Files in secsse

Several Examined and Concealed States-Dependent Speciation and Extinction

NEWS.md R/RcppExports.R R/secsse_utils.R R/seccse_plot.R R/default_params_doc.R R/secsse-package.R R/secsse_sim.R R/secsse_prep.R R/secsse_loglik.R R/secsse_data.R R/secsse_ml_func_def_pars.R R/secsse_ml.R inst/doc/sim_with_secsse.Rmd inst/doc/complete_tree.Rmd inst/doc/starting_secsse.Rmd inst/doc/complete_tree.R inst/doc/sim_with_secsse.R inst/doc/plotting_states.R inst/doc/starting_secsse.R inst/doc/plotting_states.Rmd tests/testthat.R tests/testthat/test_geosse.R tests/testthat/test_hisse.R tests/testthat/test_plotting.R tests/testthat/test_secsse_sim.R tests/testthat/test_secsse_vs_cla_secsse.R tests/testthat/test_cla_secsse_ml_func_def_pars.R tests/testthat/test_ml_par.R tests/testthat/test_ml_func_def_pars.R tests/testthat/test_lambda_setup.R tests/testthat/test_cla_secsse_ml.R tests/testthat/test_integration_methods.R tests/testthat/test_secsse_cla_ct.R tests/testthat/test_secsse_ct.R vignettes/sim_with_secsse.Rmd vignettes/complete_tree.Rmd vignettes/starting_secsse.Rmd vignettes/plotting_states.Rmd man/secsse_ml_func_def_pars.Rd man/secsse_loglik_eval.Rd man/cla_id_paramPos.Rd man/q_doubletrans.Rd man/create_default_shift_matrix.Rd man/create_lambda_list.Rd man/extract_par_vals.Rd man/secsse_loglik.Rd man/create_q_matrix.Rd man/cla_secsse_loglik.Rd man/plot_state_exact.Rd man/create_default_lambda_transition_matrix.Rd man/cla_secsse_ml.Rd man/phylo_vignette.Rd man/event_times.Rd man/cla_secsse_ml_func_def_pars.Rd man/sortingtraits.Rd man/default_params_doc.Rd man/fill_in.Rd man/create_mu_vector.Rd man/traits.Rd man/prepare_full_lambdas.Rd man/id_paramPos.Rd man/secsse_sim.Rd man/secsse-package.Rd man/secsse_ml.Rd man/example_phy_GeoSSE.Rd man/expand_q_matrix.Rd