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ropensci / taxa

taxonomic classes for R
https://docs.ropensci.org/taxa
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Importing new version of functions from metacoder #3

Closed zachary-foster closed 8 years ago

zachary-foster commented 8 years ago

Hi @sckott. Sorry I have not talked to you about this repo in a while. We are about to submit metacoder to CRAN and submit its publication. I have talked to my advisor, Niklaus Grunwald, and he is OK with moving the taxonomy class (called taxmap in metacoder) and its associated functions into taxa and continuing development there.

The functions have changed quite a bit since you last saw them. The manipulation functions are now modelled after dplyr. They are basically an adaptation of dplyr to a pair of data.frames in the same object: tabular data (called 'observations') mapped to hierarchical data (called taxa). There is also support for "virtual columns" in both tables that can be used like normal columns in most situations. Everything is still S3, but I am ok with changing this.

There are tests and full help pages with examples that should allow you to make sense of things. To get an overall idea of how this set of functions is intended to be used see how metacoder uses them here:

https://grunwaldlab.github.io/metacoder_documentation/vignettes--03--manipulating_taxonomic_data.html https://grunwaldlab.github.io/metacoder_documentation/vignettes--04--hierarchical_subsampling.html

The website just went up and a few pages dont work yet, but those should.

Let me know if you have problems/questions.

zachary-foster commented 8 years ago

hmm, the checks passed on my computer. I will look into this soon

sckott commented 8 years ago

thanks, having a look

zachary-foster commented 8 years ago

Nice.

I replaced the example dataset so the function examples in the man pages should work now.

sckott commented 8 years ago

@zachary-foster looks good to me. merging.

opening up a new issue to talk about where to go from here