NEWS

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secsse 3.1.0 (2024-04-30)

Version 3.1.0 fixes a bug in the simulation code that caused trait changes during speciation to not be tracked appropriately. This could, for instance, interfere with conditioning and this bug especially impacted ClaSSE-type simulations.

Minor changes

• Added explicit check of the order of states, states are no longer assumed to be numerically or alphabetically sorted.
• Added multiple additional simulation checks

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

• The function expand_q_matrix is now deprecated, please use q_doubletrans

Minor changes

• Added conditioning of simulation of complete trees on complete tree size
• Fixed some issues with setting pool_init_states
• Added option to return a histogram of simulated tree sizes, across all successful and failed trees.

secsse 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

• Function name changes:
  • create_lambda_matrices() is now called create_lambda_list()
  • create_transition_matrix() is now called create_q_matrix()
  • create_mus() is now called create_mu_vector()
  • create_default_q_list() is now called create_default_shift_matrix()
  • create_default_lambda_list () is now called create_default_lambda_transition_matrix()
  • create_default_q_list() is now called create_default_shift_matrix()
• Package data files renamed:
  • phylo_Vign is now called phylo_vignette
  • traitinfo is now called traits
  • phy is now called example_phy_GeoSSE
• plot_state_exact() argument steps renamed to num_steps and argument focal_tree renamed to phy for consistency with other functions.

Major changes

• Vastly improve the computational speed of "cla_" likelihood calculation.
• Optimization of parallelization resulting in better scaling with more threads and faster run time for standard secsse and cla_secsse likelihood calculations.

Minor changes

• Added a NEWS.md file to track changes to the package.
• Documentation reworked into default_params_doc().
• Several documentation formatting improvements and linking. Documentation now follows and allows for roxygen2 markdown.
• A new vignette:
  • Using secsse with complete phylogenies (with extinction) vignette("complete_tree", package = "secsse")
• A new pkgdown website!
  • It contains all the documentation and vignettes of the package, along with additional interesting information like the Secsse versions article with details on performance and the development history of secsse.
• Revise, combine and simplify the Using SecSSE ML search and Setting up a secsse analysis into the Starting secsse vignette vignette("starting_secsse", package = "secsse").
• secsse_sim() argument conditioning now defaults to "obs_states" from "none".
• No longer Import package 'stringr' and Suggest package 'testit'.
• New organisation of code in .R, .cpp and .h files. (Developer side).
• Start archiving in Zenodo, with new .zenodo.json metadata file.

Bug fixes

• secsse_sim() fix bug causing error when simulating trees with extinct species.

secsse 2.6.0 (2023-07-06)

Major changes

• C++ code base for the standard likelihood, making smarter use of parallelization, this marks another 10-fold increase in speed.

Minor changes

• Add a number of helper functions: fill_in(), create_default_q_list(), create_default_transition_list(), create_mus()
• Implemented necessary changes to comply with CRAN clang16 build and solve issue with the boost odeint library uninitialized variable (see https://github.com/boostorg/odeint/issues/59 and more details at https://github.com/rsetienne/DAISIE/pull/158)
• Updated Copyright license to the Boost Software License, Version 1.0 for included C++ code (R code remains GPL>=3).

Bug fixes

• Fix memory leaks

secsse 2.5.0 (2023-05-03)

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()).

secsse 2.0.0 (2019-06-25)

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.

secsse 1.0.0 (2019-01-30)

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.