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Merged
elegios merged 5 commits into from
Apr 27, 2026
Merged

Divmodels change #50

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6b104a1
Changed changelog so that it is based on the latest release
ronquist Mar 26, 2026
4eba651
Added more info about the changes in the divmodels pull request
ronquist Mar 26, 2026
f5458be
Added comment about the import of math.tppl in model files
ronquist Mar 27, 2026
761b4db
Merge branch 'treeppl:master' into divmodels-change
ronquist Apr 23, 2026
865cae1
Remove mention of math imports, implied by other comments and a bit t…
elegios Apr 23, 2026
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12 changes: 12 additions & 0 deletions docs/changelog.md
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Expand Up @@ -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
Expand All @@ -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

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