This package and included functions was developed for the American chestnut landscape genomics manuscript. The aim was to develop a method for estimating the number of individuals to sample from a population in order to capture a predefined percentage of diversity within a breeding population.
The preprint for the article can be found at bioRxiv: https://doi.org/10.1101/2023.05.30.542850
A vcf file or genotype matrix can be used
To install package:
install.packages("devtools") #If not already installed
library(devtools)
devtools::install_github("alex-sandercock/castgen")
library("castgen")
The output will be provided in the terminal following the completion of all iterations:
Number of trees to sample = 22.0
95% Confidence Intervals = (16.378127142052662, 27.621872857947338)
Iterations performed = 5
The capture_diversity functions were converted from a Python function https://github.com/alex-sandercock/Capture_genomic_diversity. These R versions of the function are much (much) faster to run and have the option to run in parallel depending on cores available.
