read_ function examples (manpages and vignette)

[antagomir]

The read_phyloseq, read_biom2phyloseq etc useq datasets from QIITA and DynamicsIBD. We had to remove these data sets from the package due to Bioc constraints for package size (4Mb). I have commented out the respective parts in the documentation (Rd files as well as docs/Rmd files) but these need to be updated. One solution is to make a separate example data repository online together with the tutorial. The larger data sets can then be fetched from there on-the-fly, This will require access to internet connection however.

[antagomir]

Or a separate data package is also an option.

[microsud]

I have created a microbiomedatarepo which can be accessed via the microbiomeutilties R package function get_microbiome_data. This datarepo contains a subset of studies included in the MicrobiomeHD database from Duvallet et al 2017: Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nature communications as phyloseq objects. One way would be to make the datarepo broader with *.biom and other test files. Alternatively, replicating a similar repository under the microbiome organistion would be possible. This would mean providing a new fucntion within microbiome R package. However, I do not have access to create new repos here.

[antagomir]

@binmat has just prepared phyloseq data packages for David and Ravel data sets, and in microbiome pkg we have phyloseq objects for three studies. More likely to come. In my view, the best way would be to be to follow standard practices and prepare either data objects that can be loaded with data(..) command; or entire data packages. But for examples & tutorials we also need other formats (such as biom), therefore an example data repository should be useful. If you agree, we could move microbiomedatarepo under microbiome organization in Guthub (perhaps the repository name can then be shortened to just data?) until a better solution emerges? You have now full rights, I had not noticed this.