NEWS.md

In OchoaLab/simgenphen: Simulate Genotypes and Phenotypes

simgenphen 0.0.0.9000 (2021-08-27)

• First commit of public version
• Includes full tests for all functions
• Nothing exported or documented yet

simgenphen 0.0.1.9000 (2021-08-27)

• Documented and exported all functions!
• Function sim_pop now also returns admix_proportions_1, the admixture proportions of the founders, distinguished from admix_proportions which is the admixture proportions of the final generation (different if G > 1).
• Function sim_geno:
• First parameter is renamed from admix_proportions to admix_proportions_1 to emphasize that it should be the admixture proportions of the founders!
• Optional parameter p_anc_input is renamed to p_anc.
• Function sim_gen_phen debugged to use founder admixture proportions to draw genotypes for founders. The previous version had the bug because sim_geno did not return founder admixture proportions, only last-generation values, but the bug only manifested if G > 1. Bug was very recently introduced (compared to previous non-public code in a separate repository).
• Function sim_bim added parameter pos_gap.

simgenphen 0.0.2.9000 (2021-09-03)

• Added package documentation with runnable examples.
• Also updated examples in individual functions to better match the package entry examples.

simgenphen 0.0.3.9000 (2021-09-03)

• Added README with examples from package documentation.

simgenphen 0.0.4.9000 (2022-02-21)

• Function sim_geno fixed a bug that fixed loci were redrawn without respecting p_anc if provided (no bug for p_anc = NULL).
• Functions sim_geno and sim_gen_phen added option beta for a Beta distribution for ancestral allele frequencies.

simgenphen 0.0.5.9000 (2023-02-01)

• Function sim_gen_phen added element p_anc to return list, needed in order to reuse the simulated genotypes to simulate new traits for them (for example, with different heritabilities).
• Updated unit tests for function sim_bim to expect column alt before ref in return tibble (a change inherited from dependency genio::make_bim() made in genio version 1.1.0.9000 (2022-04-20))

OchoaLab/simgenphen documentation built on Feb. 10, 2023, 3:32 p.m.