Analysis of Outbreaks with Sequence Data

Global functions | |
---|---|

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_whbottleneck | Source code |

choose_whmodel | Source code |

copy2pbe0 | Source code |

copy2pbe1 | Source code |

cycleYN | Source code |

destroy_pbe | Source code |

distmatrix_phybreak | Source code |

edmondsiterative | 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_gentimes | Source code |

lik_sampletimes | Source code |

lik_topology_host | Source code |

likseq | Source code |

likseqenv | 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 |

maketransplot | Source code |

mcctree | Source code |

mpcinfector | Source code |

mtcctree | Source code |

nfarray | Source code |

nflist | Source code |

nthsample | Source code |

obkData2phybreak | Source code |

pathtocycle | 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 |

plotTrans | Man page Source code |

postinfector | 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 |

ptr | 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 |

rinfectors | Source code |

rinftimes | 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 |

sctwh3 | Source code |

sim.phybreak | Man page Source code |

sim_additionalsamples | Source code |

sim_outbreak | Source code |

sim_outbreak_size | Source code |

sim_phybreak | Man page Source code |

sim_phylotree | Source code |

sim_sequences | 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 |

transtreecount | Source code |

transtreeedmonds | 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 |

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