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

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<-