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.
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.