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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 {pr}114

Update:

  • Remove num_causal dependence on simulating effect sizes {pr}107
  • Add options to simulate effect sizes from random_sign in fixed value trait model {pr}109
  • Add frequency dependence architecture in sim_trait function, and allele frequency is given as an output as well {pr}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 {pr}112
  • Add option to input the causal site IDs, instead of randomly selecting them in sim_phenotype and sim_trait functions {pr}124
  • Add normalise_phenotypes function to normalize the simulated phenotypes {pr}130
  • Add delta degrees of freedom input in normalise_phenotypes function {pr}136
  • Add normalise_genetic_value function to normalize the genetic values {pr}145

Fix:

  • Raise error when there are no individuals {pr}97
  • Raise error when incorrect values are given in the num_causal argument {pr}99
  • Remove # pragma: no cover in certain functions {pr}119
  • Modify default input arguments of sim_trait, sim_env and sim_phenotype functions {pr}120
  • Add verification.py for statistical tests {pr}129
  • Add statistical tests against external simulators {pr}132
  • Change the dtype of trait_id input in genetic_value function {pr}134
  • Add density plot in verification.py {pr}138
  • Add multithreading in verification.py {pr}139
  • Conduct exact tests against AlphaSimR, simplePHENOTYPES and the simulation framework described in ARG-Needle paper in verification.py {pr}140

Documentation:

  • Modify introduction {pr}96
  • Document ploidy {pr}98
  • Documentation for the new sim_trait function {pr}115
  • Documentation for random_sign input in trait distribution models {pr}122
  • Modify phrasing in documentation {pr}123
  • Documentation for specifying causal site IDs {pr}126
  • Documentation for modifying the numericalization of genotypes {pr}133
  • Modify the frequency dependence explanation in the documentation {pr}141
  • Fix typo in documentation {pr}142

[0.0.1] - 2023-09-05

Highlights:

Documentation:

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:

Fix:

  • Hide private functions and classes {pr}73
  • Modify docstring explanations and examples {pr}76

Documentation:

  • Create infrastructure for documentation {pr}77
  • Build initial documentation {pr}78
  • Add Changelog to documentation {pr}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