Man pages for thednainus/pangeaZA
Analyses and models for PANGEA data from South Africa (ZA).
| generate_model0 | Generate a simple HIV epidemic model for use by phydynR |
| get_sequences | Title Get fasta sequences from PANGEA dataframe |
| getsubtres | partition the tree into a set of clades within the desired... |
| getsubtresRecursively | partition the tree into a set of clades within the desired... |
| m0R.t | Compute R(t) by integrating over future hazard of removal and... |
| mcmcfit0.0 | Runs parallel mcmc chains in order to fit model0 |
| root_and_drop_tips | Title Root phylogenetic tree and drop outgroup sequences |
| rrcgr | Prunes redundant close global reference sequences for... |
| rrcgr2 | remove redundant cgr |
| sa_treedater | Does a treedater analysis for gag, env or pol and usign the... |
| setup.model.equations | Setup Model Equations |
| summary_model0 | Generate tables and plots for fits of model0 |
| trajectories_model0 | Make tfgys for multiple sets of input files |
