expand_pop2ind: Expand Population-Level Metadata to Individual-Level Data...

In pygmyperch/melfuR: A collection of ugly R functions for analysis of SNP and spatial data.

Expand Population-Level Metadata to Individual-Level Data Frame

Description

This function expands population-level metadata to an individual-level data frame by merging metadata with individual data from a 'genlight' or 'genind' object.

Usage

expand_pop2ind(geno, meta.data)

Arguments

geno	A 'genlight' or 'genind' object containing the genotype data.
meta.data	A data frame containing population-level metadata. This data frame must include a column named 'site' that corresponds to the population names in the 'genlight' or 'genind' object.

Details

The function extracts individual sample names and their population assignments from the 'genlight' or 'genind' object. Population-level metadata such as XY coordinates or environmental data are expanded to individual-level metadata using a left join on the 'site' column. The resulting individual-level data frame is saved as a CSV file named "individual_env_data.csv".

Value

A data frame containing individual-level data with expanded metadata.

Examples

## Not run: 

# Example genlight object
library(adegenet)
library(dartR.base)
data(nancycats)

genlight_obj <- gi2gl(nancycats[pop(nancycats) %in% levels(pop(nancycats))[1:3]])

# Example metadata
meta_data <- data.frame(
  site = c("P01", "P02", "P03"),
  env_var1 = c(10.5, 20.3, 15.2),
  env_var2 = c(100, 200, 150),
  stringsAsFactors = FALSE
)

# Expand population-level metadata to individual-level
individual_data <- expand_pop2ind(genlight_obj, meta_data)

# Example genind object
genind_obj <- nancycats[pop(nancycats) %in% levels(pop(nancycats))[1:3]]
individual_data_genind <- expand_pop2ind(genind_obj, meta_data)

## End(Not run)

pygmyperch/melfuR documentation built on Aug. 26, 2024, 12:48 a.m.