Files in Giappo/sls
Likelihood model for diversification processes with single lineage rate shifts
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/default_param_doc.R
R/sls_ML.R
R/sls_conditionings.R
R/sls_convolutions.R
R/sls_dummy_functions.R
R/sls_l_2_brts.R
R/sls_likelihoods_bisse.R
R/sls_likelihoods_div.R
R/sls_likelihoods_nee.R
R/sls_likelihoods_nodiv.R
R/sls_main.R
R/sls_main_utils.R
R/sls_sim.R
R/sls_sim_utils.R
R/sls_utils.R
README.md
appveyor.yml
man/DFT.Rd
man/IDFT.Rd
man/P_transition_matrix.Rd
man/Pc_1shift.Rd
man/cat2.Rd
man/combine_ddd.Rd
man/combine_ddd_nodiv.Rd
man/combine_pns.Rd
man/combine_pns0.Rd
man/combine_pns_nodiv.Rd
man/create_data_file_name.Rd
man/create_results_file_name.Rd
man/cut_loglik_from_name.Rd
man/d_t.Rd
man/default_params_doc.Rd
man/e_t.Rd
man/get_function_names.Rd
man/get_model_names.Rd
man/get_param_names.Rd
man/get_pkg_name.Rd
man/loglik_DDD.Rd
man/loglik_bisse.Rd
man/loglik_bisse2.Rd
man/loglik_bisse_shift.Rd
man/loglik_bisse_shift2.Rd
man/loglik_preshift.Rd
man/loglik_preshift2.Rd
man/loglik_preshift_nodiv.Rd
man/loglik_preshift_unobs.Rd
man/loglik_sls_p.Rd
man/loglik_sls_p2.Rd
man/loglik_sls_p2_nodiv.Rd
man/loglik_sls_p_dummy.Rd
man/loglik_sls_p_dummy_nodiv.Rd
man/loglik_sls_p_nodiv.Rd
man/loglik_sls_q.Rd
man/loglik_sls_q_nodiv.Rd
man/main_save_files.Rd
man/one_minus_pt.Rd
man/one_minus_ut.Rd
man/p_t.Rd
man/pars_transform_back.Rd
man/pars_transform_forward.Rd
man/phase_factor.Rd
man/pn.Rd
man/pn_bar.Rd
man/print_info.Rd
man/sim_adapt_l_matrix_size.Rd
man/sim_check_survival.Rd
man/sim_conditioning.Rd
man/sim_cut_l_matrix.Rd
man/sim_decide_event.Rd
man/sim_get_brts.Rd
man/sim_get_motherclade.Rd
man/sim_get_n_0.Rd
man/sim_get_pars.Rd
man/sim_get_pool.Rd
man/sim_get_shifts_info.Rd
man/sim_get_standard_l_2.Rd
man/sim_get_t_0.Rd
man/sim_initialize_data_new_clade.Rd
man/sim_read_l_1.Rd
man/sim_sample_deltas.Rd
man/sim_use_event.Rd
man/sls_ML.Rd
man/sls_check_input.Rd
man/sls_conds.Rd
man/sls_l_2_brts.Rd
man/sls_loglik_rhs.Rd
man/sls_logliks_div.Rd
man/sls_logliks_dummy.Rd
man/sls_logliks_experiment.Rd
man/sls_logliks_nodiv.Rd
man/sls_main.Rd
man/sls_main_dummy.Rd
man/sls_ml_dummy.Rd
man/sls_n_0s.Rd
man/sls_sim.Rd
man/ut.Rd
pics/AppVeyor.png
pics/Codecov.png
pics/TravisCI.png
sls.Rproj
tests/testthat.R
tests/testthat/test-pars_transform.R
tests/testthat/test-sls_conditionings.R
tests/testthat/test-sls_convolutions.R
tests/testthat/test-sls_dummy.R
tests/testthat/test-sls_likelihoods_bisse.R
tests/testthat/test-sls_likelihoods_div.R
tests/testthat/test-sls_likelihoods_nee.R
tests/testthat/test-sls_likelihoods_nodiv.R
tests/testthat/test-sls_main.R
tests/testthat/test-sls_ml.R
tests/testthat/test-sls_sim.R
tests/testthat/test-sls_sim_utils.R
tests/testthat/test-sls_utils.R
tests/testthat/test-style.R
vignettes/sls_pipeline.Rmd
