Notes - Mathematica functions: newlyInfective, makeSomeInfective

[PaulMelloy]

These are just notes to assist in understanding the model workflow, no comments needed.

infectPlantsAt = list / data.frame of coordinates

• which is parsed through packetsFromLocations (which just wraps coordinates into the first element if a list, and adds a 1 to the second element )
  additionalNewlyInfectiveList <- infectPlantsAt i.e. list(c("x","y"),1)

Then additionalNewlyInfectiveList is used in function makeSomeInfective() and never used again.

makeSomeInfective

• A sporePacket refers to additionalNewlyInfectiveList mentioned above.
• sporesInPacket is numeric and 1 on the first run
• paddockUninfectiveGrowingPoints a data.table for each 1x1m unit all containing the values -1 at the start.
  (a) coords with values less than -0.5 are added to infectiveElementsList (for coords from additionalNewlyInfectiveList) ; then
  (b) paddockUninfectiveGrowingPoints (for coords from additionalNewlyInfectiveList) are updated with refUninfectiveGrowingPoints (40 the seeding_rate)
  (c) (i) infectionsNew <- paddockUninfectiveGrowingPoints which are then less than sporesInPacket (1 as allocated in packetsFromLocations)(none on first run with coords from additionalNewlyInfectiveList) ) and
  (ii) update that paddockUninfectiveGrowingPoints value <- 0
  (d) (i) infectionsNew <- sporesInPacket (1) when paddockUninfectiveGrowingPoints is equal or greater than sporesInPacket ( additionalNewlyInfectiveList coords on first run) and
  (ii) update paddockUninfectiveGrowingPoints value <- paddockUninfectiveGrowingPoints - infectionsNew (first run: 40 - 1)
• finally paddockInfectiveGrowingPoints (note: Infective not uninfective) <- paddockInfectiveGrowingPoints + infectionsNew (first run: 0 + 1)

Therefore on the first run the function makes the following changes to global environment variables

• infectiveElementsList contains coords from additionalNewlyInfectiveList)
• paddockUninfectiveGrowingPoints at coords from additionalNewlyInfectiveList contain value 40
• paddock__Infective__GrowingPoints at coords is updated to contain value 1