summary.pyRAD.loci: Summary method for 'pyRAD.loci' objects
In RADami: Phylogenetic Analysis of RADseq Data

Description Usage Arguments Details Value Note Author(s) See Also

This function provides the summary stats used by many functions in RADami

1 2	## S3 method for class 'pyRAD.loci' summary(object, ...)

`object`	an object of class `pyRAD.loci`
`...`	not currently used, but maintained for consistency with default `summary` method

This is currently called by default by read.pyRAD, creating a list object called radSummary in value for that object.

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

Probably these functions could be teased apart to be more useful and save space, but for now they are left as is. At this point, there is actually a fair bit of redundancy.

Andrew Hipp

read.pyRAD, print.pyRAD.loci

RADami documentation built on May 30, 2017, 8:23 a.m.