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

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

rl{ 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<- }