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TIBHannover/BacDiveR v0.5.0-beta

Katrin Leinweber

This R package provides a programmatic interface for the Bacterial Diversity Metadatabase (Söhngen et al. 2014 & 2016) of the DSMZ (German Collection of Microorganisms and Cell Cultures). BacDiveR helps you conduct your microbial research better and faster, by:

  • downloading the BacDive datasets you want to investigate off-line, and by

  • providing you with a way to document and report your searches and downloads, in a reproducible manner (.R scripts and/or .Rmd files).

It was also built to serve as a demonstration object during TIB's "FAIR Data & Software" workshop.

See TIBHannover.GitHub.io/BacDiveR for more details, /news there for the changelog, and GitHub.com/TIBHannover/BacDiveR for the latest source code.

Changelog for BacDiveR v0.5.0-beta

  • Added syncing of release versions to Zenodo, starting with 10.5281/zenodo.1308061

  • The JSON downloads are no longer purged of all space characters pre-emptively to prevent jsonlite from complaining about invalid encoding (#43). Instead, only \r, \n and \t are repaired to \\r, \\n and \\t, which jsonlite expects. This leads to different output (newline & tabs, where previously only spaces occured)! Thus, if you are parsing BacDiveR output in any way, you may need to adjust that. Because I consider this unlikely given the "maturing" status, and because no API surface was changed, I don't consider this a major change in the SemVer.org sense.

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