v3.0.1

v3.0.1

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.
• Fix Zenodo metadata integration.
• CITATION file uses new 'bibentry()`.

v3.0.0

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.