R/phylosamp_funcs.R
prob_trans_mtsl.Rd
This function calculates the probabilitiy that two cases are linked by direct transmission given that they have been linked by phylogenetic criteria. The multiple-transmission and single-linkage method assumes the following:
Each case \(i\) is, on average, the infector of R
cases in the population (\(N\))
Each case \(i\) is allowed to be linked by the linkage criteria to only one other case \(j\) in the sampled population (\(M\)).
prob_trans_mtsl(chi, eta, rho, M, R)
chi | scalar or vector giving the specificity of the linkage criteria |
---|---|
eta | scalar or vector giving the sensitivity 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 |
R | scalar or vector giving the effective reproductive number of the pathogen |
scalar or vector giving the probability of transmission between two cases given linkage by phylogeneitic criteria
Other prob_trans:
prob_trans_mtml()
,
prob_trans_stsl()
John Giles, Shirlee Wohl, and Justin Lessler
prob_trans_mtsl(eta=1, chi=1, rho=0.5, M=100, R=1) # Perfect sensitivity and specificity#> [1] 1prob_trans_mtsl(eta=0.99, chi=0.9, rho=1, M=50, R=1)#> [1] 0.8626143prob_trans_mtsl(eta=0.99, chi=0.9, rho=0.5, M=100, R=1)#> [1] 0.6284302