Man pages for smitdave/MASH
MASH (Modular Analysis and Simulation for Human Health)

add2Q_endPfMOIPfMOI 'Human' Event: Add PfMOI Clearance Event to Event Queue
add2Q_endPfSIPfSI 'Human' Event: Add PfSI Clearance Event to Event Queue
add2Q_endprophylaxisPfMOIPfMOI 'Human' Event: Add PfMOI End of Chemoprophylaxis Event...
add2Q_endprophylaxisPfSIPfSI 'Human' Event: Add PfSI End of Chemoprophylaxis Event to...
add2Q_feverPfMOIPfMOI 'Human' Event: Add PfMOI Fever Event to Event Queue
add2Q_feverPfSIPfSI 'Human' Event: Add PfSI Fever Event to Event Queue
add2Q_gsvaccinatePfMOIPfMOI 'Human' Event: Add PfMOI GS Vaccination Event to Event...
add2Q_gsvaccinatePfSIPfSI 'Human' Event: Add PfSI GS Vaccination Event to Event...
add2Q_gswanePfMOIPfMOI 'Human' Event: Add PfMOI GS Waning Protection Event to...
add2Q_gswanePfSIPfSI 'Human' Event: Add PfSI GS Waning Protection Event to...
add2Q_infectHumanPfMOIPfMOI 'Human' Event: Add PfMOI Infection Event to Event Queue
add2Q_infectHumanPfSIPfSI 'Human' Event: Add PfSI Infection Event to Event Queue
add2Q_pevaccinatePfMOIPfMOI 'Human' Event: Add PfMOI PE Vaccination Event to Event...
add2Q_pevaccinatePfSIPfSI 'Human' Event: Add PfSI PE Vaccination Event to Event...
add2Q_pewanePfMOIPfMOI 'Human' Event: Add PfMOI PE Waning Protection Event to...
add2Q_pewanePfSIPfSI 'Human' Event: Add PfSI PE Waning Protection Event to...
add2Q_SimBitePfMOIPfMOI SimBite 'Human' Event: Add PfMOI Simulated Bite Event...
add2Q_treatPfMOIPfMOI 'Human' Event: Add PfMOI Treatment Event to Event Queue
add2Q_treatPfSIPfSI 'Human' Event: Add PfSI Treatment Event to Event Queue
addCohort_MacroEmergeMACRO: Calculate Emerging Adults for 'MacroPatch'
addCohort_MicroEL4PMICRO 'Landscape' Method: Get Emerging Adults from ImagoQ and...
addCohort_MicroEL4PSiteMICRO 'Landscape' Method: Get Emerging Adults from ImagoQ and...
addCohort_MicroEmergeMICRO 'Landscape' Method: Get Emerging Adults from ImagoQ and...
addCohort_MicroEmergeSiteMICRO 'Landscape' Method: Get Emerging Adults from ImagoQ and...
allocEggQAllocate EggQ
allocImagoQAllocate ImagoQ
AquaEmergeLambdaPlot_utilityPlot Lambda for Emerge Module
AquaticSiteMICRO-Site Aquatic Habitat Class Definition
betaRootAFind shape1 (alpha) Parameter of Beta Distribution for Given...
betaRootBFind shape2 (beta) Parameter of Beta Distribution for Given...
calcLambda_MicroEL4PCalculate Lambda for EL4P Aquatic Ecology Module
calculateBionomics_utilityM-BITES Utility: Calculate Ross-MacDonald Bionomics from...
colLuminosity_utilityBrighten or Darken Colors
EggQMICRO Egg Queue
EL4PAquatic Ecology EL4P Class
EL4P.Landscape.FitFit EL4P Aquatic Ecology Module to 'Landscape'
EL4P.Mesh.FitFit EL4P Aquatic Ecology Module to Mesh of K
EL4P.ParametersInitialize EL4P Aquatic Ecoogy Module Parameters
emergingAdults_MacroEmergeMACRO: Calculate Emerging Adults from ImagoQ for 'MacroPatch'
endPfMOIPfMOI 'Human' Event: PfMOI Infection Event
endPfSIPfSI 'Human' Event: PfSI Clearance Event
endprophylaxisPfMOIPfMOI 'Human' Event: PfMOI End of Chemoprophylaxis Event
endprophylaxisPfSIPfSI 'Human' Event: PfSI End of Chemoprophylaxis Event
event_endPfMOIPfMOI 'Human' Event: Generate PfMOI Clearance Event
event_endPfSIPfSI 'Human' Event: Generate PfSI Clearance Event
event_endprophylaxisPfMOIPfMOI 'Human' Event: Generate PfMOI End of Chemoprophylaxis...
event_endprophylaxisPfSIPfSI 'Human' Event: Generate PfSI End of Chemoprophylaxis...
event_feverPfMOIPfMOI 'Human' Event: Generate PfMOI Fever Event
event_feverPfSIPfSI 'Human' Event: Generate PfSI Fever Event
event_gsvaccinatePfMOIPfMOI 'Human' Event: Generate PfMOI GS Vaccination Event
event_gsvaccinatePfSIPfSI 'Human' Event: Generate PfSI GS Vaccination Event
event_gswanePfMOIPfMOI 'Human' Event: Generate PfMOI GS Waning Protection...
event_gswanePfSIPfSI 'Human' Event: Generate PfSI GS Waning Protection Event
event_infectHumanPfMOIPfMOI 'Human' Event: Generate PfMOI Infection Event
event_infectHumanPfSIPfSI 'Human' Event: Generate PfSI Infection Event
event_pevaccinatePfMOIPfMOI 'Human' Event: Generate PfMOI PE Vaccination Event
event_pevaccinatePfSIPfSI 'Human' Event: Generate PfSI PE Vaccination Event
event_pewanePfMOIPfMOI 'Human' Event: Generate PfMOI PE Waning Protection...
event_pewanePfSIPfSI 'Human' Event: Generate PfSI PE Waning Protection Event
event_SimBitePfMOIPfMOI SimBite 'Human' Event: Generate PfMOI Simulated Bite...
event_treatPfMOIPfMOI 'Human' Event: Generate PfMOI Treatment Event
event_treatPfSIPfSI 'Human' Event: Generate PfSI Treatment Event
extend_PatchesImagoQExtend 'MacroPatch' ImagoQ (Emerging Adults Queue)
feeding_PfMOIPfMOI 'MicroMosquitoFemale' Method: Host Feeding
feeding_PfSIPfSI 'MicroMosquitoFemale' Method: Host Feeding
FeedingSiteMICRO Feeding Site Class Definition
feverPfMOIPfMOI 'Human' Event: PfMOI Infection Event
feverPfSIPfSI 'Human' Event: PfSI Fever Event
gammaRatesGamma Distributed Biting Rates
getEIP_MacroMosquitoPopSet 'MacroMosquitoPop' getEIP
get_lambda_MicroEmergeMICRO 'AquaticSite' Method: Get Lambda
get_MicroHuman_ActivitySpaceMICRO: Get 'Human' ActivitySpace
get_MicroHuman_FemalePopPointerMICRO: Get 'Human' 'MicroMosquitoPopFemale' Pointer
get_MicroHuman_LandscapePointerMICRO: Get 'Human' 'Landscape' Pointer
get_MicroHumanPop_FemalePopPointerMICRO: Get 'HumanPop' 'MicroMosquitoPopFemale' Pointer
get_MicroHumanPop_LandscapePointerMICRO: Get 'HumanPop' 'Landscape' Pointer
get_MicroHumanPop_TilePointerMICRO: Get 'HumanPop' 'MicroTile' Pointer
get_MicroHuman_TilePointerMICRO: Get 'Human' 'MicroTile' Pointer
get_MicroKernel_movement_BROMICRO Search Kernels: 'MicroTile' Access MvAll Object for...
get_MicroKernel_movement_BROMMICRO Search Kernels: 'MicroTile' Access MvAll Object for...
get_MicroKernel_movement_FULLMICRO Search Kernels: 'MicroTile' Access MvAll Object for...
get_MicroKernel_movement_MaleMICRO Search Kernels: 'MicroTile' Access MvAll Object for...
get_PatchesEggQGet 'MacroPatch' EggQ (Egg Batches)
get_PatchesImagoQGet 'MacroPatch' ImagoQ (Emerging Adults Queue)
get_seasonGet 'MacroPatch' Seasonal Emergence
ggColOffset_utilitySample Equally from Color Space with Offset
ggCol_utilitySample Equally from Color Space
gsvaccinatePfMOIPfMOI 'Human' Event: PfMOI GS Vaccination Event
gsvaccinatePfSIPfSI 'Human' Event: PfSI GS Vaccination Event
gswanePfMOIPfMOI 'Human' Event: PfMOI GS Waning Protection Event
gswanePfSIPfSI 'Human' Event: PfSI GS Waning Protection Event
HistoryGenericGeneric History
HistoryTravelTravel History
HumanHuman Class Definition
HumanEventQHuman Event Queue
Human_get_PfMOI_PARPfMOI 'Human' Method: Get PfMOI_PAR
Human_get_PfSI_PARPfSI 'Human' Method: Get PfSI_PAR
humanPfMOIPfMOI Human Stage Pathogen Class
humanPfSIPfSI Human Stage Pathogen Class
HumanPopHumanPop Class Definition
HumanPop_get_PfMOI_historyPfMOI 'HumanPop' Method: Get PfMOI Histories
HumanPop_get_PfMOI_PARPfMOI 'HumanPop' Method: Get PfMOI_PAR
HumanPop_get_PfSI_historyPfSI 'HumanPop' Method: Get PfSI Histories
HumanPop_get_PfSI_PARPfSI 'HumanPop' Method: Get PfSI_PAR
HumanPop.ParametersMICRO: Initialize HumanPop Parameters for 'HumanPop'
HumanPop_set_humanPfMOIPfMOI 'HumanPop' Method: Set Human-stage PfMOI Object
HumanPop_set_humanPfSIPfSI 'HumanPop' Method: Set Human-stage PfSI Object
HumanPop_set_PfMOI_PARPfMOI 'HumanPop' Method: Set PfMOI Paramters for a 'HumanPop'
HumanPop_set_PfSI_PARPfSI 'HumanPop' Method: Set PfSI Paramters for a 'HumanPop'
Human_set_humanPfMOIPfMOI 'Human' Method: Set Human-stage PfMOI Object
Human_set_humanPfSIPfSI 'Human' Method: Set Human-stage PfSI Object
ImagoQMICRO Imago Queue
importMicroMosquitoHistory_utilityM-BITES Utility: Import JSON Mosquito Histories
infectHumanPfMOIPfMOI 'Human' Event: PfMOI Infection Event
infectHumanPfSIPfSI 'Human' Event: PfSI Infection Event
infectiousBite_PfMOIPfMOI 'Human' Method: Infectious Bite on Human
infectiousBite_PfSIPfSI 'Human' Method: Infectious Bite on Human
init_MACRO_PfMOIPfMOI 'HumanPop' Method: Initialize MACRO PfMOI Infections
init_MACRO_PfSIPfSI 'HumanPop' Method: Initialize MACRO PfSI Infections
init_MacroTile_PfMOIMACRO PfMOI 'MacroTile' Method: Initialize MACRO PfMOI...
init_MacroTile_PfSIMACRO PfSI 'MacroTile' Method: Initialize MACRO PfSI...
init_MicroHuman_ActivitySpaceMICRO 'Human' Method: Initialize Activity Space
init_MicroHumanPop_ActivitySpaceMICRO 'HumanPop' Method: Initialize Activity Space
init_MICRO_PfMOIPfMOI 'HumanPop' Method: Initialize MICRO PfMOI Infections
init_MICRO_PfSIPfSI 'HumanPop' Method: Initialize MICRO PfSI Infections
init_Pathogens_MicroMosquitoFemale_PfMOIPfMOI Helper Code for Pathogen Initialization in...
init_Pathogens_MicroMosquitoFemale_PfSIPfSI Helper Code for Pathogen Initialization in...
init_Pathogens_MicroMosquitoPopFemale_PfMOIPfMOI Helper Code for Pathogen Initialization in...
init_Pathogens_MicroMosquitoPopFemale_PfSIPfSI Helper Code for Pathogen Initialization in...
K2psi_MicroEL4PConvert K and Regression Coefficient into Psi
LandscapeMICRO Landscape Class Definition
Landscape.Aqua.ParametersMICRO: Generate Parameters for 'Landscape' 'AquaticSite'
Landscape.Feeding.ParametersMICRO: Generate Parameters for 'Landscape' 'FeedingSite'
Landscape.ParametersMICRO: Generate Parameters for 'Landscape' Object
layEggs_MacroMosquitoPop'MacroMosquitoPop' layEggs
lmTest_PfMOIPfMOI 'Human' Method: Light Microscopy Test
lmTest_PfSIPfSI 'Human' Method: PfSI Light Microscopy Test
MacroHuman_add2Q_BitesMACRO 'Human' Method: add2Q_Bites
MacroHuman_add2Q_returnHomeadd2Q_returnHome
MacroHuman_add2Q_takeTripadd2Q_takeTrip
MacroHuman_event_returnHomeevent_returnHome
MacroHuman_event_takeTripevent_takeTrip
MacroHuman_expectedBitesMACRO 'Human' Method: expectedBites
MacroHuman_get_locationMACRO: Get 'Human' location
MacroHuman_get_MosquitoPointerGet 'Human' 'MacroMosquitoPop' Pointer
MacroHuman_get_myEIRGet 'Human' myEIR
MacroHuman_get_PatchesPointerGet 'Human' 'MacroPatch' Pointer
MacroHuman_get_patchIDGet 'Human' patchID
MacroHuman_get_TilePointerGet 'Human' 'MacroTile' Pointer
MacroHuman_get_travelGet 'Human' travel
MacroHuman_get_travelHistoryHumanReturn 'Human' Travel History
MacroHuman_get_travelHistoryHumanPopReturn 'HumanPop' Travel History
MacroHuman_go_PatchSet 'Human' go_Patch
MacroHuman_init_travelMACRO 'Human' Method: Initialize Travel
MacroHuman_json_travelHistoryWrite 'HumanPop' Travel History to JSON
MacroHumanPop_get_patchIDMACRO 'HumanPop' Method: Get all patchID
MacroHumanPop_set_patchIDMACRO 'HumanPop' Method: Set all patchID
MacroHuman_queueInfectiousBitesMACRO 'HumanPop' Method: queueInfectiousBites
MacroHuman_returnHomereturnHome
MacroHuman_set_locationMACRO: Set 'Human' location
MacroHuman_set_MosquitoPointerSet 'Human' 'MacroMosquitoPop' Pointer
MacroHuman_set_myEIRSet 'Human' myEIR
MacroHuman_set_PatchesPointerSet 'Human' 'MacroPatch' Pointer
MacroHuman_set_patchIDSet 'Human' patchID
MacroHuman_set_TilePointerSet 'Human' 'MacroTile' Pointer
MacroHuman_set_travelSet 'Human' travel
MACRO.Humans.SetupMACRO: Initialize Additional Methods & Fields in 'Human' and...
MacroHuman_sumKappa_PfMOIMACRO: Update 'Human' PfMOI kappa For a Patch
MacroHuman_sumKappa_PfSIMACRO: Update 'Human' PfSI kappa For a Patch
MacroHuman_takeTriptakeTrip
MacroHuman_updateKappaMACRO: Update 'HumanPop' kappa For all Patches
MacroMosquitoPopMACRO Mosquito Population Class Definition
MACRO.MosquitoPop.ParametersInitialize MosquitoPop Parameters for 'MacroMosquitoPop'
MacroPatchMACRO Patch Class Definition
MACRO.Patch.Emerge.SetupInitialize Additional Methods & Fields in 'MacroPatch' for...
MACRO.Patch.ParametersInitialize MACRO Patch Parameters for 'MacroPatch'
MacroTileMACRO Tile Class Definition
MACRO.Tile.ParametersInitialize MACRO Tile Parameters for 'MacroTile'
makeLambda_MacroMACRO: Generate Seasonal Emergence (Lambda) for 'Emerge'...
makeLambda_MicroEmergeMICRO: Generate Seasonal Emergence (Lambda) for 'Emerge'...
manage_PatchesImagoQManage 'MacroPatch' ImagoQ (Emerging Adults Queue)
MASH-packageMASH (Modular Analysis and Simulation for Human Health)
mbitesBRO_BloodMealMBITES-BRO: Bloodmeal Energetics for 'MicroMosquitoFemale'
mbitesBRO_boutBMBITES-BRO: Blood Feeding Bout 'MicroMosquitoFemale'
mbitesBRO_boutOMBITES-BRO: Egg Laying Bout 'MicroMosquitoFemale'
mbitesBRO_boutRMBITES-BRO: Post-Prandial Resting Bout 'MicroMosquitoFemale'
mbitesBRO_cohort_humanEncounterMBITES-BRO-Cohort: Human Host Encounter for...
mbitesBRO_cohort_oneMosquito_MBITESMBITES-BRO-Cohort: Run Simulation for 'MicroMosquitoFemale'
MBITES.BRO.Cohort.SetupMBITES-BRO-Cohort: Initialize Additional Methods & Fields in...
mbitesBRO_cohort_simCohortMBITES-BRO-Cohort: Human Host Encounter for...
mbitesBro_enterHouseMBITES-BRO: Attempt to Enter a House for...
mbitesBRO_get_MySiteTypeMBITES-BRO: Return Site Type 'MicroMosquitoFemale'
mbitesBRO_get_restHazMBITES-BRO: Get Resting Hazards for 'MicroMosquitoFemale'
mbitesBRO_get_surviveFlightProbMBITES-BRO: Get Baseline Survival Probability for...
mbitesBRO_get_WTSMBITES-BRO: Return Landing Spot Weights for...
mbitesBRO_humanEncounterMBITES-BRO: Human Host Encounter for 'MicroMosquitoFemale'
mbitesBRO_landingSpotMBITES-BRO: Land After Flight 'MicroMosquitoFemale'
mbitesBRO_layEggs_EL4PMBITES-BRO: Lay Eggs for 'EL4P' 'MicroMosquitoFemale'
mbitesBRO_layEggs_EmergeMBITES-BRO: Lay Eggs for 'Emerge' 'MicroMosquitoFemale'
mbitesBro_newSpotMBITES-BRO: Generate New Landing Spot for...
mbitesBro_oneBoutMBITES-BRO: One Bout 'MicroMosquitoFemale'
mbitesBro_oneMosquito_MBITESMBITES-BRO: Run Simulation for 'MicroMosquitoFemale'
MBITES.BRO.ParametersGenerate Parameters for M-BITES 'BRO' Module
mbitesBro_Pop_MBITESMBITES-BRO: Run Simulation for 'MicroMosquitoPopFemale'
MBITES.BRO.SetupMBITES-BRO: Initialize Additional Methods & Fields in...
MbitesBRO_timingExponentialMBITES-BRO: Exponential Timing for 'MicroMosquitoFemale'
mbitesBRO_zooEncounterMBITES-BRO: Non-Human Host Encounter for...
mbitesCohort_chooseHostMBITES-Cohort: Host Choosing for 'MicroMosquitoFemale'
MBITES.Cohort.SetupInitialize Cohort Methods for M-BITES
MBITES.FULL.ParametersGenerate Parameters for M-BITES 'Full' Module
mbitesGeneric_chooseHostMBITES-Generic: Host Choosing for 'MicroMosquitoFemale'
MbitesGeneric_isActiveMBITES-Generic: Active Check for 'MicroMosquitoFemale' and...
MbitesGeneric_isAliveMBITES-Generic: Alive Check for 'MicroMosquitoFemale' and...
mbitesGeneric_pEnergySurvivalMBITES-Generic: Probability of Death due to Energy Reserves...
mbitesGeneric_pOverFeedMBITES-Generic: Probaility of Overfeeding due to Bloodmeal...
mbitesGeneric_pReFeedMBITES-Generic: Probaility to re-enter Blood Feeding Cycle...
mbitesGeneric_pSenesceMBITES-Generic: Probability of Death due to Senescence for...
mbitesGeneric_pSugarBoutMBITES-Generic: Probability to Queue Sugar Bout due to Energy...
mbitesGeneric_pTatterMBITES-Generic: Probability of Death due to Wing Tattering...
mbitesGeneric_rBatchSizeBmsMBITES-Generic: Egg Batch Size due to Bloodmeal Size for...
mbitesGeneric_rBatchSizeNormMBITES-Generic: Draw Normally-distributed Egg Batch Size for...
mbitesGeneric_rBloodMealSizeMBITES-Generic: Draw Bloodmeal Size for 'MicroMosquitoFemale'
mbitesGeneric_rEggMaturationTimeNormMBITES-Generic: Normally-distributed Egg Maturation Time for...
mbitesGeneric_rEggMaturationTimeOffMBITES-Generic: No Egg Maturation Time for...
mbitesGeneric_rTatterSizeMBITES-Generic: Wing Tattering for 'MicroMosquitoFemale'
MBITES.Generic.SetupInitialize Generic Methods for M-BITES
mbitesGeneric_surviveFlightMBITES-Generic: Flight Survival for 'MicroMosquitoFemale'
mbitesGeneric_surviveRestingMBITES-Generic: Resting Survival for 'MicroMosquitoFemale'
meshK_MicroEL4PFit Psi on Mesh of K Values
MICRO.EL4P.SetupInitialize EL4P Aquatic Ecology Module
MICRO.Emerge.SetupInitialize Emerge Aquatic Ecology Module
MICRO.Humans.SetupMICRO: Initialize Additional Methods & Fields in 'Human' and...
MicroKernel_DistanceMatMICRO Search Kernels: Calculate Euclidean Distance Matrix
MicroKernel_exactAllMICRO Search Kernels: Exact Movement Object Between All Point...
MicroKernel_exactMvObMICRO Search Kernels: Exact Movement Object Between Two Point...
MicroKernel_moveMe_BROMICRO Search Kernels: 'MicroMosquitoFemale' Movement Function...
MicroKernel_moveMe_BROMMICRO Search Kernels: 'MicroMosquitoFemale' Movement Function...
MicroKernel_moveMe_FULLMICRO Search Kernels: 'MicroMosquitoFemale' Movement Function...
MicroKernel_moveMe_MaleMICRO Search Kernels: 'MicroMosquitoMale' Movement Function...
MicroKernelPlot_utilityMICRO Search Kernels: Plot Kernel Functions
MicroKernel_PowerKernelMICRO Search Kernels: Calculate Power Kernel
MicroKernel_prSortMICRO Search Kernels: Sort ID and Probabilities
MicroKernel_SampleMvOb_MicroMosquitoPopFemaleMICRO Search Kernels: 'MicroMosquito' Sample MvOb
MicroLandscapePlot_utilityPlot a MICRO Landscape
MicroMosquitoFemaleMICRO Female Mosquito Class Definition
MicroMosquitoMaleMICRO Male Mosquito Class Definition
MicroMosquitoPopFemale_clear_pop'MicroMosquitoPopFemale' Method: Push Emerging Mosquitoes to...
MicroMosquitoPopFemale_extend_pop'MicroMosquitoPopFemale' Method: Extend the Population Vector
MicroMosquitoPopFemale_push_pop'MicroMosquitoPopFemale' Method: Push Emerging Mosquitoes to...
MicroMosquitoPopFemale_update_nullPop'MicroMosquitoPopFemale' Method: Update 'nullPop' Index of...
MicroMosquitoPopFemale_update_pop'MicroMosquitoPopFemale' Method: Update Adult Population
MicroMosquitoPopFemale_which_alive'MicroMosquitoPopFemale' Method: Find Indices of Alive...
MicroMosquitoPop.SetupSetup MICRO Mosquito Population & M-BITES Module for a...
MicroTileMICRO Tile Class Definition
MosquitoFemaleHistoryMosquito Female History Class
mosquitoPfMOIPfMOI Mosquito Stage Pathogen Class
mosquitoPfSIPfSI Mosquito Stage Pathogen Class
newEggEmpty Egg Batch Slot for EggQ
newImagoGenerate a ImagoQ Slot
oneDay_MacroEmergeGet 'MacroPatch' Seasonal Emergence
oneDay_RMMACRO 'MacroMosquitoPop' Method: oneDay_RM
oneStep_MicroEL4PMICRO 'Landscape' Method: EL4P One Day Dynamics
oneStep_MicroEL4PSiteMICRO 'AquaticSite' Method: EL4P One Day Dynamics
oneStep_MicroEmergeMICRO 'Landscape' Method: Emerge One Day Dynamics
oneStep_MicroEmergeSiteMICRO 'AquaticSite' Method: Emerge One Day Dynamics
ovipositionEq_oneHistory_utilityM-BITES Utility: Calculate Counts of Oviposition at...
ovipositionEq_utilityM-BITES Utility: Calculate Empirical Probability of...
pevaccinatePfMOIPfMOI 'Human' Event: PfMOI PE Vaccination Event
pevaccinatePfSIPfSI 'Human' Event: PfSI PE Vaccination Event
pewanePfMOIPfMOI 'Human' Event: PfMOI PE Waning Protection Event
pewanePfSIPfSI 'Human' Event: PfSI PE Waning Protection Event
PfMOI_increment_PfIDPfMOI 'HumanPop' Method: Increment PfID
PfMOI.ParametersInitialize PfMOI Module Parameters
PfMOI.SetupInitialize PfMOI MODULE
PfMOI_ttClearPf_IndependentPfMOI 'Human' Method: Duration of Infection
PfMOI_ttClearPf_InteractionPfMOI 'Human' Method: Duration of Infection with Pathogen...
PfMOI_ttFeverPfPfMOI 'Human' Method: Timing of Fever Incident
PfMOI_ttGSWanePfPfMOI 'Human' Method: Duration of protection by GS...
PfMOI_ttInfectionPfPfMOI 'Human' Method: Duration of Latency
PfMOI_ttPEWanePfPfMOI 'Human' Method: Duration of protection by PE...
PfMOI_ttSusceptiblePfPfMOI 'Human' Method: Duration of Protection from...
PfMOI_ttTreatPfPfMOI 'Human' Method: Timing of Treatment
PfSI_increment_PfIDPfSI 'HumanPop' Method: Increment PfID
PfSI.ParametersInitialize PfSI Module Parameters
PfSI.SetupInitialize PfSI MODULE
PfSI_ttClearPfPfSI 'Human' Method: Duration of Infection
PfSI_ttFeverPfPfSI 'Human' Method: Timing of Fever Incident
PfSI_ttGSWanePfPfSI 'Human' Method: Duration of protection by GS Vaccination
PfSI_ttInfectionPfPfSI 'Human' Method: Duration of Latency
PfSI_ttPEWanePfPfSI 'Human' Method: Duration of protection by PE Vaccination
PfSI_ttSusceptiblePfPfSI 'Human' Method: Duration of Protection from...
PfSI_ttTreatPfPfSI 'Human' Method: Timing of Treatment
plot_PfSIplot_PfSI
plot_PfSIOneTrajectoryplot_PfSI_oneTrajectory
pointsClusteredGenerate Matern Clustering Point Pattern for Landscape Sites
pointsLatticeGenerate Regular Grid (Lattice) Point Pattern for Landscape...
pointsOverdispersedGenerate Overdispersed (SSI) Point Pattern for Landscape...
pointsPoissonGenerate Poisson Point Pattern for Landscape Sites
probeHost_PfMOIPfMOI 'Human' Method: Host Probing
probeHost_PfSIPfSI 'Human' Method: Host Probing
probeHost_SimBitePfMOIPfMOI 'Human' Method: Simulated Host Probing
probing_PfMOIPfMOI 'MicroMosquitoFemale' Method: Host Probing
probing_PfSIPfSI 'MicroMosquitoFemale' Method: Host Probing
psi2K_cf_MicroEL4PRegress K on Psi and Return Coefficients
psi2K_plot_MicroEL4PPlot Regression of K on Psi
psiFit_MicroEL4PObjective Function for Fitting Psi
queueBitesNegBinom_SimBitePfSIPfSI SimBite 'HumanPop' Method: Generate Negative Binomial...
queueBites_SimBitePfMOIPfMOI SimBite 'HumanPop' Method: Queue SimBites for...
queueVaccination_SimBitePfMOIPfMOI SimBite 'HumanPop' Method: Queue Vaccination for...
rdtTest_PfMOIPfMOI 'Human' Method: Rapid Diagnostic Test
rdtTest_PfSIPfSI 'Human' Method: PfSI Rapid Diagnostic Test
RiskQMICRO Risk Queue
run2eq_MicroEL4PRun a Single Aquatic Population to Equilibrium
sampleIx_utilitySample Indices
SEARCH.MicroKernel.SetupMICRO Search Kernels: Initialize Additional Methods & Fields...
set_FemalePop_MicroTileMICRO 'MicroTile': Re-initialize 'MicroMosquitoPopFemale'
set_lambda_MicroEmergeMICRO 'AquaticSite' Method: Set Lambda
set_MicroHuman_ActivitySpaceMICRO: Set 'Human' ActivitySpace
set_MicroHuman_FemalePopPointerMICRO: Set 'Human' 'MicroMosquitoPopFemale' Pointer
set_MicroHuman_LandscapePointerMICRO: Set 'Human' 'Landscape' Pointer
set_MicroHumanPop_FemalePopPointerMICRO: Set 'HumanPop' 'MicroMosquitoPopFemale' Pointer
set_MicroHumanPop_LandscapePointerMICRO: Set 'HumanPop' 'Landscape' Pointer
set_MicroHumanPop_TilePointerMICRO: Set 'HumanPop' 'MicroTile' Pointer
set_MicroHuman_TilePointerMICRO: Set 'Human' 'MicroTile' Pointer
set_PatchesEggQSet 'MacroPatch' EggQ (Egg Batches)
set_PatchesImagoQSet 'MacroPatch' ImagoQ (Emerging Adults Queue)
set_seasonSet 'MacroPatch' Seasonal Emergence
SimBite_MeanBitesSimulate Biting Process from Population Mean Number of Bites
SimBitePfMOIPfMOI SimBite 'Human' Event: PfMOI Simulated Bite Event
SimBitePfMOI.SetupInitialize SimBite PfMOI Module
SimBitePfSI.SetupInitialize SimBite PfSI Module
SimBite_WaitingTimeSimulate Biting Process from Population Mean Waiting Time...
simMacroMACRO 'MacroTile' Simulate MACRO Dynamics
sim_MicroHuman_ActivitySpaceMICRO 'Human' Method: Initialize Activity Space
sim_MicroHumanPop_ActivitySpaceMICRO 'HumanPop' Method: Simulate Activity Space
simMICRO_oneStepMICRO 'MicroTile': Run Simulation one Time Step
siteAgesGenerate Ages for 'HumanPop'
sitePopsGenerate Site Sizes for 'HumanPop'
treatPfMOIPfMOI 'Human' Event: PfMOI Treatment Event
treatPfSIPfSI 'Human' Event: PfSI Treatment Event
updateLandscape_MicroEL4PUpdate 'Landscape' and 'AquaticSite' after Fitting EL4P...
util_List2DfUtility: Convert List to Data Frame
util_PfSIHistoryPfSI: Calculate State Space Occupancy Vector
util_PfSIoneHistoryPfSI: Write One Human History
util_PfSISlicePfSI: Empty Occupancy Vector
smitdave/MASH documentation built on Aug. 17, 2017, 8:42 a.m.