From 7aa0cb432936168e14976f7f8d9bfdacc29cc029 Mon Sep 17 00:00:00 2001 From: daikitag <48062118+daikitag@users.noreply.github.com> Date: Wed, 6 Mar 2024 23:41:07 +0000 Subject: [PATCH] Version 0.1.0 Release Update the changelog for version0.1.0 release --- CHANGELOG.md | 46 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 45 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4559cdd..01504c2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,49 @@ # 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: @@ -60,4 +104,4 @@ Initial alpha release of the package. - Daiki Tagami - Gertjan Bisschop -- Jerome Kelleher \ No newline at end of file +- Jerome Kelleher