Files in mdkarcher/phylodyn
Statistical Tools for Phylodynamics
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/BNPR_PS_fixedBeta.R
R/GP_isochronous.R
R/INLA_tools.R
R/Newick_Files.R
R/Phyloinfer.R
R/Tajima.R
R/calculate.R
R/coal_lik.R
R/coal_lik_BSMC.R
R/coalsieve.R
R/datasets.R
R/gp_nieps.R
R/hist2heat.R
R/model_check.R
R/old_functions.R
R/performance_measures.R
R/phylodyn.R
R/plotting_tools.R
R/pow_ESS.R
R/read_newick.R
R/simple_models.R
R/statgentools.R
R/trajectories.R
R/wrappers.R
R/xml_makers.R
README.md
data/Bottle_20c.rda
data/NY_flu.rda
data/regional_flu.rda
inst/CITATION
man/BNPR.Rd
man/BNPR_samp_only.Rd
man/Bottle_20c.Rd
man/NY_flu.Rd
man/boombust_traj.Rd
man/bottleneck_traj.Rd
man/coal_check.Rd
man/coalsim.Rd
man/create_F.Rd
man/cyclic_traj.Rd
man/exp_traj.Rd
man/find_info2.Rd
man/generate_newick.Rd
man/hist2heat.Rd
man/initialize_params.Rd
man/inla.models.Rd
man/log_samp_mat.Rd
man/logistic_traj.Rd
man/loglik_ESS.Rd
man/loglik_ESS_pref.Rd
man/logposterior_ESS.Rd
man/logposterior_ESS_pref.Rd
man/logprior_ESS.Rd
man/logprior_ESS_pref.Rd
man/make_alignment.Rd
man/make_taxa.Rd
man/mcmc_sampling.Rd
man/mesa_traj.Rd
man/ml_exp_coal.Rd
man/phylodyn-package.Rd
man/plot_BEAST.Rd
man/plot_BNPR.Rd
man/plot_MCMC.Rd
man/plot_mrw.Rd
man/plot_res.Rd
man/plot_seasonality.Rd
man/plot_seasonality_beast.Rd
man/posterior_coal_check.Rd
man/posterior_samp_check.Rd
man/pref_sample.Rd
man/read_times.Rd
man/regional_flu.Rd
man/samp_check.Rd
man/sample_tree.Rd
man/sloped_traj.Rd
man/smcp_sampling.Rd
man/steep_cyc_traj.Rd
man/summarize_phylo.Rd
man/traj_beta.Rd
man/unif_traj.Rd
tests/testthat.R
tests/testthat/test_anything.R
vignettes/CovariatesComparison.Rmd
vignettes/LocalGenealogies.Rmd
vignettes/LongPhyloinfer.Rmd
vignettes/ModelSelectEbov.Rmd
vignettes/ModelSelectFlu.Rmd
vignettes/NewYorkInfluenza.Rmd
vignettes/RegionalInfluenza.Rmd
vignettes/RegionalSeasonality.Rmd
vignettes/SimpleBNPR.Rmd
vignettes/SimplePPC.Rmd
vignettes/SimplePhyloinfer.Rmd
vignettes/Simulation.Rmd
vignettes/SimulationStudy.Rmd
