MBITES.BRO.Parameters: Generate Parameters for M-BITES 'BRO' Module

In smitdave/MASH: MASH (Modular Analysis and Simulation for Human Health)

Description

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

Usage

MBITES.BRO.Parameters(B_wts = rep(1, 5), R_wts = rep(1, 5), O_wts = rep(1,
  5), 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),
  B_surv = 0.85, B_succeed = 0.8, B_time = 3/4, surviveH = 1,
  probeH = 1, surviveprobeH = 1, feedH = 1, surviveZ = 1, feedZ = 1,
  R_surv = 0.9, R_time = 0.8, O_surv = 0.8, O_succeed = 0.7,
  O_time = 1.3, bm.a = 7.5, bm.b = 2.5, REFEED = FALSE, rf.a = 60,
  rf.b = 5000, OVERFEED = FALSE, of.a = 5, of.b = 5000,
  SENESCE = FALSE, sns.a = 0.1, sns.b = 100, TATTER = FALSE,
  ttsz.p = 0.5, ttsz.a = 5, ttsz.b = 95, ttr.a = 15, ttr.b = 500,
  bs.m = 30, bs.v = 5, maxBatch = 30, emt.m = 3, emt.v = 1,
  eggT = 0, eggP = 0, energyPreG = 0, PfEIP = 12, Q = 0.9)

Arguments

B_wts	landing spot weights
R_wts	landing spot weights
O_wts	landing spot weights
InAndOut	matrix of landing probabilities
B_surv	Blood feeding bout baseline survival probability mbitesGeneric_surviveFlight
B_succeed	Blood feeding bout probability of success (if succeed call mbitesGeneric_chooseHost)
B_time	Blood feeding bout mean time elapsed (in days); alternatively the waiting time until next state transition
surviveH	human host encounter survival probability of initial encounter (proceed to probe)
probeH	human host encounter probability undeterred and begin probing
surviveprobeH	human host encounter survival probability of probing
feedH	human host encounter probability to successfully blood feed
surviveZ	non-human host encounter survival probability of initial encounter (proceed to feed)
feedZ	non-human host encounter probability to successfully blood feed
R_surv	Post Prandial Resting bout baseline survival probability mbitesGeneric_surviveFlight
R_time	Post Prandial Resting bout mean time elapsed (in days); alternatively the waiting time until next state transition
O_surv	Egg Laying bout baseline survival probability mbitesGeneric_surviveFlight
O_succeed	Egg Laying bout probability of success (if successfull call layEggs)
O_time	Egg Laying bout mean time elapsed (in days); alternatively the waiting time until next state transition
bm.a	shape param for bloodmeal size (see mbitesGeneric_rBloodMealSize)
bm.b	shape param for bloodmeal size (see mbitesGeneric_rBloodMealSize)
REFEED	control boolean for refeeding behavior during resting bout
rf.a	exp param for refeeding as function of bmSize (see mbitesGeneric_pReFeed)
rf.b	exp param for refeeding as function of bmSize (see mbitesGeneric_pReFeed)
OVERFEED	control boolean for overfeeding during mbitesBRO_BloodMeal
of.a	exp param for overfeeding as function of bmSize (see mbitesGeneric_pOverFeed)
of.b	exp param for overfeeding as function of bmSize (see mbitesGeneric_pOverFeed)
SENESCE	control boolean for senesce mortality during mbitesGeneric_surviveFlight
sns.a	exp param for senescence (see mbitesGeneric_pSenesce)
sns.b	exp param for senescence (see mbitesGeneric_pSenesce)
TATTER	control boolean for wing tattering during mbitesGeneric_surviveFlight
ttsz.p	zero-inflation for tattering damage (see mbitesGeneric_rTatterSize)
ttsz.a	shape param for tattering damage (see mbitesGeneric_rTatterSize)
ttsz.b	shape param for tattering damage (see mbitesGeneric_rTatterSize)
ttr.a	exp param for tattering survival (see mbitesGeneric_pTatter)
ttr.b	exp param for tattering survival (see mbitesGeneric_pTatter)
bs.m	mean of normally-distributed egg batch size (used in mbitesGeneric_rBatchSizeNorm)
bs.v	standard deviation of normally-distributed egg batch size (used in mbitesGeneric_rBatchSizeNorm)
maxBatch	maximum egg batch size (used in mbitesGeneric_rBatchSizeBms)
emt.m	mean of normally-distributed egg batch maturation time (used in mbitesGeneric_rEggMaturationTimeNorm)
emt.v	standard deviation of normally-distributed egg batch maturation time (used in mbitesGeneric_rEggMaturationTimeNorm)
eggT	minimum time to egg maturation
eggP	minimum provision to produce eggs
energyPreG	pre-gonotrophic energy requirement
PfEIP	entomological inoculation period for Plasmodium falciparum during MicroMosquitoFemale$probing()
Q	human blood index (used in mbitesCohort_chooseHost)

Value

a named list of parameters

Examples

MBITES.BRO.Parameters()

smitdave/MASH documentation built on May 30, 2019, 5:02 a.m.