phangorn (version 2.12.1)

baseFreq: Summaries of alignments

Description

baseFreq computes the frequencies (absolute or relative) of the states from a sample of sequences. glance computes some useful information about the alignment. composition\_test computes a ${\chi }^2$-test testing if the state composition for a species differs.

Usage

baseFreq(obj, freq = FALSE, all = FALSE, drop.unused.levels = FALSE)
# S3 method for phyDat
glance(x, ...)
composition_test(obj)

Value

baseFreq returns a named vector and glance a one row data.frame.

Arguments

obj, x

as object of class phyDat

freq

logical, if 'TRUE', frequencies or counts are returned otherwise proportions

all

all a logical; if all = TRUE, all counts of bases, ambiguous codes, missing data, and alignment gaps are returned as defined in the contrast.

drop.unused.levels

logical, drop unused levels

...

further arguments passed to or from other methods.

Author

Klaus Schliep

See Also

phyDat, base.freq, glance

Examples

data(Laurasiatherian)
data(chloroplast)
# base frequencies
baseFreq(Laurasiatherian)
baseFreq(Laurasiatherian, all=TRUE)
baseFreq(Laurasiatherian, freq=TRUE)
baseFreq(chloroplast)
glance(Laurasiatherian)
glance(chloroplast)
composition_test(Laurasiatherian)[1:10,]