MBITES.FULL.Parameters: Generate Parameters for M-BITES 'Full' Module
In smitdave/MASH: MASH (Modular Analysis and Simulation for Human Health)

Description Usage Arguments Value Examples

Generate named list of parameters used throughout M-BITES 'Full' Module. All arguments have default values which are listed below before the definition.

MBITES.FULL.Parameters(enterhouse.a = 9, enterhouse.b = 1, feedHaz.a = 99,
  feedHaz.b = 1, aquaHaz.a = 99, aquaHaz.b = 1, sugarHaz.a = 99,
  sugarHaz.b = 1, swarmHaz.a = 99, swarmHaz.b = 1, F.t = 1,
  B.t = 0.75, R.t = 1.5, L.t = 0.75, O.t = 1, M.t = 1.5, S.t = 0.5,
  F.s = 0.99, B.s = 0.99, L.s = 0.99, O.s = 0.99, M.s = 0.95,
  S.s = 0.95, F.p = 0.95, B.p = 0.98, R.p = 0.98, L.p = 0.8,
  O.p = 0.98, M.p = 0.98, S.p = 0.98, maleM.s = 0.99, maleM.p = 0.95,
  Q = 0.9, reFeed = 0.01, bm.a = 7.5, bm.b = 2.5, rf.a = 60,
  rf.b = 5000, of.a = 5, of.b = 5000, S.a = 20, S.b = 10, S.u = 1/7,
  S.sa = 15, S.sb = 5, sf.a = 7.5, sf.b = 4.5, B.energy = 1/10,
  energyPreG = 0, preGsugar = 0, preGblood = 0, eggP.min = 0.5,
  sns.a = 0.085, sns.b = 100, ttsz.p = 0.5, ttsz.a = 5, ttsz.b = 95,
  ttr.a = 15, ttr.b = 500, maxBatch = 30, E.p = 0.5, Emax = 90,
  Eb = 0.9, eEndm = 180, eEndV = 30, surviveH = 1, probeH = 1,
  surviveprobeH = 1, feedH = 1, surviveL = 1, feedL = 1, SUGAR = TRUE,
  ESTIVATION = FALSE, MATE = TRUE, SENESCE = TRUE, TATTER = TRUE,
  REFEED = TRUE, OVERFEED = TRUE, HISTORY = TRUE, batchSize = "bms",
  eggMatT = "off", InAndOut = matrix(c(c(4, 2, 1, 0, 1), c(2, 1, 1, 0, 1),
  c(2, 1, 1, 0, 2), c(1, 1, 1, 0, 1), c(6, 4, 2, 1, 0)), byrow = FALSE, ncol =
  5), Fwts = rep(1, 5), Rwts = rep(1, 5), Lwts = rep(1, 5),
  Owts = rep(1, 5), Mwts = rep(1, 5), Swts = rep(1, 5), eggT = 0,
  eggP = 0, Pathogen = "PfSI")

`enterhouse.a`	= 9, # beta house entry parameters
`enterhouse.b`	= 1, # beta house entry parameters
`feedHaz.a`	= 99, # beta feeding site hazard weights
`feedHaz.b`	= 1, # beta feeding site hazard weights
`aquaHaz.a`	= 99, # beta aqua site hazard weights
`aquaHaz.b`	= 1, # beta aqua site hazard weights
`sugarHaz.a`	= 99, # beta sugar site hazard weights
`sugarHaz.b`	= 1, # beta sugar site hazard weights
`swarmHaz.a`	= 99, # beta swarm site hazard weights
`swarmHaz.b`	= 1, # beta swarm site hazard weights
`F.t`	= 1, #blood feed search bout timing
`B.t`	= 0.75, #blood feed attempt bout timing
`R.t`	= 1.5, #resting bout timing
`L.t`	= 0.75, #egg laying search bout timing
`O.t`	= 1, #egg laying attempt bout timing
`M.t`	= 1.5, #mating bout timing
`S.t`	= 0.5, #sugar feeding bout timing
`F.s`	= 0.99,
`B.s`	= 0.99,
`L.s`	= 0.99,
`O.s`	= 0.99,
`M.s`	= 0.95,
`S.s`	= 0.95,
`F.p`	= 0.95,
`B.p`	= 0.98,
`R.p`	= 0.98,
`L.p`	= 0.80,
`O.p`	= 0.98,
`M.p`	= 0.98,
`S.p`	= 0.98,
`maleM.s`	= .99,
`maleM.p`	= .95,
`Q`	= 0.9, #human blood index
`reFeed`	= 0.01, #probability to refeed post resting bout
`bm.a`	= 7.5, #shape param for bloodmeal size
`bm.b`	= 2.5, #shape param for bloodmeal size
`rf.a`	= 60, #exp param for refeeding as function of bmSize
`rf.b`	= 5e3, #exp param for refeeding as function of bmSize
`of.a`	= 5, #exp param for overfeeding as function of bmSize
`of.b`	= 5e3, #exp param for overfeeding as function of bmSize
`S.a`	= 20, #exp param for death as function of energy
`S.b`	= 10, #exp param for death as function of energy
`S.u`	= 1/7, #energy expenditure for each bout
`S.sa`	= 15, #exp param for sugar bout as function of energy
`S.sb`	= 5, #exp param for sugar bout as function of energy
`sf.a`	= 7.5, #shape param for sugar feed size
`sf.b`	= 4.5, #shape param for sugar feed size
`B.energy`	= 1/10, #scaling factor energy from a bloodmeal
`energyPreG`	= 0, #pre-gonotrophic energy requirement
`preGsugar`	= 0,
`preGblood`	= 0,
`sns.a`	= 0.085, #exp param for senescence
`sns.b`	= 100, #exp param for senescence
`ttsz.p`	= 0.5, #zero-inflation for tattering damage
`ttsz.a`	= 5, #shape param for tattering damage
`ttsz.b`	= 95, #shape param for tattering damage
`ttr.a`	= 15, #exp param for tattering survival
`ttr.b`	= 500, #exp param for tattering survival
`maxBatch`	= 30, #maximum batch size
`E.p`	= 0.5, # probability of surviving estivation
`Emax`	= 90, # onset of the dry season; a day of the calendar year
`Eb`	= 0.9,
`eEndm`	= 180, # end of estivation; a day of the calendar year
`eEndV`	= 30,
`surviveH`	= 1,
`probeH`	= 1,
`surviveprobeH`	= 1,
`feedH`	= 1,
`surviveL`	= 1,
`feedL`	= 1,
`SUGAR`	= TRUE,
`ESTIVATION`	= FALSE,
`MATE`	= TRUE,
`SENESCE`	= TRUE, #senesce
`TATTER`	= TRUE, #tattering
`REFEED`	= TRUE,
`OVERFEED`	TRUE; simulate overfeeding? See `overFeed`
`HISTORY`	TRUE; record history? Needed for `cohortBionomics`, see `historyTrack`
`batchSize`	"bms"; switches for how egg batch size is calculated, should be either "bms" or "norm", see `BatchSize.bms` or `BatchSize.norm`
`eggMatT`	"off"; switches for how egg maturation is calculated, should be either "off" or "norm", see `eggMaturationTime.off` or `eggMaturationTime.norm`
`InAndOut`	matrix of weights for landing spot, see `newSpot`
`Fwts`	rep(1,5); blood feeding search bout landing spot weights, see `newSpot`
`Rwts`	rep(1,5); resting bout landing spot weights, see `newSpot`
`Lwts`	rep(1,5); egg laying search bout landing spot weights, see `newSpot`
`Owts`	rep(1,5); egg laying attempt bout landing spot weights, see `newSpot`
`Mwts`	rep(1,5); mating bout landing spot weights, see `newSpot`
`Swts`	rep(1,5); sugar bout landing spot weights, see `newSpot`
`eggT`	the minimum time before eggs are mature
`eggP`	the minimum provision before eggs are mature
`Pathogen`	name of the PATHOGEN module to use, can be in "PfSI", "PfMOI"