filter.by: Identify names of loci for which at the requested taxa are...
In RADami: Phylogenetic Analysis of RADseq Data

Description Usage Arguments Details Value Author(s) See Also

Returns the names of loci for which the requested taxa are present at some threshold

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filter.by(dat, taxa, req = NULL,
          threshInds = 3, threshTaxa = 2,
          use.tidyName = FALSE, ...)

`dat`	an object of class `pyRAD.loci` or `summary.pyRAD.loci`
`taxa`	a list of character vectors of taxa or individuals
`req`	a character vector listing taxa that are required; defaults to none
`threshInds`	a vector of integers corresponding to taxa, indicating the threshold number of individuals
`threshTaxa`	a single integer, indicating how many taxa are required at their `threshInds` level to export a locus
`use.tidyName`	whether to use the `tidyName` function for matching taxon names; useful if there is a mix of uppercase, lowercase, special characters etc. that are not really essential for distinguishing taxa
`...`	extra arguments to `tidyName`

Not currently called by any other functions in this package, but useful for quickly identifying loci for which data are present in a specified number of individuals

A list with two items:

`loci`	a character vector of loci that satisfy the filter criteria
`loc.mat`	a boolean matrix indicating for each locus which taxa satisfy their individuals threshold

Andrew Hipp

subset.pyRAD.loci

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