Version 0.1.0 Release

Update the changelog for version0.1.0 release

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
+- Jerome Kelleher