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05-writing.Rmd
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05-writing.Rmd
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# (PART) Writing {-}
# Writing
## Writing group
<!-- **TODO: (Eric)** -->
# R Markdown
## Setup
See [Setup/R Markdown](#rmd-setup).
## Slides
October 21 2019 - Basic R Markdown
[Slides](https://slides.robitalec.ca/basic-rmd.html)
[Resources](https://gitlab.com/robit.a/workshops/-/archive/master/workshops-master.zip?path=basic-rmd)
```{r, echo = FALSE}
knitr::include_url('https://slides.robitalec.ca/basic-rmd.html')
```
## Basic markdown
Wrap a word with single asterisks for *italics* and double asterisks for **bold**.
```
Wrap a word with single asterisks for *italics* and double asterisks for **bold**.
```
Surround inline code chunks with single `` `backticks` `` or full code blocks with triple backticks:
````
```
yum <- is.delicious('gorgonzola')
yum
[1] TRUE
```
````
Tables can be made with a [markdown table generator](http://www.tablesgenerator.com/markdown_tables#) (or by hand), or with functions, for example: `knitr::kable`.
```{r, echo = TRUE, eval = FALSE}
knitr::kable(diamonds)
```
```{r, echo = FALSE, eval = TRUE}
library(data.table)
library(ggplot2)
data(diamonds)
setDT(diamonds)
knitr::kable(diamonds[1:5])
```
<!-- **TODO: images** -->
## YAML
<!-- **TODO: link basic YAML Rmd** -->
<!-- **TODO: add classic error not working because tabs instead of spaces** -->
### Rendering multiple output formats {#rmd-multiple-output}
To render multiple output formats from the same R Markdown document, use this example. We remap the knit button / shortcut to rendering all the output formats specified.
<script src='https://gitlab.com/snippets/1976028.js'></script>
## BibTeX
### Setting italics in references
Setting italics in your `.bibtex` references is as simple as wrapping the words in `\emph{}`. For example:
```latex
\emph{Escherichia coli}
```
## Tables
Lots of options are available for generating markdown tables from R objects,
or text.
Manually/copy-paste
* [Tables Generator](https://www.tablesgenerator.com/markdown_tables)
R packages
* `knitr::kable`
* [`pander`](http://rapporter.github.io/pander/)
* [`gt`](https://gt.rstudio.com/)
* [`flextable`](https://ardata-fr.github.io/flextable-book/)
* [`xtable`](https://cran.r-project.org/web/packages/xtable/vignettes/xtableGallery.pdf)
Note: differences between these packages are mainly in syntax but more importantly
also in the possible output formats. Some only work with HTML output, some only
PDF, etc.
## Reflow lines
If this is a manuscript, and you are noticing (especially in Git) everything is
on a few really long lines, simply reflow using the shortcut (CTRL+SHIFT+/) or
remember to hit enter at the end of a line.
<!-- **TODO: example image of this** -->
## Presentations with `xaringan`
Yihui Xie made a great package for generating HTML presentations in R Markdown: [`xaringan`](https://bookdown.org/yihui/rmarkdown/xaringan.html).
All of Alec's slides use this package, see [Slides](#slides).
### Incremental ggplot slides
An example for building your ggplots incrementally using this example `xaringan` document.
<script src='https://gitlab.com/snippets/1954903.js'></script>
<!-- ## Manuscript notes -->
<!-- use PDF for supplements, latex changes for fig caps -->
<!-- flextable for office tables -->