phyloseq: phyloseq-deprecated – R documentation

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phyloseq-deprecated

Depcrecated functions in the phyloseq package.

Description

These will be migrated to "defunct" status in the next release, and removed completely in the release after that. These functions are provided for compatibility with older version of the phyloseq package. They may eventually be completely removed.

Usage

deprecated_phyloseq_function(x, value, ...)

Arguments

`x`	For assignment operators, the object that will undergo a replacement (object inside parenthesis).
`value`	For assignment operators, the value to replace with (the right side of the assignment).
`...`	For functions other than assignment operators, parameters to be passed to the modern version of the function (see table).

Details

`plot_taxa_bar`	now a synonym for `plot_bar`
`taxaplot`	now a synonym for `plot_bar`
`taxtab`	now a synonym for `tax_table`
`taxTab`	now a synonym for `tax_table`
`sampleData`	now a synonym for `sample_data`
`samData`	now a synonym for `sample_data`
`sam_data`	now a synonym for `sample_data`
`speciesSums`	now a synonym for `taxa_sums`
`sampleSums`	now a synonym for `sample_sums`
`nspecies`	now a synonym for `ntaxa`
`species.names`	now a synonym for `taxa_names`
`sampleNames`	now a synonym for `sample_names`
`sample.names`	now a synonym for `sample_names`
`getSamples`	now a synonym for `get_sample`
`getSpecies`	now a synonym for `get_taxa`
`rank.names`	now a synonym for `rank_names`
`getTaxa`	now a synonym for `get_taxa_unique`
`sample.variables`	now a synonym for `sample_variables`
`getVariable`	now a synonym for `get_variable`
`merge_species`	now a synonym for `merge_taxa`
`otuTable`	now a synonym for `otu_table`
`speciesarerows`	now a synonym for `taxa_are_rows`
`speciesAreRows`	now a synonym for `taxa_are_rows`
`plot_richness_estimates`	now a synonym for `plot_richness`
`import_qiime_sampleData`	now a synonym for `import_qiime_sample_data`
`filterfunSample`	now a synonym for `filterfun_sample`
`genefilterSample`	now a synonym for `genefilter_sample`
`prune_species`	now a synonym for `prune_taxa`
`subset_species`	now a synonym for `subset_taxa`
`tipglom`	now a synonym for `tip_glom`
`taxglom`	now a synonym for `tax_glom`
`tre`	now a synonym for `phy_tree`
`show_mothur_list_cutoffs`	now a synonym for `show_mothur_cutoffs`
`sam_data<-`	now a synonym for `sample_data<-`
`sampleData<-`	now a synonym for `sample_data<-`
`tre<-`	now a synonym for `phy_tree<-`
`speciesAreRows<-`	now a synonym for `taxa_are_rows<-`
`otuTable<-`	now a synonym for `otu_table<-`
`taxTab<-`	now a synonym for `tax_table<-`

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23