get a sample list of possible transmission pair assignments
sampleTransmissionPairs(tree, g, e, nSamples, sampTime = c("eachAfterGettingInfected", "bothAtInfection", "atTips"))
| tree | a phylo object with N tips. |
|---|---|
| g | numerical vector of length the number of nodes in the tree: the known viral genetic contributions at the tips and internal nodes. |
| e | numerical vector of length N: the known environmental deviations at the tips. |
| nSamples | : number of samples. Each sample corresponds to an assignment of the internal nodes of the tree with tip-labels and the correalation of the formed set of source-recipient phenotypes. |
| sampTime | : a character indicating how the phenotypes for the pairs shall be formed. Currently two possible values are supported : eachAfterGettingInfected - the source phenotype is measured at the moment of infection from its own source, the recipient phenotype is measured at the moment it got infected from the source; bothAtInfection - the source and the recipient phenotypes are taken at the moment of infection from source to recipient. atTips - the source and the recipient phenotypes are measured at their corresponding tips in the tree. |
a list of nSamples matrices, each matrix having tree columns representing source phenotype, recipient phenotype and time of the infection from the root