Where to put header.tex to change page to Landscape Rmarkdown - r-markdown

I read here how to add what is needed to give me the ability to change my page to landscape:
enter link description here
However I have saved the header.tex file everyplace I could think of and I still end up getting the following error:
Called from: (function (e)
{
if (inherits(e, "shiny.silent.error"))
return()
handle <- getOption("shiny.error")
if (is.function(handle))
handle()
})(list(message = "pandoc document conversion failed with error 43",
call = NULL))
Browse[1]>
I know this is do to me typing \blandscape and \elandscape because the PDF works as soon as I delete those commands. What I need help with is figuring out where to save the header.tex file to so that Rmarkdown knows how to locate it. Thanks in advance for everyone's your help!
Follow up:
Taking scoa's advice about adding it to my header I edited the top of my Rmd file to the following. Unfortunately it still didn't work.
---
title: "Lake Report"
output: pdf_document
header-includes:
- \usepackage{lscape}
- \newcommand{\blandscape}{\begin{landscape}}
- \newcommand{\elandscape}{\end{landscape}}
---
\newpage
\blandscape
```{r Non-Seasonal MK results, echo=FALSE}
# MKanalysis <- reactive(HM_MK(data = NonSeasonalData(),n = 4))
kable(MKanalysis(), caption = "Non-Seasonal Trend Analysis")
```
The results of the Mann Kendall analysis....
\elandscape
Latex program/verision: pdfTex, Version 3.14159265-2.6-1.40.17

Save the header.tex in the same directory your Rmd file is. Also, rather than an external file, you could just add those commands in your yaml front matter, a more portable solution:
---
title: "Lake Report"
output: pdf_document
header-includes:
- \usepackage{lscape}
- \newcommand{\blandscape}{\begin{landscape}}
- \newcommand{\elandscape}{\end{landscape}}
---

Related

Unable to find file 'path/NA' when knitting to word_document2 using tbl_summary but works for PDF, HTML etc

before you click "next", this is not a path file error.
I am building on a blogpost: https://labrtorian.com/2019/08/26/rmarkdown-template-that-manages-academic-affiliations/
It works well for scientific papers.
My problem is:
In Rmarkdown when calling a data frame I am returned with the error about not being able to find file 'path/NA'
---
output:
bookdown::word_document2:
pandoc_args:
- --reference-doc=Extras/Reference_Document.docx
keep_tex: TRUE
---
```{r MRE}
library(gtsummary)
a <- c(10,20,30,40)
b <- c('book', 'pen', 'textbook', 'pencil_case')
c <- c(TRUE,FALSE,TRUE,FALSE)
d <- c(2.5, 8, 10, 7)
df <- data.frame(a,b,c,d)
tbl_summary(df)
tbl_summary
which returns:
Error: could not find file '/Users/brianbrummer/Documents/Rstudio/Affilitations_template/NA'
Execution halted
So what gives? I would usually know how to fix a "path not found" error, but not a file...and the file is NA?
files referenced in YAML can be found:
https://github.com/bridaybrummer/author_affiliations_extras.git
Thanks in advance
I did some digging and found the issue and a solution. First, if you update your yaml to call the reference document like this, you won't get the error any longer.
---
output:
word_document:
reference_doc: Reference_Document.docx
---
The issue was with the flextable package. If you're looking for community service points, you can post this reprex to their github page to alert them to the issue.
---
output:
word_document:
pandoc_args:
- --reference-doc=Reference_Document.docx
---
```{r MRE}
mtcars |>
flextable::flextable()
```

When I use RStudio to Generate PDF File,I Met this Error :! Missing number, treated as zero

When I use RStudio to Generate PDF File,I Met this Error :
Missing number, treated as zero.
<to be read again>
(
l.349 \begin
{minipage}[b]{\linewidth}\raggedright
错误: LaTeX failed to compile bookdown.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See bookdown.log for more info.
停止执行
When I open the tex file:
\begin{minipage}[b]{\linewidth}\raggedright
独立性和可持续性
\end{minipage}
the Rmd file is
---
CJKmainfont: PingFangSC-Regular
fontsize: "12pt"
indent: true
header-includes:
- \usepackage{xeCJK}
output:
pdf_document:
keep_tex: yes
latex_engine: xelatex
toc: yes
toc_depth: 1
template: latex/template.tex
documentclass: ctexbook
link-citations: yes
geometry: [b5paper, tmargin=2.5cm, bmargin=2.5cm, lmargin=3.5cm, rmargin=2.5cm]
colorlinks: yes
---
latex/template.tex:
https://github.com/yihui/bookdown-chinese/blob/master/latex/template.tex
How can I fix it? if I comment the code (#template:latex/template.tex) the Errors would be gone
You will successfully render the following Rmd to a pdf without any error.
Although #Stéphane Laurent commented here that you may need to add a diameter to \linewidth, I do not think that is cause of the problem you faced, since the Rmd below using \linewidth, not 1\linewidth, works fine.
The real problem may lay in other parts of your Rmd file, I suspect. However, you must post a reproducible example like the one I show in this answer, as I commented here, and present the contents of the .log file that is created when you knit your Rmd file.
---
header-includes:
- \usepackage{ctex}
output:
pdf_document: default
---
\begin{minipage}[b]{\linewidth}\raggedright
独立性和可持续性
\end{minipage}

Problem with ligatures in Rmarkdown / bookdown pdf output

In my Rmarkdown project, I'm having trouble in correctly exporting ligatures in PDF file.
font-config.tex file -
\usepackage{fontspec}
\setmainfont{Noto Sans}
YAML front-matter in Rmd file -
---
title: "test"
author: "author"
date: "22/02/2021"
output:
pdf_document:
latex_engine: xelatex
includes:
in_header: font-config.tex
---
The following text is in hindi language.
गुरु
Output shown in PDF -
Output expected -
The Nakula font is correctly displayed, but it does not have bold-face type font.
The Noto Sans font I'm using works fine in html output, but have problem with ligature in PDF output.
I tried, the pandoc documentation and other similar questions on stackoverflow and tex.stackexchange, but no luck.
I'm new to TeX, and hopefully it has a very simple solution.
This may work for you, following the information given here:
---
title: "Hindi"
author: "bttomio"
output:
pdf_document:
latex_engine: xelatex
header-includes:
- \usepackage{fontspec}
- \setmainfont{Noto Sans}
- \usepackage{polyglossia}
- \setdefaultlanguage{hindi}
- \setotherlanguage{english}
- \newfontfamily\devanagarifont[Scale=MatchUppercase]{Nakula}
- \newfontfamily\devtransl[Mapping=DevRom]{Times New Roman}
---
The following text is in hindi language.
गुरु
-output

Setting citation_package option under pdf_document in YAML Header and using rmarkdown::pdf_document function

The help file of the pdf_document function of the Rmarkdown CRAN package says that the function is defined with the following options:
pdf_document(toc = FALSE, toc_depth = 2, number_sections = FALSE,
fig_width = 6.5, fig_height = 4.5, fig_crop = TRUE,
fig_caption = TRUE, dev = "pdf", df_print = "default",
highlight = "default", template = "default", keep_tex = FALSE,
latex_engine = "pdflatex", citation_package = c("none", "natbib",
"biblatex"), includes = NULL, md_extensions = NULL,
pandoc_args = NULL, extra_dependencies = NULL)
I am under the impression that I could add any of these arguments as options under pdf_document in the output section of the YAML header in my Rmarkdown document. Is this correct? The document managed to compile when I used the following options/arguments of pdf_document: toc, number_sections, fig_caption, df_print, and keep_tex. However, when I add citation_package to the list, I get an error in compiling. For instance, consider the following template Rmarkdown document.
---
title: "Untitled"
author: "Unknown"
date: "4/18/2019"
output:
pdf_document:
# toc: true
number_sections: true
fig_caption: true
df_print: kable
keep_tex: true
citation_package: biblatex
bibliography: sample_bib.bib
csl: /Users/Shared/Zotero/styles/multidisciplinary-digital-publishing-institute.csl
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
I love R [#rcoreteamLanguageEnvironmentStatistical2018].
The sample_bib.bib mentioned is the bib file that looks like
#software{rcoreteamLanguageEnvironmentStatistical2018,
location = {{Vienna, Austria}},
title = {R: {{A Language}} and {{Environment}} for {{Statistical Computing}}},
url = {https://www.R-project.org/},
version = {3.5.1},
organization = {{R Foundation for Statistical Computing}},
date = {2018},
author = {{R Core Team}}
}
However, I was unable to knit this Rmarkdown document. I got the following error.
/usr/local/bin/pandoc +RTS -K512m -RTS rmarkdown_pdf_document.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output rmarkdown_pdf_document.tex --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmarkdown/rmd/latex/default-1.17.0.2.tex --number-sections --highlight-style tango --pdf-engine pdflatex --biblatex --variable graphics=yes --variable 'geometry:margin=1in' --variable 'compact-title:yes'
output file: rmarkdown_pdf_document.knit.md
INFO - This is Biber 2.7
INFO - Logfile is 'rmarkdown_pdf_document.blg'
INFO - Reading 'rmarkdown_pdf_document.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'sample\_bib.bib' for section 0
ERROR - Cannot find 'sample\_bib.bib'!
INFO - ERRORS: 1
Error: Failed to build the bibliography via biber
Execution halted
Warning message:
LaTeX Warning: Citation 'rcoreteamLanguageEnvironmentStatistical2018' on page 1
undefined on input line 137.
LaTeX Warning: Empty bibliography on input line 169.
Package rerunfilecheck Warning: File `rmarkdown_pdf_document.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex) rmarkdown_pdf_document
(biblatex) and rerun LaTeX afterwards.
Luckily, this problem is easily fixed by moving the "citation_package" from an option under pdf_document to a separate line in the YAML header. Or:
---
title: "Untitled"
author: "Unknown"
date: "4/18/2019"
output:
pdf_document:
# toc: true
number_sections: true
fig_caption: true
df_print: kable
keep_tex: true
citation_package: biblatex
bibliography: sample_bib.bib
csl: /Users/Shared/Zotero/styles/multidisciplinary-digital-publishing-institute.csl
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
I love R [#rcoreteamLanguageEnvironmentStatistical2018].
Upon knitting this adjusted Rmarkdown document, the result is a pdf_document.
So my question is: Was I right that you could add any of the arguments found in the pdf_document help file on CRAN as options under "pdf_document" in the YAML header in a Rmarkdown file? Or, upon using this particular citation_package argument/option, could this be a possible bug in the rmarkdown::pdf_document() function?
ALSO POSTED ON RMARKDOWN's GITHUB; see for additional comments.

How to add an index to a PDF rendered from an Rmarkdown document using Rstudio on Windows?

The example document below is intended to include an index after the appendix. In a Sweave document, Rstudio would run a shell escape command to create the index .idx file, but I've not been able to find a way to do this for an Rmarkdown document. Is there a simple header command I'm missing?
---
title: "Untitled"
output:
pdf_document:
toc: yes
header-includes:
- \usepackage{makeidx}
- \makeindex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# R Markdown
This is an \index{R Markdown} 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>.
# Appendix - A
End of the document
\printindex
I've tried this from both the Knit button and using:
rmarkdown::render(rmd.file, output_format = "pdf_document", clean = FALSE)
I'm looking for a solution that can run as part of an automated process.
UPDATE:
I was able to get the index to work by changing the output type to bookdown::pdf_document2. The additional latex packages were required for a combination of indexing, cross referencing, and formatting.
---
title: "Untitled"
output:
bookdown::pdf_document2:
toc: no
geometry: margin=0.8in
header-includes:
- \usepackage{attachfile2}
- \usepackage{booktabs}
- \usepackage{caption}
- \usepackage{float}
- \usepackage[utf8]{inputenc}
- \usepackage{makeidx}
- \makeindex
- \usepackage{multirow}
- \usepackage{setspace}
- \usepackage{relsize}
- \usepackage[table]{xcolor}
- \setcounter{tocdepth}{5}
- \setcounter{secnumdepth}{0}
- \hypersetup{unicode=true,pdfusetitle,bookmarks=true,bookmarksnumbered=true,bookmarksopen=true,bookmarksopenlevel=2,breaklinks=false,backref=false,colorlinks=true,linkcolor=blue}
---
While this would work when manually pushing the create PDF button, the call to rmarkdown::render() still does not process the indexing.