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Remove reference to GIT setup
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paulklemm committed Mar 12, 2018
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38 changes: 12 additions & 26 deletions Readme.md
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<!-- TOC -->

- [⚓️ SonaR `R` Back-End for use with OpenCPU](#⚓️-sonar-r-back-end-for-use-with-opencpu)
- [Git Setup](#git-setup)
- [Temporary Building Process](#temporary-building-process)
- [TODO](#todo)
- [Problems with Roxygen](#problems-with-roxygen)
- [File permissions of `data` folder when editing inside of Docker image](#file-permissions-of-data-folder-when-editing-inside-of-docker-image)
- [Principal Component Analysis](#principal-component-analysis)
- [Links](#links)
* [⚓️ SonaR `R` Back-End for use with OpenCPU](#⚓️-sonar-r-back-end-for-use-with-opencpu)
* [Temporary Building Process](#temporary-building-process)
* [TODO](#todo)
* [Problems with Roxygen](#problems-with-roxygen)
* [File permissions of `data` folder when editing inside of Docker image](#file-permissions-of-data-folder-when-editing-inside-of-docker-image)
* [Principal Component Analysis](#principal-component-analysis)
* [Links](#links)

<!-- /TOC -->

# ⚓️ SonaR `R` Back-End for use with OpenCPU

## Git Setup

This repo knows two origins:

```bash
# From https://stackoverflow.com/questions/14290113/git-pushing-code-to-two-remotes
git remote set-url --add --push origin git@github.molgen.mpg.de:paulklemm/snr.git
git remote set-url --add --push origin git@github.sf.mpg.de:pklemm/sona-R.git
# Check with `git remote show origin`
```

This is neccessary since the `R` devtools allow for easy installation of packages on Github.com.

## Temporary Building Process

The public data is attached to this package as public data set in the `data/` folder. Using the `.onLoad()` function in the `zzz.R` file, the data is loaded on package load to ensure fast access times. Since this package is automatically loaded in the OpenCPU server, the public data is available to all sessions instantly.
Expand All @@ -34,8 +20,8 @@ Currently the way to rebuild the public dataset is to run the `create_public_dat

## TODO

- Automatically build the package in the docker image using a CRON Job
- Include additional functionality distinguishing between private and public data
* Automatically build the package in the docker image using a CRON Job
* Include additional functionality distinguishing between private and public data

## Problems with Roxygen

Expand Down Expand Up @@ -65,9 +51,9 @@ I checked `prcomp`, `fast.prcomp` and `princomp`. The latter is the fastest and

See also

- [https://stackoverflow.com/questions/8299460/what-is-the-fastest-way-to-calculate-first-two-principal-components-in-r](https://stackoverflow.com/questions/8299460/what-is-the-fastest-way-to-calculate-first-two-principal-components-in-r)
- [https://www.rdocumentation.org/packages/gmodels/versions/2.16.2/topics/fast.prcomp](https://www.rdocumentation.org/packages/gmodels/versions/2.16.2/topics/fast.prcomp)
* [https://stackoverflow.com/questions/8299460/what-is-the-fastest-way-to-calculate-first-two-principal-components-in-r](https://stackoverflow.com/questions/8299460/what-is-the-fastest-way-to-calculate-first-two-principal-components-in-r)
* [https://www.rdocumentation.org/packages/gmodels/versions/2.16.2/topics/fast.prcomp](https://www.rdocumentation.org/packages/gmodels/versions/2.16.2/topics/fast.prcomp)

## Links

- [How to include and preload data in OpenCPU packages](https://www.opencpu.org/posts/scoring-engine/) ([.onLoad call](https://github.com/rwebapps/tvscore/blob/master/R/onLoad.R))
* [How to include and preload data in OpenCPU packages](https://www.opencpu.org/posts/scoring-engine/) ([.onLoad call](https://github.com/rwebapps/tvscore/blob/master/R/onLoad.R))

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