Syphilis Model: Timing of Progression to Primary Stage

[karina-d-wallrafen]

Currently, any active node in the incubating stage of syphilis infection is eligible for progression to the primary stage (Line 136 of module-fx.R reads idsEligPri <- which(active == 1 & syph.stage == 1)). Since the infection function is called before the disease progression function, this means that it's possible for a node to become infected and immediately progress from the incubating to the primary stage within the same time step.

Changing Line 136 to idsEligPri <- which(active == 1 & syph.stage == 1 & infTime < at) would ensure that there is at least a one time step delay between infection and progression to the primary stage.