Man pages for dhelekal/CaveDive
Phylodynamics for Clonal Expansion
| build_coal_tree | Generate a Newick string representation of a tree... |
| build_coal_tree.structured | Generate a Newick string representation of a tree... |
| coalescent_loglh | Compute likelihood of a realisation of a homogeneous... |
| discard_burn_in.expansionsMCMC | Discard burn in iterations |
| expansions_infer | Run rjmcmc inference on the provided preprocessed phylogeny,... |
| expansionsMCMC | Constructs object of class expansionsMCMC |
| expansions_simulate | Simulate parameters and event times for a genealogy with... |
| exponential_coalescent_loglh | Compute likelihood of a realisation of an exponential growth... |
| extract_lineage_times | Extracts Lineage times (but faster) from a parent phylogeny... |
| homogenous_coal.log_lh | Compute likelihood of a realisation of a homogeneous... |
| homogenous_coal.simulate | Simulate homogenous coalescent, |
| inhomogenous_coal.log_lh | Compute likelihood of a realisation of an inhomogeneous... |
| inhomogenous_coal.simulate | Simulate inhomogenous coalescent, |
| inv_rates | Numerically invert rates |
| logexp_coalescent_loglh | Compute likelihood of a realisation of an half/logistic... |
| mcmc2data.frame | Converts MCMC output into two data frames, one conaining... |
| plot_event_summary | Plots mcmc output as several panels |
| plot.expansionsMCMC | Plot results |
| plot_structured_tree | Plots a structured tree with different lineages distinguished... |
| plot_tree_freq | Plots tree branch frequency histogram |
| preprocess_phylo | Preprocess phylogeny to speed up likelihood computation |
| run_expansion_inference | Run rjmcmc inference on the provided phylogeny and supplied... |
| sat_coalescent_loglh | Compute likelihood of a realisation of an half/logistic... |
| simulate_clonal_tree | Simulate an instance of coalescent process with local... |
| simulate_expansion_phylo | A phylogeny containing clonal expansions. Note: The resulting... |
| standard_priors | Generates a list of priors of the form described in the paper... |
| structured_coal.likelihood | Compute likelihood for preprocessed phylogeny |
| structured_coal.simulate | Simulate expansion structured coalescent Population size must... |
