summary.phylofactor: Summarize phylofactor objects

In reptalex/phylofactor: phylofactor

Summarize phylofactor objects

Description

Summarize phylofactor objects

Usage

## S3 method for class 'phylofactor'
summary(PF, taxonomy = NULL, factor = NULL,
  taxon.trimming = "sup", output.signal = T)

Arguments

PF	phylofactor object
taxonomy	taxonomy (optional) for taxonomic trimming. First column contains tree tip-labels, second column has semicolon-delimited taxonomic character strings.
factor	Integer (optional). If NULL, will use print.phylofactor
taxon.trimming	Chracter string. How to trim taxonomic groups. Must be either "sup" (group by shortest unique prefix for every taxon in group distinguishing it from taxa in complementary group), "taxon" for taxon levels in second column of taxonomy, or "species" for no taxonomic binning.
output.signal	logical - whether or not to output signal. Will attempt to call model.fcn or customized choice.fcn to estimate signal (and thus relative importance) for each taxonomic group from taxon.trimming.

Value

phylofactor.summary object containing data, group summary and, with input taxonomy, taxonomic break-down of signal

reptalex/phylofactor documentation built on Feb. 28, 2024, 3:19 p.m.