Man pages for phylodyn
Statistical Tools for Phylodynamics
| BNPR | Bayesian nonparametric phylodynamic reconstruction. |
| boombust_traj | Boom and bust trajectory |
| Bottle_20c | Bottle_20c |
| bottleneck_traj | Bottleneck trajectory |
| 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 |
| inla.models | INLA wrapper |
| logistic_traj | Seasonal logistic trajectory |
| 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_BNPR | Plot a BNPR output |
| plot_mrw | Plot Mean Relative Widths |
| plot_res | Plot SMCP Results |
| plot_seasonality | Plot Seasonality |
| 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 |
| 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. |
