README.md
In dcgerard/phwelike: Code from Jiang, Ren, and Wu (2021) in Package Form

phwelike

This contains the code from Jiang et al (2021), in package form so it is easier for me to compare in simulations. You can see the results of these comparisons in Gerard (2022).

The original repo that contains the code from Jiang et al (2021) is located at https://github.com/LiboJiang/DoubleReduction.

The main functions are

main_multi(): Fit main_p2() across many loci.
main_p2(): Calculate maximum likelihood esimates of double reduction and allele frequency in tetraploids using all genotypes.
main_p3(): Calculate maximum likelihood esimates of double reduction and allele frequency in tetraploids using just heterozygous/homozygous.
sim_p(): Simulate genotypes at equilibrium in tetraploids. However, there is a mistake in Jiang et al (2021) and these genotypes are not actually simulated at equilibrium. See Gerard (2022) for details.
sim_p3(): Simulate heterozygous/homozygous at equilibrium in tetraploids. However, there is a mistake in Jiang et al (2021) and these are not actually simulated at equilibrium. See Gerard (2022) for details.

David Gerard’s work was supported by the National Science Foundation under Grant No. 2132247. The opinions, findings, and conclusions or recommendations expressed are those of the author and do not necessarily reflect the views of the National Science Foundation.

The work of Jiang et al (2021) was supported by grant 201404102 from the State Administration of Forestry of China and grant 32070601 from the National Natural Science Foundation of China.

Please note that the phwelike project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

Gerard D (2022). “Double reduction estimation and equilibrium tests in natural autopolyploid populations.” Biometrics In press. doi:10.1111/biom.13722.
Jiang, Libo, Xiangyu Ren, and Rongling Wu. 2021. “Computational Characterization of Double Reduction in Autotetraploid Natural Populations.” The Plant Journal 105 (6): 1703–9. doi:10.1111/tpj.15126