Files in rsetienne/secsse
Several Examined and Concealed States-Dependent Speciation and Extinction
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/cpp_lint.yml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
.vscode/genenv.R
.vscode/launch.json
.vscode/settings.json
.vscode/tasks.json
.zenodo.json
DESCRIPTION
LICENSE
LICENSE.note
NAMESPACE
NEWS.md
R/RcppExports.R
R/default_params_doc.R
R/seccse_plot.R
R/secsse-package.R
R/secsse_data.R
R/secsse_loglik.R
R/secsse_ml.R
R/secsse_ml_func_def_pars.R
R/secsse_prep.R
R/secsse_sim.R
R/secsse_utils.R
README.md
_pkgdown.yml
data/example_phy_GeoSSE.rda
data/phylo_vignette.rda
data/traits.rda
inst/CITATION
inst/COPYRIGHTS
inst/LICENSE_1_0.txt
man/cla_id_paramPos.Rd
man/cla_secsse_loglik.Rd
man/cla_secsse_ml.Rd
man/cla_secsse_ml_func_def_pars.Rd
man/create_default_lambda_transition_matrix.Rd
man/create_default_shift_matrix.Rd
man/create_lambda_list.Rd
man/create_mu_vector.Rd
man/create_q_matrix.Rd
man/default_params_doc.Rd
man/event_times.Rd
man/example_phy_GeoSSE.Rd
man/expand_q_matrix.Rd
man/extract_par_vals.Rd
man/figures/Codecov.png
man/figures/github_actions_logo.png
man/fill_in.Rd
man/id_paramPos.Rd
man/phylo_vignette.Rd
man/plot_state_exact.Rd
man/prepare_full_lambdas.Rd
man/q_doubletrans.Rd
man/secsse-package.Rd
man/secsse_loglik.Rd
man/secsse_loglik_eval.Rd
man/secsse_ml.Rd
man/secsse_ml_func_def_pars.Rd
man/secsse_sim.Rd
man/sortingtraits.Rd
man/traits.Rd
secsse.Rproj
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/config.h
src/odeint.h
src/secsse_eval.cpp
src/secsse_loglik.cpp
src/secsse_loglik.h
src/secsse_rhs.h
src/secsse_sim.cpp
src/secsse_sim.h
tests/testthat.R
tests/testthat/test_cla_secsse_ml.R
tests/testthat/test_cla_secsse_ml_func_def_pars.R
tests/testthat/test_geosse.R
tests/testthat/test_hisse.R
tests/testthat/test_integration_methods.R
tests/testthat/test_lambda_setup.R
tests/testthat/test_ml_func_def_pars.R
tests/testthat/test_ml_par.R
tests/testthat/test_plotting.R
tests/testthat/test_secsse_cla_ct.R
tests/testthat/test_secsse_ct.R
tests/testthat/test_secsse_sim.R
tests/testthat/test_secsse_vs_cla_secsse.R
vignettes/.gitignore
vignettes/complete_tree.Rmd
vignettes/plotting_states.Rmd
vignettes/secsse_performance.Rmd
vignettes/sim_with_secsse.Rmd
vignettes/starting_secsse.Rmd
vignettes/timing_data.RData
