species_nucleotide_diversity_pts: nucleotide diversity by species arguments: * infobold a...

In Grelot/geogendivr: Geographic Gene Diversity in R

Description

nucleotide diversity by species arguments: * infobold a dataframe with taxonomy+sequence dna information * buffer.Within a dataframe with row as indiv seq and col as rls pts with TRUE/FALSE presence/absence id of sequence infobold within a given buffer around a given rls pts * rls.pts.index index of the RLS pts it calculates * alignment of sequences by species * number of sequences by species * nucleotide diversity it returns a dataframe with taxonomy and nucleotide diversity and number of sequences by species species with not enough sequences to calculate nucleotide diversity are removed

Usage

species_nucleotide_diversity_pts(
  rls.pts.index,
  infobold,
  boldWithinRLS,
  MinimumNumberOfSequencesBySpecies
)

Grelot/geogendivr documentation built on Sept. 3, 2020, 6:25 p.m.