Man pages for mdkarcher/phylodyn
Statistical Tools for Phylodynamics
| BNPR | Bayesian nonparametric phylodynamic reconstruction. |
| BNPR_samp_only | Nonparametric estimate of sampling intensity |
| boombust_traj | Boom and bust trajectory |
| Bottle_20c | Bottle_20c |
| bottleneck_traj | Bottleneck trajectory |
| coal_check | Predictive check for coalescent model |
| coalsim | Simulate from inhomogeneous, heterochronous coalescent |
| create_F | Generates a matrix with ranked tree shape information |
| cyclic_traj | Cyclical trajectory |
| exp_traj | Exponential trajectory |
| find_info2 | Extracts all sufficient statistics for inferring Ne from... |
| generate_newick | Returns a phylo object from the argumentes generated with... |
| hist2heat | Plot heatmap of a histogram |
| initialize_params | Set fixed parameters for prior, likelihood, and posterior... |
| inla.models | INLA wrapper |
| logistic_traj | Seasonal logistic trajectory |
| loglik_ESS | Compute the log-likelihood using the set-up for ESS (sampling... |
| loglik_ESS_pref | Compute the log-likelihood using the set-up for ESS (sampling... |
| logposterior_ESS | Compute the log-posterior using the set-up for ESS (sampling... |
| logposterior_ESS_pref | Compute the log-posterior using the set-up for ESS (sampling... |
| logprior_ESS | Compute the log-prior using the set-up for ESS (sampling... |
| logprior_ESS_pref | Compute the log-prior using the set-up for ESS (sampling... |
| log_samp_mat | Calculate posterior sampling intensities |
| make_alignment | Make alignment BEAST XML block |
| make_taxa | Make taxa BEAST XML block |
| mcmc_sampling | MCMC Sampling |
| mesa_traj | Mesa trajectory |
| ml_exp_coal | Maximum likelihood exponential model |
| NY_flu | New York Influenza Genealogy |
| phylodyn-package | Tools for analyzing genealogy and genome sequence data using... |
| plot_BEAST | Plot trajectory estimate and credible intervals |
| plot_BNPR | Plot a BNPR output |
| plot_MCMC | Plot an MCMC output |
| plot_mrw | Plot Mean Relative Widths |
| plot_res | Plot SMCP Results |
| plot_seasonality | Plot Seasonality |
| plot_seasonality_beast | Plot seasonal overlays |
| posterior_coal_check | Posterior predictive check for coalescent model |
| posterior_samp_check | Posterior predictive check for inhomogenous Poisson process... |
| pref_sample | Sample preferentially |
| read_times | Extracts coalescent times from a Multi-Phylo object |
| regional_flu | Regional Influenza Genealogy |
| samp_check | Predictive check for sampling model |
| sample_tree | Sample a phylo tree |
| sloped_traj | Sloped trajectory |
| smcp_sampling | SMC' sampler-inference from local genealogies |
| steep_cyc_traj | Steep cyclical trajectory |
| summarize_phylo | Summarize a phylogeny. |
| traj_beta | Raise a trajectory function to a power |
| unif_traj | Uniform trajectory. |
