diff --git a/docs/changelog.md b/docs/changelog.md index c2d62fe..0617a71 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -14,14 +14,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- Added math functions, distribution types and functions, and tree types and functions to the library. The code is in separate library files (`math.tppl`, `distributions.tppl` and `trees.tppl`) in the `src/lib/` directory. +- Added diversification model example for the birth-death diffusion (BDD) model, version 2 (analogous to ClaDS2). +- Added diversification model versions with hard-coded delayed sampling. +- Added constant-rate birth-death (CRBD) model using weights based on analytical likelihood rather than simulation. + ### Changed +- Moved the functions `exp`, `log`, `sqrt`, `minInt`, `maxInt`, `floor`, `ceil`, `round` from the `standard.tppl` library file to `math.tppl`. + ### Deprecated ### Removed +- Removed the `Tree` type from the `standard.tppl` library file. An identical type, called `ClockTree`, is now in the `trees.tppl` library file. This change allows a more convenient interface, in that a user can synonymize a local custom `Tree` type with `ClockTree`, or any other tree type in the standard library that is appropriate for the model script. + ### Fixed +- Changed the `rho` parameter (leaf sampling probability) in the data files for the diversification model scripts from `2.0` to `0.5`. + ### Security ## v0.3 @@ -44,3 +55,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Using `debug` to print strings no longer crashes ### Security +