Man pages for JamesStimson/transnp
Transmission inference using SNP data

addAlignmentadd alignments to list
createMLTreescreate maximum likelihood trees from a list of alignments
createTimedTreescreate timed trees from a list of maximum likelihood trees
estimatetreeestimate a tree
estimate.treeestimate a tree
filterInfectedDateFilter record on specified date of infection
filterPossibleWiwFilter record on specified allowable transmission matrix
filterTransPairFilter record on specified directed transmission pair
getGenerationTimesGet generation times
getInfectionDatesGet infection dates
getInfectionTimesGet infection times
getLikelyInfectorsGet infection likelihoods for a given case
getNumberUnsampledGet the number of unsampled cases
getTimesToSamplingGet infection-to-sampling times
getTTreeDistInfoCreate list of wiw information in order to compute...
infer_multiTTree_shareParamSimultaneously infer transmission trees given phylogenetic...
networkPlotSimple visualisation of transmission tree with visNetwork
networkTPlotDynamic plot of the transmission network with edges weighted...
plotGenerationTimeDensityPlot generation time density for chosen case
plot_gen_timesPlot histogram of generation times for each cluster
plotInfectionDateDensityPlot infection date density for chosen case
plotSampleTimeDensityPlot time to sampling (from infection) for chosen case
plot_times_to_sampPlot histogram of times to sampling for each cluster
plotTransTreeSummaryPlot transmission network with posterior probabilities at or...
plot_unsampled_casesPlot histogram of the number of unsampled cases for each...
setUpDatescreate list of dates to match alignments
simulTransTreesSimultaneously infer transmission trees given phylogenetic...
JamesStimson/transnp documentation built on June 18, 2018, 2 a.m.