Files in franciscorichter/emphasis
Evolutionary Modeling on Phylogenetic Applications with Simulations and Importance Sampling
.DS_Store
.Rbuildignore
.gitattributes
.github/workflows/main.yml
.gitignore
DESCRIPTION
Documentation/Usage_DE.R
Documentation/documentation_benchmarking.Rmd
Documentation/documentation_benchmarking.nb.html
Documentation/documentation_estimation.Rmd
Documentation/documentation_estimation.nb.html
Documentation/documentation_notebook.Rmd
Documentation/documentation_simulation.Rmd
Documentation/documentation_simulation.nb.html
LICENSE
NAMESPACE
R/.DS_Store
R/RcppExports.R
R/emphasis.R
R/generateNonHomogeneousExp.R
R/generatePhyloPD.R
R/learn_de.R
R/learning_DE.R
R/learning_DE_mod.R
R/learning_EM.R
R/learning_GAM.R
R/learning_GMM.R
R/pd_ML.R
R/simulation_PD_spec_ext.R
R/simulation_augmentPD.R
R/simulation_generatePhyloDDD.R
R/simulation_generatePhyloPD.R
R/simulation_tree_pd.R
R/visualization_learning.R
R/visualization_lik_vis.R
R/visualization_process_and_plot.R
R/zdep_learning_emphasis_de_factorial.R
R/zdep_util.R
README.md
circ.png
docs/Simulation.R
docs/Simulation.Rmd
docs/Simulation.html
emphasis.Rproj
emphasis_logo.png
emphasis_logo_circ.png
inst/include/augment_tree.hpp
inst/include/div_tree.hpp
inst/include/emphasis.hpp
inst/include/model.hpp
inst/include/model_helpers.hpp
inst/include/phylodiv_tree.hpp
inst/include/precision_weights.hpp
inst/include/sbplx.hpp
inst/include/state_guard.hpp
man/AugmentMultiplePhyloPD.Rd
man/ExponentialRate.Rd
man/augmentPD.Rd
man/check_convergence.Rd
man/dd_ML_est.Rd
man/e_cpp.Rd
man/em_cpp.Rd
man/emphasis-package.Rd
man/emphasis.Rd
man/emphasis_de.Rd
man/emphasis_de_factorial.Rd
man/generateNonHomogeneousExp.Rd
man/generatePhyloPD.Rd
man/loglikelihood.Rd
man/m_cpp.Rd
man/mcGrid.Rd
man/nhExpRand.Rd
man/pd_ML.Rd
man/rate_t.Rd
man/rescale_tree.Rd
man/sim_tree_is_extinct_pd.Rd
man/sim_tree_pd_R.Rd
man/sim_tree_pd_cpp.Rd
man/sim_tree_pd_grid.Rd
man/simulate_evolution.Rd
man/simulate_single_pd_tree_cpp.Rd
man/train_GAM.Rd
pythonProject/.idea/.gitignore
pythonProject/.idea/.name
pythonProject/.idea/Py.iml
pythonProject/.idea/inspectionProfiles/profiles_settings.xml
pythonProject/.idea/misc.xml
pythonProject/.idea/modules.xml
pythonProject/.idea/vcs.xml
src/E_step.cpp
src/M_step.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/augment_tree.cpp
src/div_tree.cpp
src/generateNonHomogeneousExp-e621a0d0.o.tmp
src/generateNonHomogeneousExp.cpp
src/loglik.cpp
src/mcem.cpp
src/phylodiv_tree.cpp
src/rcpp_mce.cpp
src/rcpp_mcem.cpp
src/rcpp_mcm.cpp
src/rinit.cpp
src/rinit.h
src/rsbplx.cpp
src/unpack.h
vignettes/Simulation.Rmd
vignettes/documentation_estimation.Rmd
