BiocStyle header specification
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@ioannisvardaxis-11763
Last seen 2.7 years ago
Norway/Oslo

Hi,

I am trying to use BiocStyle to create vignette in R markdown. I read the instructions but i dont get the results i want so I was wondering what I have done wrong. I dont understand where I should place the first chuck which loads latex2. If i do it this way i get two pages with double author etc.

---
title: "pkg"
author: "author"
date: "`r doc_date()`"
package: "`r BiocStyle::pkg_ver('pkg')`"
output:
 BiocStyle::pdf_document2
vignette: >
 %\VignetteIndexEntry{pkg}
 %\VignetteEngine{knitr::rmarkdown}
 %\VignetteEncoding{UTF-8}
---

```{r style,eval=TRUE,echo=FALSE,results='hide'}
BiocStyle::latex2()
```

<!-- Title -->
\bioctitle[pkg]{long pkg name}
\author{author {\email{author mail}}}
\date{`r Sys.Date()`}

\maketitle


Best

biocstyle • 993 views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 19 minutes ago
United States

You already have set the author and title in the yaml section:

---
title: "pkg"
author: "author"
date: "`r doc_date()`"
package: "`r BiocStyle::pkg_ver('pkg')`"
output:
 BiocStyle::pdf_document2
vignette: >
 %\VignetteIndexEntry{pkg}
 %\VignetteEngine{knitr::rmarkdown}
 %\VignetteEncoding{UTF-8}
---

The extra title section you add below is then adding in the same thing, a second time.

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0
Entering edit mode

hi, thanks for the answer.

I know, but if I dont do that then i cannot use :\bioctitle[pkg]{long pkg name} and the package will only have a sort name

actually i cannot use any of the biocstyle options in the yalm since biocstyle has to be loaded after the yalm. Therefore everythink is doubled.

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0
Entering edit mode

In an .Rmd document, you don't need the code chunk which calls BiocStyle::latex2(), as the setup is already done by specifying output: BiocStyle::pdf_document2 in the document header. The short/long titles in r markdown are currently not implemented, for now you can only have one title specified in document header. However, I might add this in near future, so stay tuned.

Cheers,

Andrzej

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0
Entering edit mode

Ok thanks.

One last question, i try to add email etc in yaml but it doesn't appear on the pdf:

---
title: "pkg"
author: "author"
email: email@..
date: "`r doc_date()`"
package: "`r BiocStyle::pkg_ver('pkg')`"
output:
 BiocStyle::pdf_document2
vignette: >
 %\VignetteIndexEntry{pkg}
 %\VignetteEngine{knitr::rmarkdown}
 %\VignetteEncoding{UTF-8}
---

Any solution to that?

Best

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0
Entering edit mode

Try the following:

author:
  - name: first author
    email: email@...
    affiliation: in case you want to provide one
  - name: another author
    email: ...
    affiliation: ...
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0
Entering edit mode

In case you missed it, the devel version of BiocStyle::pdf_document2 supports now the shorttitle yaml option for specifying headers.

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