API for mdkarcher/phylodyn
Statistical Tools for Phylodynamics
| Global functions | |
|---|---|
| BNPR | Man page Source code |
| BNPR_PS | Man page Source code |
| BNPR_samp_only | Man page Source code |
| Bottle_20c | Man page |
| ESS | Source code |
| ESS2 | Source code |
| ESS3 | Source code |
| ESS_betas_ll | Source code |
| ESS_betas_ll2 | Source code |
| ESS_betas_ll3 | Source code |
| ESS_ext_ll | Source code |
| ESS_none_ll | Source code |
| GP.posterior | Source code |
| GP.posterior2 | Source code |
| GP.prior | Source code |
| MH_betas | Source code |
| MH_betas_rscan | Source code |
| MH_betas_rscan2 | Source code |
| MH_betas_rscan3 | Source code |
| Met | Source code |
| NY_flu | Man page |
| Q.matrix | Source code |
| Q_matrix | Source code |
| U | Source code |
| U_kappa | Source code |
| U_split | Source code |
| U_split_smc | Source code |
| bias | Source code |
| boombust_traj | Man page Source code |
| boombust_traj_inv | Source code |
| bottleneck_traj | Man page Source code |
| bottleneck_traj_inv | Source code |
| branching_sampling_times | Source code |
| bring_branch_lengths | Source code |
| burnin_subsample | Source code |
| calculate_estimates | Source code |
| coal_check | Man page Source code |
| coal_lik_init | Source code |
| coal_loglik | Source code |
| coal_loglik_smc | Source code |
| coal_samp_fns_loglik | Source code |
| coal_samp_loglik | Source code |
| coal_stats | Source code |
| coal_to_exp | Source code |
| coalsim | Man page Source code |
| coalsim_thin | Source code |
| coalsim_tt | Source code |
| compute_pos_summ | Source code |
| compute_pos_summ2 | Source code |
| compute_pos_summ3 | Source code |
| condense_stats | Source code |
| create_F | Man page Source code |
| cyclic_traj | Man page Source code |
| cyclic_traj_inv | Source code |
| dev | Source code |
| envelope | Source code |
| exp_coal_lik_init | Source code |
| exp_coal_loglik | Source code |
| exp_to_KS | Source code |
| exp_traj | Man page Source code |
| exp_traj_inv | Source code |
| find.children.length | Source code |
| find_info2 | Man page Source code |
| find_sufficient | Source code |
| float2gray | Source code |
| gen_INLA_args | Source code |
| gen_summary | Source code |
| generate_newick | Man page Source code |
| generate_newick_old | Source code |
| get_data | Source code |
| get_tips_and_times | Source code |
| gp_nieps_iso | Source code |
| group_data | Source code |
| group_sufficient | Source code |
| hazard_uniroot_stepfun | Source code |
| heterochronous_gp_stat | Source code |
| heterochronous_gp_stat_old | Source code |
| hist2heat | Man page Source code |
| infer_coal | Source code |
| infer_coal_deriv | Source code |
| infer_coal_samp | Source code |
| infer_coal_samp_exper | Source code |
| infer_samp | Source code |
| infer_samp_exper | Source code |
| initialize_params | Man page Source code |
| inla.models | Man page Source code |
| int_invexp_interval | Source code |
| integrate_step_fun | Source code |
| joint_stats | Source code |
| lambda.prior | Source code |
| lambda_prior | Source code |
| location.thinned.uniform | Source code |
| location.thinned.uniform2 | Source code |
| log_betas_prior | Source code |
| log_betas_prior2 | Source code |
| log_betas_prior3 | Source code |
| log_f_prior_kappa | Source code |
| log_field_prior | Source code |
| log_inorm_prior | Source code |
| log_inorm_prior3 | Source code |
| log_kappa_prior | Source code |
| log_mvnorm_prior | Source code |
| log_samp_int | Source code |
| log_samp_mat | Man page Source code |
| log_sampling_intensity | Source code |
| log_tau_prior | Source code |
| logistic_traj | Man page Source code |
| logistic_traj_inv | Source code |
| loglik_ESS | Man page Source code |
| loglik_ESS_pref | Man page Source code |
| logposterior_ESS | Man page Source code |
| logposterior_ESS_pref | Man page Source code |
| logprior_ESS | Man page Source code |
| logprior_ESS_pref | Man page Source code |
| make_alignment | Man page Source code |
| make_taxa | Man page Source code |
| mcmc_ESS | Source code |
| mcmc_sampling | Man page Source code |
| mesa_traj | Man page Source code |
| mesa_traj_inv | Source code |
| ml_exp_coal | Man page Source code |
| number.thinned | Source code |
| phylodyn | Man page |
| phylodyn-package | Man page |
| plot_BEAST | Man page Source code |
| plot_BNPR | Man page Source code |
| plot_BNPR_old | Source code |
| plot_INLA | Source code |
| plot_INLA_ii | Source code |
| plot_INLA_inv | Source code |
| plot_MCMC | Man page Source code |
| plot_mrw | Man page Source code |
| plot_res | Man page Source code |
| plot_seasonality | Man page Source code |
| plot_seasonality_beast | Man page Source code |
| posterior_coal_check | Man page Source code |
| posterior_samp_check | Man page Source code |
| precBM | Source code |
| pref_sample | Man page Source code |
| pref_sample_betafun | Source code |
| read_times | Man page Source code |
| regional_flu | Man page |
| relwid | Source code |
| relwid_emp | Source code |
| samp_check | Man page Source code |
| samp_check_exp | Source code |
| samp_check_exp2 | Source code |
| samp_loglik | Source code |
| samp_loglik3 | Source code |
| samp_loglik_pow | Source code |
| samp_stats | Source code |
| samp_to_chisq | Source code |
| samp_to_exp | Source code |
| samp_to_exp2 | Source code |
| sample_tree | Man page Source code |
| sampling | Source code |
| sampling_ESS | Source code |
| sampling_ESS2 | Source code |
| sampling_ESS3 | Source code |
| shade_band | Source code |
| sigmoidal | Source code |
| slice.sampling | Source code |
| sloped_traj | Man page Source code |
| sloped_traj_inv | Source code |
| smcp_sampling | Man page Source code |
| steep_cyc_traj | Man page Source code |
| steep_cyc_traj_inv | Source code |
| sufficient_stats | Source code |
| sufficient_stats2 | Source code |
| summarize_phylo | Man page Source code |
| summarize_phylo2 | Source code |
| traj_beta | Man page Source code |
| unif_traj | Man page Source code |
| unif_traj_inv | Source code |
| update_burnin_subsample | Source code |
| variation | Source code |
| whiten_kappa | Source code |
