Following this post, I'm trying to put #YihuiXie 's answer in practice with the PLOS template of rticles but it doesn't work. Any help would be very appreciated!
Below in a minimal example:
---
title: Title of submission to PLOS journal
author:
- name: Me
affiliation: Here
# output: rticles::plos_article
output:
bookdown::pdf_document2:
base_format: rticles::plos_article
---
# Introduction
Some text \#ref(fig:fig1)
# References {#references .unnumbered}
The error message reads
Error in pdf_book(..., base_format = rmarkdown::pdf_document) : formal argument "base_format" matched by multiple actual arguments
Calls: <Anonymous> -> create_output_format -> do.call -> <Anonymous>
Execution halted
You cannot change the base_format for bookdown::pdf_document2. You can do so for bookdown::pdf_book, though:
---
title: Title of submission to PLOS journal
author:
- name: Me
affiliation: Here
#output: rticles::plos_article
output:
bookdown::pdf_book:
base_format: rticles::plos_article
---
# Introduction
Some text \#ref(fig:fig1)
# References {#references .unnumbered}
Note to other readers: Make sure that .../rticles/rmarkdown/templates/plos_article/skeleton/PLOS-submission.eps is present in that directory.
Related
I am getting following error while Knit my RMarkdown file.
Parser error: while parsing a block mapping at line 1, column 1 did not find expected key at line 2, column 11
Calls: <Anonymous> ... parse_yaml_front_matter -> yaml_load -> <Anonymous>
Execution halted*
I understand it's my yaml header which is following -
---
title: "Data Wrangling Assessment"
author: ""ABC 11111""
subtitle:
output:
word_document: default
html_document:
df_print: paged
html_notebook: default
---
Can anyone please help me to troubleshoot?
The issue is that you wrapped the author name in doubled double quotes. If you want to quote the author name you have to
escape the inner double quotes using \", e.g. "\"ABC 11111\""
replace the outer double quotes with single quotes, e.g. '"ABC 11111"'
---
title: "Data Wrangling Assessment"
author: "\"ABC 11111\""
subtitle:
output:
word_document: default
html_document:
df_print: paged
html_notebook: default
---
My document is simply this
---
title: "The Visual Speech (VISP) Handbook"
author: "Fredrik Karlsson & Linda Sandström"
site: bookdown::bookdown_site
documentclass: book
output:
bibliography: references.bib
#bookdown::pdf_book: default
bookdown::gitbook: default
biblio-style: "apalike"
link-citations: true
---
# Preface {-}
[#R-base]
and I have a reference file:
> dir(pattern = "*.bib")
[1] "references.bib"
but I am unable to find this bib file when knitting the book:
Error in eval(parse(text = name)) : object 'references.bib' not found
Calls: ... create_output_format ->
create_output_format_function -> eval -> eval Please delete _main.Rmd
after you finish debugging the error. Execution halted
Any ideas on how to set this up properly (in Rstudio)
Thanks!
Fredrik
It's just a location problem in the code (see more information here).
You could try:
---
title: "The Visual Speech (VISP) Handbook"
author: "Fredrik Karlsson & Linda Sandström"
site: bookdown::bookdown_site
documentclass: book
output:
#bookdown::pdf_book: default
bookdown::gitbook: default
bibliography: references.bib
biblio-style: "apalike"
link-citations: true
---
# Preface {-}
[#R-base]
I'd like to rmarkdown::render a R document without indicating the yaml options within the document itself.
Ideally that could be an argument on rmarkdown::render or knitr::spin like what you can do to pass params (see the Rmarkdown reference book). Typically I'd like author, date and the output options too.
I think this is possible because spining the following document without specifying anything I get the following output (so there must be a template of default args that I can hopefully change)
As an example, how could I do to render a document that would give me the same output as say the below (but of course without specifying the yaml in the document ie no yaml whatsoever in the document)
---
title: "Sample Document"
output:
html_document:
toc: true
theme: united
pdf_document:
toc: true
highlight: zenburn
---
#' # Title
Hello world
#+ one_plus_one
1 + 1
You can pass yaml options as parameters too. For example:
---
params:
title: "add title"
author: "add author"
output: pdf_document
title: "`r params$title`"
author: "`r params$author`"
---
This is my document text.
Then, in a separate R script:
rmarkdown::render("my_doc.rmd",
params=list(title="My title",
author="eipi10"))
You could cat a sink into a tempfile.
xxx <- "
#' # Title
Hello world
#+ one_plus_one
1 + 1
"
tmp <- tempfile()
sink(tmp)
cat("
---
title: 'Sample Document'
output:
html_document:
toc: true
theme: united
pdf_document:
toc: true
highlight: zenburn
---", xxx)
sink()
w.d <- getwd()
rmarkdown::render(tmp, output_file=paste(w.d, "myfile", sep="/"))
I am trying to create an R markdown file but when I do I get the following error:
Line 2:
Error in .Call(C_str Sub_replacement, str, from, to, NULL, value) :
Incorrect number of arguments (5), expecting 6 for 'C_str Sub Replacement'
Calls: <Anonymous> ... indir -> inline exec -> <Anonymous> -> str_sub<- -> .Call
I have tried searching the internet and can not find an answer to this specific error. I am running R-3.3.0 and using R Studio.
I have updated the packages - knitr, markdown and yaml.
The following is my set up:
---
title: "Setting up a DQASS PC"
author: "DKMillington"
date: "`r format(Sys.Date(), '%d/%m/%Y')`"
header-includes:
- \usepackage{amsmath}
output:
rmarkdown::html_vignette:
css: mystyle.css
toc: true
number_sections: true
---
```{r, echo = FALSE, message = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
library(dqass)
```
Thank you for your time in advance.
Dale
I am using the bookdown package in R to write a gitbook, but I don't want the final book to have the sharing links to facebook, twitter. I am using something like this in the YAML
---
title: "A Minimal Book Example"
author: "SN"
date: "`r Sys.Date()`"
output:
bookdown::gitbook
gitbook_config:
sharing:
facebook: false
twitter: false
documentclass: book
link-citations: yes
description: "This book ... ."
---
but I am getting an error
Error in yaml::yaml.load(enc2utf8(string), ...) :
Scanner error: mapping values are not allowed in this context at line 6, column 19
Calls: <Anonymous> ... yaml_load_utf8 -> mark_utf8 -> <Anonymous> -> .Call
Execution halted
Can anyone help me in setting options in YAML so that no sharing options show up in the final rendering?
thanks!
SN
Two mistakes:
You omitted a colon after bookdown::gitbook;
gitbook_config should be config.
---
title: "A Minimal Book Example"
author: "SN"
date: "`r Sys.Date()`"
output:
bookdown::gitbook:
config:
sharing:
facebook: false
twitter: false
documentclass: book
link-citations: yes
description: "This book ... ."
---