# . Let c = c 1. v five. If c , then simulate U DU?; `t

From here, we Sms scattered all through the genome [2,25,53,56,57,58,59.Materials and Approaches M. tuberculosis strains] sample only a proportion of the infectious set from each stratum at each time ^ point t when calculating P it . Let c = c + 1. v 5. If c , then simulate U DU?; `t , let ^t ?M ; U , and return to step 3. ^ v If c > , then let I t be the set containing all c - 1 elements of ^t and continue to step 5. six. Calculate the approximated likelihood component for time t, ^ Lt ?Yi2S t?exp??^ S it ? ; t?? ? ^ S it ? ; t?;Y ?1 ?exp^ ^ i2I t? nI tP c? ^ ^ ^t exactly where X it ?r ? ^ O ; j? as ahead of, and r t ?`t . j2I t T 7. Let t = t+1. If t q ^ j2I tk OT ; j?be the estimate with the infectious pressure exerted on susceptible person i from stratum k ^ at time t. Here, r tk is the empirical sampling proportion from the sampled infectious set for the ^ stratum, I tk may be the total set of infectious folks in strata k at time t, and I tk is definitely the randomly sampled set of infectious men and women obtained by way of SRS (with replacement) from ^ strata k with empirical sampling proportion r tk . The sum of infectious pressures from every stratum exerted on person i at time t is known as the total infectious stress and calculated as ^ Z it ?m X ^ Z itk : k?As before, for tiny infectious sets, i.e., jI tk j q, we use the entire infectious set and don't sample. Beneath a spatial-stratification scheme, we use q = five. Thus, the approximation of the probability of infection is ??^ ^ ??Pit ' P it ?1 ?exp S it ? ; t?; which is substituted into our likelihood function. We refer to this model as the SSS-ILM. We consider a three-dimensional infection matrix, Q, with dimensions tmax ?m ?n that include components corresponding to integer identification numbers for every single farm. We use the notation Q ; C; D to refer for the farm ID positioned at time B, stratum C, and cell D within matrix Q. We also define a two-dimensional matrix, W, with dimensions tmax ?m that contain the number of infectious men and women in every stratum at every time point (up till the presence of empty cells). Therefore, for each mixture of t = 1, . . ., tmax and k = 1, . . ., m, W ; k ?jQ ; k; , where W ; k represents the number of infectious individuals at time t, in stratum k. We use the following algorithm to calculate the approximated likelihood function below the spatial stratification scheme: ^ 1. Let L tk ?0 8 t ?1; .