Man pages for JamesStimson/transnp
Transmission inference using SNP data
| addAlignment | add alignments to list |
| createMLTrees | create maximum likelihood trees from a list of alignments |
| createTimedTrees | create timed trees from a list of maximum likelihood trees |
| estimatetree | estimate a tree |
| estimate.tree | estimate a tree |
| filterInfectedDate | Filter record on specified date of infection |
| filterPossibleWiw | Filter record on specified allowable transmission matrix |
| filterTransPair | Filter record on specified directed transmission pair |
| getGenerationTimes | Get generation times |
| getInfectionDates | Get infection dates |
| getInfectionTimes | Get infection times |
| getLikelyInfectors | Get infection likelihoods for a given case |
| getNumberUnsampled | Get the number of unsampled cases |
| getTimesToSampling | Get infection-to-sampling times |
| getTTreeDistInfo | Create list of wiw information in order to compute... |
| infer_multiTTree_shareParam | Simultaneously infer transmission trees given phylogenetic... |
| networkPlot | Simple visualisation of transmission tree with visNetwork |
| networkTPlot | Dynamic plot of the transmission network with edges weighted... |
| plotGenerationTimeDensity | Plot generation time density for chosen case |
| plot_gen_times | Plot histogram of generation times for each cluster |
| plotInfectionDateDensity | Plot infection date density for chosen case |
| plotSampleTimeDensity | Plot time to sampling (from infection) for chosen case |
| plot_times_to_samp | Plot histogram of times to sampling for each cluster |
| plotTransTreeSummary | Plot transmission network with posterior probabilities at or... |
| plot_unsampled_cases | Plot histogram of the number of unsampled cases for each... |
| setUpDates | create list of dates to match alignments |
| simulTransTrees | Simultaneously infer transmission trees given phylogenetic... |
