API for donkeyshot/phybreak
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
donkeyshot/phybreak documentation built on Aug. 16, 2018, noon