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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

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