Initial edit vignettes

.gitignore

@@ -5,3 +5,5 @@
 inst/data
 docaux/
 inst/doc
+inst/shiny/include/*.html
+vignettes/*.html

inst/shiny/include/about.md

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-This application was written by Dieter Menne at [Menne Biomed Consulting, Tübingen](https://www.menne-biomed.de).
+This application was written by Dieter Menne at [Menne Biomed Consulting, Tübingen](https://www.menne-biomed.de), in cooperation with the Department of Gastroenterology of the University Hospital of Zürich and Claraspital Basel. Thanks to Benjamin Misselwitz, Mark Fox, Werner Schwizer and Andreas Steingötter.
 
 - All code is GPL-3 Open Source and available on github.
 - The core routines to fit data are in package [breathtestcore](https://github.com/dmenne/breathtestcore), also on [CRAN](https://cran.r-project.org/web/packages/breathtestcore/index.html). [Code examples](https://dmenne.github.io/breathtestcore/reference/nlme_fit.html) are provided to run an analysis under R.

vignettes/FAQ.Rmd

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+---
+title: "FAQ for breathtestshiny"
+author: "Dieter Menne"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The `html_vignette` output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The `html_vignette` format:
+
+- Never uses retina figures
+- Has a smaller default figure size
+- Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style
+
+## Vignette Info
+
+Note the various macros within the `vignette` section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the `title` field and the `\VignetteIndexEntry` to match the title of your vignette.
+
+## Styles
+
+The `html_vignette` template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:
+
+    output: 
+      rmarkdown::html_vignette:
+        css: mystyles.css
+
+## Figures
+
+The figure sizes have been customised so that you can easily put two images side-by-side. 
+
+```{r, fig.show='hold'}
+plot(1:10)
+plot(10:1)
+```
+
+You can enable figure captions by `fig_caption: yes` in YAML:
+
+    output:
+      rmarkdown::html_vignette:
+        fig_caption: yes
+
+Then you can use the chunk option `fig.cap = "Your figure caption."` in **knitr**.
+
+## More Examples
+
+You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using `knitr::kable()`.
+
+```{r, echo=FALSE, results='asis'}
+knitr::kable(head(mtcars, 10))
+```
+