secsse 3.0.1

Version 3.0.1 patches some inaccuracies in simulation functions, and deprecates expand_q_matrix, as this was making some incorrect assumptions.

Breaking changes

Minor changes

3.0.0

Version 3.0.0 extends the C++ code base used for the standard likelihood to the “cla_” likelihood, harnessing the same computation improvement.

Breaking changes

Major changes

Minor changes

Bug fixes

2.6.0

Major changes

Minor changes

Bug fixes

2.5.0

Version 2.5.0 appeared in 2021 on GitHub and was published in May 2023 on CRAN. Version 2.5.0 marks the first version using C++ to perform the integration, and it used tbb (from the RcppParallel package) to perform multithreading. This marks a ten fold increase in speed over previous versions. Secondly, 2.5.0 introduces the function secsse_sim() to simulate a diversification process using the (cla) secsse framework. Lastly, in version 2.5.0 functions were added to allow visualisation of inferred rates of speciation across the tree (e.g. plot_state_exact() and secsse_loglik_eval()).

2.0.0

Version 2.0.0 appeared in June of 2019 on CRAN and extended the package with the cla framework, e.g. including state shifts during speciation / asymmetric inheritance during speciation.

1.0.0

The first version of secsse appeared in January of 2019 on CRAN. It used the package deSolve to solve all integrations, and could switch between either using a fully R based evaluation, or use FORTRAN to speed up calculations. Furthermore, using the foreach package, within-R parallelization was implemented. However, parallelization only situationally improved computation times, and generally, computation was relatively slow.