API for donkeyshot/phybreak
Analysis of Outbreaks with Sequence Data
| Global functions | |
|---|---|
| .cycleYN | Source code |
| .edmondsiterative | Source code |
| .infarray | Source code |
| .inflist | Source code |
| .likseq | Source code |
| .likseqenv | Source code |
| .mcctree | Source code |
| .mpcinfector | Source code |
| .mtcctree | Source code |
| .pathtocycle | Source code |
| .postinfector | Source code |
| .ptr | Source code |
| .rinfectors | Source code |
| .rinftimes | Source code |
| .sctwh3 | Source code |
| .transtreecount | Source code |
| .transtreeedmonds | Source code |
| AvianFluH7N7_2003 | Man page |
| ESS | Man page Source code |
| ESS.factor | Man page Source code |
| ESS.numeric | Man page Source code |
| ESS.phybreak | Man page Source code |
| FMD_2001 | Man page |
| FMD_2007 | Man page |
| M_tuberculosis_2013 | Man page |
| accept_pbe | Source code |
| build_pbe | Source code |
| burnin.phybreak | Man page Source code |
| burnin_phybreak | Man page Source code |
| c.phybreak | Man page Source code |
| choose_distmodel | Source code |
| choose_whbottleneck | Source code |
| choose_whmodel | Source code |
| copy2pbe0 | Source code |
| copy2pbe1 | Source code |
| cuttree | Source code |
| destroy_pbe | Source code |
| distmatrix_phybreak | Source code |
| environment2phybreak | Source code |
| get.mcmc | Source code |
| get.multiPhylo | Source code |
| get.parameters | Source code |
| get.phylo | Source code |
| get.seqdata | Source code |
| get.tree | Source code |
| get_bottlenecks | Man page Source code |
| get_data | Man page Source code |
| get_mcmc | Man page Source code |
| get_multiPhylo | Man page Source code |
| get_parameters | Man page Source code |
| get_phybreak | Man page |
| get_phylo | Man page Source code |
| get_transtree | Man page Source code |
| graphicalparameters | Source code |
| infectorsets | Man page Source code |
| lik_coaltimes | Source code |
| lik_coaltimes_host | Source code |
| lik_distances | Source code |
| lik_gentimes | Source code |
| lik_sampletimes | Source code |
| lik_topology_host | Source code |
| link_s_to_t | Source code |
| logLik.phybreak | Man page Source code |
| make_nodehosts | Source code |
| make_phyloparset | Source code |
| make_phyloparsets | Source code |
| makephylotransplot | Source code |
| maketransplot | Source code |
| nthsample | Source code |
| phybreak | Man page Source code |
| phybreak2environment | Source code |
| phybreak2phylo | Source code |
| phybreak2trans | Source code |
| phybreakdata | Man page Source code |
| phylotree | Man page Source code |
| plot.phybreak | Man page Source code |
| plot.phybreakdata | Man page Source code |
| plotPhylo | Man page Source code |
| plotPhyloTrans | Man page Source code |
| plotTrans | Man page Source code |
| prepare_pbe | Source code |
| print.phybreak | Man page Source code |
| print_data | Source code |
| print_model | Source code |
| print_phybreak_general | Source code |
| print_screen_log | Source code |
| propose_pbe | Source code |
| quantile.phybreak | Man page Source code |
| rankhostsforplot | Source code |
| rewire_change_infector_complete | Source code |
| rewire_change_infector_wide | Source code |
| rewire_pathA_complete_classic | Source code |
| rewire_pathA_complete_edgewise | Source code |
| rewire_pathA_wide_classic | Source code |
| rewire_pathA_wide_edgewise | Source code |
| rewire_pathB_complete_classic | Source code |
| rewire_pathB_complete_edgewise | Source code |
| rewire_pathB_wide_classic | Source code |
| rewire_pathB_wide_edgewise | Source code |
| rewire_pathCF1_complete_classic | Source code |
| rewire_pathCF1_wide_classic | Source code |
| rewire_pathCF2_complete_classic | Source code |
| rewire_pathCF2_wide_classic | Source code |
| rewire_pathCF_complete_edgewise | Source code |
| rewire_pathCF_wide_edgewise | Source code |
| rewire_pathD_complete_classic | Source code |
| rewire_pathD_complete_edgewise | Source code |
| rewire_pathD_wide_classic | Source code |
| rewire_pathD_wide_edgewise | Source code |
| rewire_pathE_complete_classic | Source code |
| rewire_pathE_complete_edgewise | Source code |
| rewire_pathE_wide_classic | Source code |
| rewire_pathE_wide_edgewise | Source code |
| rewire_pathK_complete_classic | Source code |
| rewire_pathK_wide_classic | Source code Source code |
| rewire_pullnodes_complete | Source code |
| rewire_pullnodes_wide | Source code |
| rewire_removebnode | Source code |
| rewire_selectbnode | Source code |
| rewire_within_complete_edgewise | Source code |
| rewire_within_wide_edgewise | Source code |
| sample.phybreak | Man page Source code |
| sample_coaltimes | Source code |
| sample_phybreak | Man page Source code |
| sample_singlechildnode | Source code |
| sample_singlecoaltime | Source code |
| sample_topology | Source code |
| sim.phybreak | Man page Source code |
| sim_additionalsamples | Source code |
| sim_outbreak | Source code |
| sim_outbreak_size | Source code |
| sim_outbreak_size_spatial | Source code |
| sim_outbreak_spatial | Source code |
| sim_phybreak | Man page Source code |
| take_cnode | Source code |
| testargumentsclass_phybreak | Source code |
| testdataclass_phybreak | Source code |
| testfortree_phybreak | Source code |
| thin.phybreak | Man page Source code |
| transphylo2phybreak | Source code |
| transtree | Man page Source code |
| update_dist_exponent | Source code |
| update_dist_mean | Source code |
| update_dist_scale | Source code |
| update_host | Source code |
| update_host_keepphylo | Source code |
| update_host_phylotrans | Source code |
| update_host_withinhost | Source code |
| update_mG | Source code |
| update_mS | Source code |
| update_mu | Source code |
| update_wh_exponent | Source code |
| update_wh_level | Source code |
| update_wh_slope | Source code |
| whichgeneration | Source code |
