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It is highly recommended to use R-Studio to edit the Book of OHDSI. If you haven't done so already, make sure to install:
Once installed, run install.packages(“bookdown”) in R to install the bookdown package.
To start editing the book, first fork the TheBookOfOhdsi repo. Then clone the fork using RStudio.
You can build the entire book in RStudio in the Build tab (top right panel). Alternatively, you can build a preview just of your chapter using the preview_chapter() command.
After making your edits, commit and push them to your forked repository. From there, you can create a pull-request to the main repository.
An overview of basic Markdown syntax can be found here.
Please add figure files to a subfolder of the images folder. The subfolder should have the same name as the chapter Rmd file.
In the chapter, you can include a figure using the following piece of text:
```{r figure1, fig.cap='The prediction problem',echo=FALSE, out.width='100%'} knitr::include_graphics("images/PatientLevelPrediction/Figure1.png") ```
Here, figure1
is the label that can be used to reference the figure. You furthermore must specify a caption and the path to the figure file.
You can reference the figure in your text for example using Figure \@ref(fig:figure1) shows …
.
To add literature references to your chapter, two steps are needed:
Citations should be provided in BibTeX format. There are two ways to get BibTeX formatted citations:
Note that there is only one boob.bib file for the entire book.
The first field in the BibTeX in its label, and this label can be used to reference the citation. This can be done with and without square brackets. For example, As proposed by @reps2018
will render to `As proposed by Reps et al. (2018)`, while As proposed elsewhere [@reps2018]
will render to `As proposed elsewhere (Reps et al. 2018)`