Usage
check.NameChanges(conn, order.by = "spec")
check.Species(conn, spec, gene)
check.Markers(conn, subset, outgroup, colname = "blocks", plot = TRUE)
check.Coverage(conn, pool.markers = TRUE)
check.Clades(phy, tax)
Arguments
conn
a database connection object.
spec
character string giving the name of a species
gene
character string giving the name of a genetic marker
subset
character string giving the names of a subset of species
outgroup
character string giving the name(s) of outgroup species
order.by
a character string giving the column name that is used for ordering the output table
colname
character string: gb, sel, or blocks.
tax
a data frame containing a taxonomic classification