In Pakillo/rmdTemplates: A collection of Rmarkdown templates

^1^ Estación Biológica de Doñana (CSIC)

^2^ Universidad de Sevilla

^3^ Second Author affiliation

* Corresponding author: [e-mail]

ABSTRACT

Write your abstract here.

Keywords: Rmarkdown, reproducible science

library("knitr")

### Chunk options: see http://yihui.name/knitr/options/ ###
## Text results
opts_chunk$set(echo = FALSE, 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/")

## Plots
opts_chunk$set(fig.path = "output/figures/")

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

INTRODUCTION

Write your introduction here. You can cite bibliography like this [@Yan2011; @Sutherland2011] if you provide a BibTeX file with references. See http://rmarkdown.rstudio.com for more information.

You can even specify the desired output format for your bibliography by including a style file for a specific journal (e.g. "ecology.csl"). Many different bibliography styles (CSL files) can be obtained at http://citationstyles.org/, https://github.com/citation-style-language/styles, or https://zotero.org/styles.

METHODS

Study Area

We worked in a beautiful place with lots of trees, like Quercus suber and Laurus nobilis.

Data collection and analysis

dataset <- read.csv("mydata.csv")

We applied a linear model where

$$ y_{i} = \alpha + \beta*x_{i} $$

model <- lm(y ~ x)

We used the statistical language R r citep(citation()) for all our analyses. These were implemented in dynamic rmarkdown documents using knitr r citep(citation("knitr")) and rmarkdown r citep(citation("rmarkdown")) packages. All the multilevel models were fitted with lme4 r citep(citation("lme4")).

RESULTS

Trees in forest A grew taller than those in forest B (mean height: r mean(25, 31, 28) versus r mean(13, 19, 16) m).

And many more cool results that get updated dynamically, e.g. see Table \@ref(tab:Table-mtcars) and Fig. \@ref(fig:scatterplot). Note Tables and Figures are cross-linked and numbered automatically.

kable(head(iris), caption = "A glimpse of the famous Iris dataset.")

x <- rnorm(100)
y <- jitter(x, 1000)
plot(x, y)

DISCUSSION

Discuss.

CONCLUSIONS

Wrap up

ACKNOWLEDGEMENTS

On the shoulders of giants.

REFERENCES

write.bibtex(file = "knitcitations.bib")

::: {#refs} :::

\newpage

Supplementary Table (on new page)

kable(mtcars[10:16, ], caption = "Now a subset of mtcars dataset.")

\newpage

Supplementary Figure (on new page)

a <- sort(rnorm(100))
b <- c(rep("Group Small", 35), rep("Group Big", 65))
boxplot(a ~ b)

# set eval = FALSE if you don't want this info (useful for reproducibility) to appear 
sessionInfo()
# sessioninfo::session_info()

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