rbefdata paper

• Tentative title:

rbefdata a package to access and process data stored on a BEFdata portal instance

• Journal:

???

Read the paper

You can have a first glance on the contents in nice formatted markdown if you go to the markdown representation of the paper in this repository.

Description

This paper deals with rbefdata and discusses the functionality on a real scenario with already published data.

Authors

• Karin Nadrowski
• Anne Lang
• Claas-Thido Pfaff
• xingxing man (sorry if this is not exactly right)

Technique

Github collaboration

For the collaboration on github please create your own author branch for writing.

git checkout -b author_yourname

Work on that branch only and once and a while merge it into the master branch. This works as follows:

• Checkout the master

git checkout master

• Pull for changes in master online and merge them in

git pull --rebase

• Merge in recent changes from your author branch (can be conflicted)

git merge author_yourname

• Push the merged version online

git push

• Checkout your author branch and work on

git push

• Repeat the steps after another part is finished.

NOTE:

If you have conflicts on merging files with git you need to resolve them manually. This is usually best done in a 3 way merge tool. Conflicts happen if a part of document is modified in both the aim and the version you like to merge in. You need to pick the changes you like to keep then manually.

R Markdown and Markdown

The whole paper is written in R markdown. Markdown which is a lightweight markup language. For a description of commands that are available in Markdown see here. The R Markdown markup makes it easier to handle the inclusion of the R packages commands and output. You can use R-Studio to edit the document as it offers methods to compile the document from R Markdown to markdown and then to other document formats (e.g html) with the Knitr package.

• Using R Markdown

Work with rbefdata

As the rbefdata quires you to set your credentials to authenticate against the BEFdata portal you need to set them somewhere. But as they are like passwords you should not set it in the files that will be pushed to GitHub. For this I created .gitignore file that makes the repository ignore a secretes.R file in the paper folder. After download create it and add a line into it like this but replace with your real credentials.

bef.options("user_credentials" = "s0l0p982340987uöaf")