get.distance: Calculate Nei distance between two or more population

Description

Function to calculate Nei's distance between two or more population

Usage

get.distance(
  population,
  type = "nei",
  marker = "all",
  per.marker = FALSE,
  gen1 = NULL,
  database1 = NULL,
  cohorts1 = NULL,
  id1 = NULL,
  gen2 = NULL,
  database2 = NULL,
  cohorts2 = NULL,
  id2 = NULL,
  database.list = NULL,
  gen.list = NULL,
  cohorts.list = NULL
)

Value

Population list

Arguments

population: population list
type: Chose type of distance to compute (default: Neis standard genetic distance "nei"). Alt: Reynolds distance ("reynold"), Cavalli-Sforza ("cavalli"), Neis distance ("nei_distance"), Neis minimum distance ("nei_minimum")
marker: Vector with SNPs to consider (Default: "all" - use of all markers)
per.marker: Set to TRUE to return per marker statistics on genetic distances
gen1: Quick-insert for database (vector of all generations to consider)
database1: First Groups of individuals to consider
cohorts1: Quick-insert for database (vector of names of cohorts to consider)
id1: Individual IDs to search/collect in the database
gen2: Quick-insert for database (vector of all generations to consider)
database2: Second Groups of individuals to consider
cohorts2: Quick-insert for database (vector of names of cohorts to consider)
id2: Individual IDs to search/collect in the database
database.list: List of databases to consider (use when working with more than 2 populations)
gen.list: Quick-insert for database (vector of all generations to consider)
cohorts.list: Quick-insert for database (vector of names of cohorts to consider)

Examples

Run this code

data(ex_pop)
get.distance(ex_pop, database1 = cbind(1,1), database2 = cbind(1,2))

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