This function provides the summary stats used by many functions in RADami
Usage
# S3 method for pyRAD.loci
summary(object, ...)
Arguments
object
an object of class pyRAD.loci
…
not currently used, but maintained for consistency with default summary method
Value
A list with of the following objects:
num.loci
an integer, indicating how many loci there are in the object
tips.per.locus
a list of character vectors, enumerating the tips in each locus
break.vectors
a named character vector of the break lines between vectors, with names
corresponding to locus names -- completely redundant with the same object in the
pyRAD.loci object
seqs.per.locus
a list of named character vectors, enumerating the sequences in each locus, named
by tips
num.inds.per.locus
an integer vector, indicating how many individuals are in each locus
variable.loci
a boolean vector, indicating which loci are variable (only using the pyRAD
break vectors)
inds.mat
a handy boolean matrix with individuals as the rows and loci as the columns;
used in several places in RADami
locus.lengths
an integer vector, indicating the length of each locus
Details
This is currently called by default by read.pyRAD, creating a list object called radSummary
in value for that object.