baseFreq {phangorn} | R Documentation |
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 class 'phyDat'
glance(x, ...)
composition_test(obj)
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. |
Value
baseFreq
returns a named vector and glance
a one row
data.frame
.
Author(s)
Klaus Schliep
See Also
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,]
[Package phangorn version 2.12.1 Index]