species_nucleotide_diversity_site: Nucleotide diversity by species

In Grelot/rgeogendiv: Geographic Genetic Diversity

Description

nucleotide diversity by species arguments: * specimen.df 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 specimen.df 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_site(
  site.ids,
  specimen.df,
  sequenceIntersectSites,
  MinimumNumberOfSequencesBySpecies,
  fishbaseValidation = FALSE
)

Arguments

site.ids	index of the site of the grid
specimen.df	a data.frame with taxonomy+sequence dna information
sequenceIntersectSites	a matrix of presence/absence TRUE/FALSE of a specimen within a site with column as site ID and row as specimen spatial points ID
MinimumNumberOfSequencesBySpecies	an integer minimum number of sequences representatives of a species in a site

Value

a data.frame with number of individuals and nucleotide diversity for each species in the site.

Grelot/rgeogendiv documentation built on Dec. 22, 2020, 5:51 a.m.