Changelog

[0.1.0] - 2024-03-07

Breaking changes:

• sim_genetic function is no longer supported, and users should be using genetic_value function instead. The new genetic_value function uses trait dataframe as an input, but random_seed is not a necessary argument, as there is no randomness involved. The frequency dependence architecture is implemented in sim_trait function instead of sim_genetic function, so users should put the alpha parameter in sim_trait function instead.

• negative input in exponential and gamma distribution trait models are no longer supported, and users should be using random_sign instead #114

Update:

• Remove num_causal dependence on simulating effect sizes #107

• Add options to simulate effect sizes from random_sign in fixed value trait model #109

• Add frequency dependence architecture in sim_trait function, and allele frequency is given as an output as well #111

• Implement genetic_value function to compute genetic values based on the trait dataframe. There is no randomness involved, and frequency dependence architecture is not implemented #112

• Add option to input the causal site IDs, instead of randomly selecting them in sim_phenotype and sim_trait functions #124

• Add normalise_phenotypes function to normalize the simulated phenotypes #130

• Add delta degrees of freedom input in normalise_phenotypes function #136

• Add normalise_genetic_value function to normalize the genetic values #145

Fix:

• Raise error when there are no individuals #97

• Raise error when incorrect values are given in the num_causal argument #99

• Remove # pragma: no cover in certain functions #119

• Modify default input arguments of sim_trait, sim_env and sim_phenotype functions #120

• Add verification.py for statistical tests #129

• Add statistical tests against external simulators #132

• Change the dtype of trait_id input in genetic_value function #134

• Add density plot in verification.py #138

• Add multithreading in verification.py #139

• Conduct exact tests against AlphaSimR, simplePHENOTYPES and the simulation framework described in ARG-Needle paper in verification.py #140

Documentation:

• Modify introduction #96

• Document ploidy #98

• Documentation for the new sim_trait function #115

• Documentation for random_sign input in trait distribution models #122

• Modify phrasing in documentation #123

• Documentation for specifying causal site IDs #126

• Documentation for modifying the numericalization of genotypes #133

• Modify the frequency dependence explanation in the documentation #141

• Fix typo in documentation #142

[0.0.1] - 2023-09-05

Highlights:

• Initial stable release of tstrait in PyPI https://pypi.org/project/tstrait/

• Initial stable release of tstrait in conda-forge

Documentation:

• tstrait description in https://tskit.dev/software/

Contributors:

• Jerome Kelleher

• Ben Jeffery

• Gertjan Bisschop

• Daiki Tagami

[0.0.1a5] - 2023-09-05

Test release of the package before releasing it to conda-forge

Contributors:

• Jerome Kelleher

• Ben Jeffery

• Gertjan Bisschop

• Daiki Tagami

[0.0.1a2] - 2023-08-25

Highlights:

• Release of tstrait documentation in https://tskit.dev/tstrait/docs/latest/

Fix:

• Hide private functions and classes #73

• Modify docstring explanations and examples #76

Documentation:

• Create infrastructure for documentation #77

• Build initial documentation #78

• Add Changelog to documentation #79

Contributors:

• Daiki Tagami

• Gertjan Bisschop

• Jerome Kelleher

[0.0.1a1] - 2023-08-22

Initial alpha release of the package.

Contributors:

• Daiki Tagami

• Gertjan Bisschop

• Jerome Kelleher