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This package and included functions were 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.
A VCF file with GT information or a genotype matrix can be used as input
To install package:
install.packages("devtools") #If not already installed
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
If you use this package, please cite:
A.M. Sandercock, J.W. Westbrook, Q. Zhang, & J.A. Holliday, A genome-guided strategy for climate resilience in American chestnut restoration populations, Proc. Natl. Acad. Sci. U.S.A. 121 (30) e2403505121, https://doi.org/10.1073/pnas.2403505121 (2024).
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.