orphan.individuals: Identify Vouchers Lacking Sequences

In andrew-hipp/morton: Tools for manipulation of phylogenetic, genetic, and other biodiversity data

Identify Vouchers Lacking Sequences

Description

Determines which specimen vouchers do not have any sequences associated with them and which do.

Usage

orphan.individuals(dat)

Arguments

dat	A matrix, the output of make.gene.matrix.

Details

Uses the function make.shared.gene.matrix internally. All returned vectors are ordered to correspond with the rows of the gene matrix.

Value

NCBI_accession	A vector of pipe-delimited NCBI accession numbers for each voucher.
taxon	A vector of the taxon name of each voucher; if multiple, names are pipe-delimited.
orphans	A vector of all vouchers which do not have any gene sequences associated with them.
notOrphans	A vector of all vouchers which have at least one gene sequence associated with them.

Author(s)

Andrew Hipp and Kasey Pham

See Also

make.gene.matrix, make.shared.gene.matrix

andrew-hipp/morton documentation built on April 7, 2024, 12:15 p.m.