checkMissingSpec: Check for Missing Species

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Create a table of species that failed to pass steps in the pipeline.

Usage

checkMissingSpec(x, provenance = ".", tag = "ingroup")

Arguments

x	An object of class dbPars or megapteraProj.
provenance	A character string as used in the column provenance the acc_<locus> tables in the postgreSQL database. Depending on your actual pipeline setup these may be "ncbi", "ncbi annotated", or "bold" as well as any user-defined strings.
tag	A character string as used in the column tag in the taxonomy table in the postgreSQL database. Depending on your choices for parameter values in taxon or taxonGuidetree these may be "ingroup (NCBI)", "extended ingroup (NCBI)", "outgroup (NCBI)", or "extended outgroup (NCBI)" as well as any user-defined strings.

Value

A data frame with two columns:

spec

Names of missing species

status

Why species is missing; might be (1) not.on.genbank (species for which no sequences were found on GenBank), (2) not.selected (species that were not selected due to below-threshold identity or coverage), or (3) not.aligned (species that were lost during the alignment process; happens rarely)

See Also

checkSpecLocus to create a barplot of the species number per locus.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.