
word_document:
reference_docx: referent-doc.docx
---
```{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>.
## Test
This is the test
Referent Document https://www.dropbox.com/scl/fi/dyww5eiga334j55t58vcp/referent-doc.docx?dl=0&rlkey=o1ejilu3dfnncar65irh5er7v
Resulting document https://www.dropbox.com/scl/fi/mieqkcvy22eeighdjaby3/Test.docx?dl=0&rlkey=8wyrci2cg0ijyxbfdw5ks1znh
In a nutshell, make a template using an already knitted document containing your content and different types of headers etc.
I had a similar problem that was fixed by knitting my document and saving the resulting word(.docx) as "template". I now had a good working file with lots of content examples.
Next, I went into this file and manually changed the styles using "styles" in the Home tab. Open up this feature in your new "template" document by using the little down arrow on the bottom right-hand corner. Click on the various paragraphs and headers in your document to see what they refer to (the style will jump about on the dropdown menu) and make your changes. Save again. Now when you want to knit a new document, it will hopefully apply your changes.
Be aware that you might get caught out by the "Body Text" and "First Paragraph", so you might need to change both of these separately.
output:
word_document:
reference_docx: template.docx
In the YAML part of your project, you have to change your referent.docx into "referent-doc.docx", surrounded by quotation marks (" "):
output:
word_document:
reference_docx: "referent-doc.docx"
# quoted with quotation marks, and here located in the same folder
P.S. Be sure to produce a good reference_doc: You need to start from a .docx file which is produced by markdown (e.g., using the knit button), in order to get a few titles, texts, figs and tables into a .docx. Then edit the styles; margin, etc. from Microsoft Word, and save it to a .docx file.
I'm having some trouble to compile an entire document from many Rmd files by using the bookdown approach.
If I knit individual .Rmd files then 'preamble.tex' included in YAML options is taken into account.
If I render the book (with both approaches described here), then 'preamble.tex' is ignored.
To make things concrete, consider the following mwe:
preamble.tex:
\usepackage{times}
index.Rmd:
---
title: "My paper"
site: "bookdown::bookdown_site"
output:
bookdown::pdf_document2:
includes:
in_header: "preamble.tex"
---
01-intro.Rmd:
# Introduction
This chapter is an overview of the methods that we propose to solve an **important problem**.
Then, by knitting 'index.Rmd' or '01-intro.Rmd' the font indicated in 'preamble.tex' is used.
However when rendering with bookdown::render_book('index.Rmd',"bookdown::pdf_book", new_session = T) it is simply ignored.
What is more, in my actual project there are other output options that end up ignored. For example, I use toc: false and it works when knitting single files, but fails when rendering the document.
In this simple example it would be okay to use a single file, but my actual project has many chapters with R chunks within each of them. Thus, building a single file doesn't seem a good idea.
I appreciate any hints on what I am missing here.
Thanks in advance.
What you are missing here is that in your YAML header, preamble.tex is included for the bookdown::pdf_document2 output format and not bookdown::pdf_book, the format you pass to the output_format argument in bookdown::render_book(). For this reason, other YAML options (like toc: true) do not work either.
Running
bookdown::render_book('index.Rmd', "bookdown::pdf_document2", new_session = T)
instead should work.
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'd like to include LaTeX environments (e.g., algorithmic from algorithmicx, mini from optidef, dcases from mathtools, etc.) in my .Rmd bookdown file. This is no problem for pdf output. But these do not render for html or docx output.
My current hack solution:
Generate the .pdf output.
Screen shot, edit, save images of interest as png
Include images conditional on output not being LaTeX
Downsides:
Obviously doesn't scale
Images are ugly in docx and html output
Screws with figure cross-referencing
There has to be a better approach, right? I was thinking that there's a way to tell rmarkdown/LaTeX that, when rendering as pdf, certain code chunks should be saved in some image format. That way they could be added back into the document as images conditional on the output document being docx or html. Is that even possible?
UPDATE: An answer to Standalone diagrams with TikZ suggests an approach involving the LaTeX standalone package. But unfortunately, it's discovered over at standalone does not work with algorithms that this does not work for the algorithm environment. Any ideas?
index.Rmd
---
title: "Bookdown"
header-includes:
- \usepackage{float}
- \floatplacement{figure}{!htb}
- \usepackage{algorithm}
- \usepackage{algpseudocode}
output:
bookdown::gitbook:
split_by: none
bookdown::pdf_book:
fig_caption: yes
keep_tex: yes
toc: no
bookdown::word_document2: default
site: bookdown::bookdown_site
---
```{r setup, include=FALSE, }
knitr::opts_chunk$set(echo = TRUE)
```
Hello zero
# First Chapter
Hello one
\begin{algorithm}
\caption{My Algo}
\begin{algorithmic}[1]
\State Do this.
\State Do that.
\end{algorithmic}
\end{algorithm}
```{r myalgo, echo=FALSE, eval = !knitr:::is_latex_output(), fig.cap="Must have text here. For cross-referencing to work."}
knitr::include_graphics("myalgo.png")
```
Hello two.
Check out this picture: \#ref(fig:myalgo)
myalgo.png
For math, R Markdown uses MathJax, and only a subset of LaTeX is available. This subset includes the basic math macros and environments, and allows you to define new macros, but doesn't support everything necessary to let you use arbitrary LaTeX packages. See http://docs.mathjax.org/en/latest/tex.html for details.
You might be able to create an environment that looks something like algorithm or algorithmic, but it's going to be a lot of work, and likely won't look as nice.
You should probably choose between PDF output with all of LaTeX available for formatting, or some flavour of HTML output with less style. For example, you could write your algorithm as
******
**Algorithm 1**: My algo
******
1. Do this.
2. Do that.
******
and it will display as
Algorithm 1: My algo
Do this.
Do that.
When using knitr and rmarkdown together to create a word document you can use an existing document to style the output.
For example in my yaml header:
output:
word_document:
reference_docx: style.docx
fig_caption: TRUE
within this style i have created a default table style - the goal here is to have the kable table output in the correct style.
When I knit the word document and use the style.docx the tables are not stylized according to the table.
Using the style inspector has not been helpful so far, unsure if the default table style is the incorrect style to modify.
Example Code:
```{r kable}
n <- 100
x <- rnorm(n)
y <- 2*x + rnorm(n)
out <- lm(y ~ x)
library(knitr)
kable(summary(out)$coef, digits=2, caption = "Test Captions")
```
I do not have a stylized document I can upload for testing unfortunately.
TL;DR: Want to stylise table output from rmarkdown and knitr automatically (via kable)
Update: So far I have found that changing the 'compact' style in the docx will alter the text contents of the table automatically - but this does not address the overall table styling such as cell colour and alignment.
Update 2: After more research and creation of styles I found that knitr seems to have no problem accessing paragraph styles. However table styles are not under that style category and don't seem to apply in my personal testing.
Update 3: Dabbled with the ReporteRs package - whilst it was able to produce the tables as a desired the syntax required to do so is laborious. Much rather the style be automatically applied.
Update 4: You cannot change TableNormal style, nor does setting a Table Normal style work. The XML approach is not what we are looking for. I have a VBA macro that will do the trick, just want to remove that process if possible.
This is essentially a combination of the answer that recommends TableNormal, this post on rmarkdown.rstudio.com and my own experiments to show how to use a TableNormal style to customize tables like those generated by kable:
RMD:
---
output:
word_document
---
```{r}
knitr::kable(cars)
```
Click "Knit Word" in RStudio. → The document opens in Word, without any custom styles yet.
In that document (not in a new document), add the required styles. This article explains the basics. Key is not to apply direct styles but to modify the styles. See this article on support.office.com on Style basics in Word.
Specifically, to style a table you need to add a table style. My version of Word is non-English, but according to the article linked above table styles are available via "the Design tab, on the Table Tools contextual tab".
Choose TableNormal as style name and define the desired styles. In my experiments most styles worked, however some did not. (Adding a color to the first column and making the first row bold was no problem; highlighting every second row was ignored.) The last screenshot in this answer illustrates this step.
Save the document, e.g. as styles.docx.
Modify the header in the RMD file to use the reference DOCX (see here; don't screw up the indentation – took me 10 minutes find this mistake):
---
output:
word_document:
reference_docx: styles.docx
---
Knit to DOCX again – the style should now be applied.
Following the steps I described above yields this output:
And here a screenshot of the table style dialog used to define TableNormal. Unfortunately it is in German, but maybe someone can provide an English version of it:
As this does not seem to work for most users (anyone but me …), I suggest we test this systematically. Essentially, there are 4 steps that can go wrong:
Wrong RMD (unlikely).
Differences in the initially generated DOCX.
Differences in how the TableNormal style is saved in the DOCX.
Differences in how the reference DOCX is used to format the final DOCX.
I therefore suggest using the same minimal RMD posted above (full code on pastebin) to find out where the results start do differ:
My initially generated DOCX.
The same document with TableNormal added: reference.docx
The final document.
The three files are generated on the following system: Windows 7 / R 3.3.0 / RStudio 0.99.896 / pandoc 1.15.2 / Office 2010.
I get the same results on a system with Windows 7 / R 3.2.4 / RStudio 0.99.484 / pandoc 1.13.1 / Office 2010.
I suppose the most likely culprits are the pandoc and the Office versions. Unfortunately, I cannot test other configurations at the moment. Now it would be interesting to see the following: For users where it does not work, what happens …
… if you start from my initial.docx?
If that does not work, what if you use my reference.docx as reference document?
If nothing works, are there eye-catching differences in the generated XML files (inside the DOCX container)? Please share your files and exact version information.
With a number of users running these tests it should be possible to find out what is causing the problems.
This was actually a known issue. Fortunately, it was solved in v2.0 or later releases of pandoc.
And I have tested the newer version, and found that there is a newly-added hidden style called "Table". Following #CL.'s suggestions to change "Table" style in reference.docx will be okay now.
In addition, look at this entry of pandoc's v2.0 release notes:
Use Table rather than Table Normal for table style (#3275). Table Normal is the default table style and can’t be modified.
As of 2021, I could not get any of the other suggested answers to work.
However, I did discover the {officedown} package, which, amongst other things, supports the styling of tables in .docx documents. You can install {officedown} with remotes::install_github("davidgohel/officedown")
To use {officedown} to render .Rmd to .docx you must replace
output:
word_document
in your document header with
output:
officedown::rdocx_document
In addition to this the {officedown} package must be loaded in your .Rmd.
As with the word_document output format, {officedown} allows us to use styles and settings from template documents, again with the reference_docx parameter.
With a reference document styles.docx, a minimal example .Rmd may look like:
---
date: "2038-01-19"
author: "The Reasonabilists"
title: "The end of time as we know it"
output:
officedown::rdocx_document:
reference_docx: styles.docx
---
```{r setup, include = FALSE}
# Don't forget about me: I'm important!
library("officedown")
```
{officedown} allows us to go one step further and specify the name of the table style to use in the document's front matter. This table style could be a custom style we created in styles.docx, or it could be one of Word's in-built styles you prefer.
Let's say we created a style My Table:
We could tell {officedown} to use this table style in our front matter as:
output:
officedown::rdocx_document:
reference_docx: styles.docx
tables:
style: My Table
Putting this altogether, knitting the minimal .Rmd:
---
date: "2038-01-19"
author: "The Reasonabilists"
title: "The end of time as we know it"
output:
officedown::rdocx_document:
reference_docx: styles.docx
tables:
style: My Table
---
```{r setup, include = FALSE}
# Don't forget about me: I'm important!
library(officedown)
```
```{r}
head(mtcars)
```
Resulting in a .docx document which looks like:
TableNormal doesn't work for me too.
On my Dutch version of Word 2016 (Office 365), I found out that I could markup tables with the style Compact.
Input (refdoc.docx contains the Compact style):
---
title: "Titel"
subtitle: "Ondertitel"
author: "`r Sys.getenv('USERNAME')`"
output:
word_document:
toc: true
toc_depth: 2
fig_width: 6.5
fig_height: 3.5
fig_caption: true
reference_docx: "refdoc.docx"
---
And RMarkdown:
# Methoden {#methoden}
```{r}
kable(cars)
```
Output:
You need to have a reference_docx: style.docx which has "Table" style in it. (see #Liang Zhang's explanation and links above).
Create a basis reference document using pandoc (source). In command line (or cmd.exe on Windows) run:
pandoc -o custom-reference.docx --print-default-data-file reference.docx
In this newly created reference.docx file, find the table created (a basic 1 row table with a caption).
While the table is selected, click "Table Design" and find "Modify Table Style":
Modify the style of the table as you wish and use this reference document in your RMD document (see the first answer by #CL.).
Using this reference document, you can also change the table and figure caption styles.
I was able to get my word output to use a default table style that I defined in a reference .docx.
Instead of 'TableNormal', the table style it defaulted to was 'Table'.
I discovered this by knitting an rmarkdown with a kable.
---
date: "December 1, 2017"
output:
word_document:
reference_docx: Template.docx
---
`r knitr::kable(source)`
Then I took a look at that generated document's XML to see what style it had defaulted to.
require(XML)
docx.file <- "generated_doc.docx"
## unzip the docx converted by Pandoc
system(paste("unzip", docx.file, "-d temp_dir"))
document.xml <- "temp_dir/word/document.xml"
doc <- xmlParse(document.xml)
tblStyle <- getNodeSet(xmlRoot(doc), "//w:tblStyle")
tblStyle
I defined the 'Table' style to put some color and borders in the reference docx. This works for one standard table style throughout the document, I haven't found a way to use different styles throughout.
This stayed true even after I opened the reference doc and edited it.