R/phylosamp_funcs.R
prob_trans_stsl.Rd
This function calculates the probabilitiy that two cases are linked by direct transmission given that they have been linked by phylogenetic criteria. The single-transmission and single-linkage method assumes the following:
Each case \(i\) is linked by transmission to only one other case \(j\) in the population (\(N\)).
Each case \(i\) is linked by the linkage criteria to only one other case \(j\) in the sampled population (\(M\)).
prob_trans_stsl(eta, chi, rho, M)
eta | scalar or vector giving the sensitivity of the linkage criteria |
---|---|
chi | scalar or vector giving the specificity of the linkage criteria |
rho | scalar or vector giving the proportion of the final outbreak size that is sampled |
M | scalar or vector giving the number of cases sampled |
scalar or vector giving the probability of transmission between two cases given linkage by phylogeneitic criteria
For perfect sensitivity, set eta = 1
.
Other prob_trans:
prob_trans_mtml()
,
prob_trans_mtsl()
John Giles, Shirlee Wohl, and Justin Lessler
prob_trans_stsl(eta=1, chi=1, rho=0.2, M=100) # perfect sensitivity and specificity#> [1] 1prob_trans_stsl(eta=1, chi=0.95, rho=0.2, M=100) # perfect sensitivity only#> [1] 0.2010021prob_trans_stsl(eta=0.99, chi=0.95, rho=0.9, M=50)#> [1] 0.898971prob_trans_stsl(eta=0.99, chi=0.95, rho=0.05, M=100)#> [1] 0.04979498