Merge upstream changes#1
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artifact$data was not being produced for stats formats because stats .csv & .tsv files were being looked for in non-existent variable
Makes the function less likely to provide an error message and makes it run more smoothly on multiple operating systems. Windows does not like the previous default.
Use default R temp directory
Fix import of "StatsDirFmt" and "DADA2StatsDirFmt"
…on the 2nd line with q2:types. This function is read_q2metadata( ) and is also used within the qza_to_phyloseq( )
Add SILVA taxonomy parsing
…ith "" column type in q2 metadata.
Add taxonomy argument in example in README
…nsitive for q2:types.
I've been having an issue (I think since an upgrade to R versions > 4.0) where qza_to_phyloseq() returns this error when multiple components are imported: > Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘prune_samples’ for signature ‘"array", "phyloseq"’ It seems to be an [error with phyloseq](joey711/phyloseq#1356), possibly related to [changes in how matrices are handled in newer versions of R](https://blog.revolutionanalytics.com/2020/04/r-400-is-released.html). Simply converting the imported matrix to dataframe before passing it to phyloseq::otu_table() seems to fix the issue.
Fix import to phyloseq
Add check for valid barcodes in decode_golay
add: error message for case when metadata file doesn't exist
added qza_to_tse function
Added support for TreeSummarizedExperiment
Support for reading ANCOM-BC results (#68)
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