Deprecate write_phyloseq

[antagomir]

This function is now marked deprecated. Instead, add an example in the tutorial.

[MADscientist314]

Just a heads up, the warning message doesn't give any solution for the deprecation.

Warning message: 'write_phyloseq' is deprecated. Use '' instead. See help("Deprecated") and help("The microbiome::write_phyloseq will be deprecated in a future release.-deprecated").

[antagomir]

Hmm yes, we were planning to just remove this functionality but perhaps it could be mentioned more explicitly or with a link to some online tutorial example.

[lxsteiner]

This would've been helpful :/ found the package through the function on https://rdrr.io/bioc/microbiome/man/write_phyloseq.html only to find out it's not there anymore.

[antagomir]

We have switched to supporting the TreeSummarizedExperiment framework for microbiome data science in R/Bioconductor. This package is not actively developed any more, although we do take care of basic maintenance.