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projects:workgroups:notes_on_writing_text_for_the_book [2019/03/13 10:23] schuemie [Keep in mind] |
projects:workgroups:notes_on_writing_text_for_the_book [2019/06/01 11:42] schuemie [Markdown syntax] |
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| 8507 | MALE| | | 8507 | MALE| | ||
| | ||
+ | Important! The number of hyphens in the second row determines how wide the table is. The relationship between number of hyphens and table width is not documented, but 10 hyphens translates into approximately 10-20% width. | ||
+ | |||
+ | You can add a table caption like this: | ||
+ | |||
+ | Table: (\#tab:conceptTable) A table with two concepts. | ||
+ | | Concept ID | Name | | ||
+ | | ---------- | ---- | | ||
+ | | 8532 | FEMALE| | ||
+ | | 8507 | MALE| | ||
+ | | ||
Footnotes: | Footnotes: | ||
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In the chapter, you can include a figure using the following piece of text: | 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%'} | + | ```{r figure1, fig.cap='The prediction problem',echo=FALSE, out.width='100%', fig.align='center'} |
knitr::include_graphics("images/PatientLevelPrediction/Figure1.png") | knitr::include_graphics("images/PatientLevelPrediction/Figure1.png") | ||
``` | ``` | ||
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You can reference the figure in your text for example using ''Figure \@ref(fig:figure1) shows ...''. | You can reference the figure in your text for example using ''Figure \@ref(fig:figure1) shows ...''. | ||
+ | |||
+ | ==== Adding ATLAS screenshots ==== | ||
+ | |||
+ | It is hard to take screenshots of ATLAS where the resulting font size in the image in the book is big enough to read. Try to keep screenshots to a minimum. If you need to make a screenshot, here are instructions for making ok screenshots: | ||
+ | |||
+ | * In Chrome, open the developer tools using Ctrl + Shift + i. | ||
+ | * Click the second button top left that looks like a mobile phone. | ||
+ | * In the main Chrome window, set the width to 1000 and the zoom to 150% | ||
+ | * Use for example the Windows Snipping Tool to capture the screen. However, you cannot include the full screen width, and for example it is best to leave out the left navigation bar. | ||
===== Adding literature references ===== | ===== Adding literature references ===== | ||
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==== Referencing in text ==== | ==== Referencing in text ==== | ||
- | 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)`// | + | The first field in the BibTeX is 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)`// |
+ | |||
+ | A convenient way of inserting citatiosn is to use the citation add-in that comes with the bookdown package: | ||
+ | |||
+ | {{:projects:workgroups:screenshot.png?400|}} | ||
+ | |||
+ | ===== Referencing OHDSI tools ===== | ||
+ | |||
+ | We will explain where to find the OHDSI tools and how to install them once in the book. All other references to OHDSI tools should just mention the tool name, and the name should be a hyperlink to the tool page. For R packages, use the Github Pages page, for example: | ||
+ | |||
+ | This done through the [FeatureExtraction](https://ohdsi.github.io/FeatureExtraction/) package. | ||
+ | |||