In Pakillo/rmdTemplates: A collection of Rmarkdown templates

library(rmarkdown)
library(knitr)

### Chunk options ###

# Modify at your will #

## Text results
opts_chunk$set(echo = TRUE, warning=TRUE, message=TRUE)

## Code decoration
opts_chunk$set(tidy=TRUE, comment = NA, highlight = TRUE)

## Cache
opts_chunk$set(cache = 2, cache.path = "output/cache/")
opts_chunk$set(cache.extra = rand_seed)

## Plots
opts_chunk$set(fig.path = "output/figures/")
opts_chunk$set(dpi = 300, fig.align = "default")   # may want 'center' sometimes

# Figure format
opts_chunk$set(dev='png')  # e.g. choose among 'pdf', 'png', 'svg'...
# may include specific dev.args as a list... see knitr help

library(knitcitations)
cleanbib()   
cite_options(citation_format = "pandoc")

if (file.exists("references.bib")) 
  refs_from_file <- read.bibtex("references.bib", check=FALSE)

library(rmdTemplates)

embed_data_html('dataset')    # write name of your dataset here

library(rmdTemplates)

embed_rmd_html("skeleton.Rmd")   # write name of the Rmd file here

Your text, code, plots here

Rmarkdown is great r citep(citation("knitr")).

You can write all your R code in chunks here and the output will appear in the final document. For example:

cat("Hello world!")

If you put a BibTeX file with references ("references.bib") in the working directory, you can cite any of them like these: @Xie_2013. Or cite by doi, e.g. r citet("10.1098/rspb.2013.1372"), thanks to knitcitations package r citep(citation("knitcitations")).

You can even specifiy the desired format for your bibliography by including a style file ("bibliostyle.csl"). See Rstudio website for more help. You can grab many different bibliography styles here: http://citationstyles.org/.

There is a chunk in the end to provide your session info at the end of the document (useful for reproducibility). Set eval=FALSE if you don't want to include that info in your document.

devtools::sessionInfo()

References

write.bibtex(file="references.bib", append=file.exists("references.bib"))

Pakillo/rmdTemplates documentation built on Sept. 16, 2022, 3:04 p.m.