R/phylosamp_funcs.R
obs_pairs_mtml.Rd
This function calculates the expected number of pairs observed in a sample of size M
.
The multiple-transmission and multiple-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 multiple cases \(j\) in the sampled population (\(M\)).
Linkage events are independent of one another (i.e, linkage of case \(i\) to case \(j\) has no bearing on linkage of case \(i\) to any other sample).
obs_pairs_mtml(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 expected number of linked pairs observed in the sample
Other obs_pairs:
exp_links()
,
obs_pairs_mtsl()
,
obs_pairs_stsl()
John Giles, Shirlee Wohl and Justin Lessler
obs_pairs_mtml(eta=1, chi=1, rho=0.5, M=100, R=1) # Perfect sensitivity and specificity#> [1] 50obs_pairs_mtml(eta=0.99, chi=0.9, rho=1, M=50, R=1)#> [1] 167obs_pairs_mtml(eta=0.99, chi=0.9, rho=0.5, M=100, R=1)#> [1] 539.5