phyloseq-deprecated: Depcrecated functions in the phyloseq package.

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

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<-

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.