Man pages for smitdave/MASH
MASH (Modular Analysis and Simulation for Human Health)
| add2Q_endPfMOI | PfMOI 'Human' Event: Add PfMOI Clearance Event to Event Queue |
| add2Q_endPfSI | PfSI 'Human' Event: Add PfSI Clearance Event to Event Queue |
| add2Q_endprophylaxisPfMOI | PfMOI 'Human' Event: Add PfMOI End of Chemoprophylaxis Event... |
| add2Q_endprophylaxisPfSI | PfSI 'Human' Event: Add PfSI End of Chemoprophylaxis Event to... |
| add2Q_feverPfMOI | PfMOI 'Human' Event: Add PfMOI Fever Event to Event Queue |
| add2Q_feverPfSI | PfSI 'Human' Event: Add PfSI Fever Event to Event Queue |
| add2Q_gsvaccinatePfMOI | PfMOI 'Human' Event: Add PfMOI GS Vaccination Event to Event... |
| add2Q_gsvaccinatePfSI | PfSI 'Human' Event: Add PfSI GS Vaccination Event to Event... |
| add2Q_gswanePfMOI | PfMOI 'Human' Event: Add PfMOI GS Waning Protection Event to... |
| add2Q_gswanePfSI | PfSI 'Human' Event: Add PfSI GS Waning Protection Event to... |
| add2Q_infectHumanPfMOI | PfMOI 'Human' Event: Add PfMOI Infection Event to Event Queue |
| add2Q_infectHumanPfSI | PfSI 'Human' Event: Add PfSI Infection Event to Event Queue |
| add2Q_pevaccinatePfMOI | PfMOI 'Human' Event: Add PfMOI PE Vaccination Event to Event... |
| add2Q_pevaccinatePfSI | PfSI 'Human' Event: Add PfSI PE Vaccination Event to Event... |
| add2Q_pewanePfMOI | PfMOI 'Human' Event: Add PfMOI PE Waning Protection Event to... |
| add2Q_pewanePfSI | PfSI 'Human' Event: Add PfSI PE Waning Protection Event to... |
| add2Q_SimBitePfMOI | PfMOI SimBite 'Human' Event: Add PfMOI Simulated Bite Event... |
| add2Q_treatPfMOI | PfMOI 'Human' Event: Add PfMOI Treatment Event to Event Queue |
| add2Q_treatPfSI | PfSI 'Human' Event: Add PfSI Treatment Event to Event Queue |
| addCohort_MacroEmerge | MACRO: Calculate Emerging Adults for 'MacroPatch' |
| addCohort_MicroEL4P | MICRO 'Landscape' Method: Get Emerging Adults from ImagoQ and... |
| addCohort_MicroEL4PSite | MICRO 'Landscape' Method: Get Emerging Adults from ImagoQ and... |
| addCohort_MicroEmerge | MICRO 'Landscape' Method: Get Emerging Adults from ImagoQ and... |
| addCohort_MicroEmergeSite | MICRO 'Landscape' Method: Get Emerging Adults from ImagoQ and... |
| allocEggQ | Allocate EggQ |
| allocImagoQ | Allocate ImagoQ |
| AquaEmergeLambdaPlot_utility | Plot Lambda for Emerge Module |
| AquaticSite | MICRO-Site Aquatic Habitat Class Definition |
| betaRootA | Find shape1 (alpha) Parameter of Beta Distribution for Given... |
| betaRootB | Find shape2 (beta) Parameter of Beta Distribution for Given... |
| calcLambda_MicroEL4P | Calculate Lambda for EL4P Aquatic Ecology Module |
| calculateBionomics_utility | M-BITES Utility: Calculate Ross-MacDonald Bionomics from... |
| colLuminosity_utility | Brighten or Darken Colors |
| EggQ | MICRO Egg Queue |
| EL4P | Aquatic Ecology EL4P Class |
| EL4P.Landscape.Fit | Fit EL4P Aquatic Ecology Module to 'Landscape' |
| EL4P.Mesh.Fit | Fit EL4P Aquatic Ecology Module to Mesh of K |
| EL4P.Parameters | Initialize EL4P Aquatic Ecoogy Module Parameters |
| emergingAdults_MacroEmerge | MACRO: Calculate Emerging Adults from ImagoQ for 'MacroPatch' |
| endPfMOI | PfMOI 'Human' Event: PfMOI Infection Event |
| endPfSI | PfSI 'Human' Event: PfSI Clearance Event |
| endprophylaxisPfMOI | PfMOI 'Human' Event: PfMOI End of Chemoprophylaxis Event |
| endprophylaxisPfSI | PfSI 'Human' Event: PfSI End of Chemoprophylaxis Event |
| event_endPfMOI | PfMOI 'Human' Event: Generate PfMOI Clearance Event |
| event_endPfSI | PfSI 'Human' Event: Generate PfSI Clearance Event |
| event_endprophylaxisPfMOI | PfMOI 'Human' Event: Generate PfMOI End of Chemoprophylaxis... |
| event_endprophylaxisPfSI | PfSI 'Human' Event: Generate PfSI End of Chemoprophylaxis... |
| event_feverPfMOI | PfMOI 'Human' Event: Generate PfMOI Fever Event |
| event_feverPfSI | PfSI 'Human' Event: Generate PfSI Fever Event |
| event_gsvaccinatePfMOI | PfMOI 'Human' Event: Generate PfMOI GS Vaccination Event |
| event_gsvaccinatePfSI | PfSI 'Human' Event: Generate PfSI GS Vaccination Event |
| event_gswanePfMOI | PfMOI 'Human' Event: Generate PfMOI GS Waning Protection... |
| event_gswanePfSI | PfSI 'Human' Event: Generate PfSI GS Waning Protection Event |
| event_infectHumanPfMOI | PfMOI 'Human' Event: Generate PfMOI Infection Event |
| event_infectHumanPfSI | PfSI 'Human' Event: Generate PfSI Infection Event |
| event_pevaccinatePfMOI | PfMOI 'Human' Event: Generate PfMOI PE Vaccination Event |
| event_pevaccinatePfSI | PfSI 'Human' Event: Generate PfSI PE Vaccination Event |
| event_pewanePfMOI | PfMOI 'Human' Event: Generate PfMOI PE Waning Protection... |
| event_pewanePfSI | PfSI 'Human' Event: Generate PfSI PE Waning Protection Event |
| event_SimBitePfMOI | PfMOI SimBite 'Human' Event: Generate PfMOI Simulated Bite... |
| event_treatPfMOI | PfMOI 'Human' Event: Generate PfMOI Treatment Event |
| event_treatPfSI | PfSI 'Human' Event: Generate PfSI Treatment Event |
| extend_PatchesImagoQ | Extend 'MacroPatch' ImagoQ (Emerging Adults Queue) |
| feeding_PfMOI | PfMOI 'MicroMosquitoFemale' Method: Host Feeding |
| feeding_PfSI | PfSI 'MicroMosquitoFemale' Method: Host Feeding |
| FeedingSite | MICRO Feeding Site Class Definition |
| feverPfMOI | PfMOI 'Human' Event: PfMOI Infection Event |
| feverPfSI | PfSI 'Human' Event: PfSI Fever Event |
| gammaRates | Gamma Distributed Biting Rates |
| getEIP_MacroMosquitoPop | Set 'MacroMosquitoPop' getEIP |
| get_lambda_MicroEmerge | MICRO 'AquaticSite' Method: Get Lambda |
| get_MicroHuman_ActivitySpace | MICRO: Get 'Human' ActivitySpace |
| get_MicroHuman_FemalePopPointer | MICRO: Get 'Human' 'MicroMosquitoPopFemale' Pointer |
| get_MicroHuman_LandscapePointer | MICRO: Get 'Human' 'Landscape' Pointer |
| get_MicroHumanPop_FemalePopPointer | MICRO: Get 'HumanPop' 'MicroMosquitoPopFemale' Pointer |
| get_MicroHumanPop_LandscapePointer | MICRO: Get 'HumanPop' 'Landscape' Pointer |
| get_MicroHumanPop_TilePointer | MICRO: Get 'HumanPop' 'MicroTile' Pointer |
| get_MicroHuman_TilePointer | MICRO: Get 'Human' 'MicroTile' Pointer |
| get_MicroKernel_movement_BRO | MICRO Search Kernels: 'MicroTile' Access MvAll Object for... |
| get_MicroKernel_movement_BROM | MICRO Search Kernels: 'MicroTile' Access MvAll Object for... |
| get_MicroKernel_movement_FULL | MICRO Search Kernels: 'MicroTile' Access MvAll Object for... |
| get_MicroKernel_movement_Male | MICRO Search Kernels: 'MicroTile' Access MvAll Object for... |
| get_PatchesEggQ | Get 'MacroPatch' EggQ (Egg Batches) |
| get_PatchesImagoQ | Get 'MacroPatch' ImagoQ (Emerging Adults Queue) |
| get_season | Get 'MacroPatch' Seasonal Emergence |
| ggColOffset_utility | Sample Equally from Color Space with Offset |
| ggCol_utility | Sample Equally from Color Space |
| gsvaccinatePfMOI | PfMOI 'Human' Event: PfMOI GS Vaccination Event |
| gsvaccinatePfSI | PfSI 'Human' Event: PfSI GS Vaccination Event |
| gswanePfMOI | PfMOI 'Human' Event: PfMOI GS Waning Protection Event |
| gswanePfSI | PfSI 'Human' Event: PfSI GS Waning Protection Event |
| HistoryGeneric | Generic History |
| HistoryTravel | Travel History |
| Human | Human Class Definition |
| HumanEventQ | Human Event Queue |
| Human_get_PfMOI_PAR | PfMOI 'Human' Method: Get PfMOI_PAR |
| Human_get_PfSI_PAR | PfSI 'Human' Method: Get PfSI_PAR |
| humanPfMOI | PfMOI Human Stage Pathogen Class |
| humanPfSI | PfSI Human Stage Pathogen Class |
| HumanPop | HumanPop Class Definition |
| HumanPop_get_PfMOI_history | PfMOI 'HumanPop' Method: Get PfMOI Histories |
| HumanPop_get_PfMOI_PAR | PfMOI 'HumanPop' Method: Get PfMOI_PAR |
| HumanPop_get_PfSI_history | PfSI 'HumanPop' Method: Get PfSI Histories |
| HumanPop_get_PfSI_PAR | PfSI 'HumanPop' Method: Get PfSI_PAR |
| HumanPop.Parameters | MICRO: Initialize HumanPop Parameters for 'HumanPop' |
| HumanPop_set_humanPfMOI | PfMOI 'HumanPop' Method: Set Human-stage PfMOI Object |
| HumanPop_set_humanPfSI | PfSI 'HumanPop' Method: Set Human-stage PfSI Object |
| HumanPop_set_PfMOI_PAR | PfMOI 'HumanPop' Method: Set PfMOI Paramters for a 'HumanPop' |
| HumanPop_set_PfSI_PAR | PfSI 'HumanPop' Method: Set PfSI Paramters for a 'HumanPop' |
| Human_set_humanPfMOI | PfMOI 'Human' Method: Set Human-stage PfMOI Object |
| Human_set_humanPfSI | PfSI 'Human' Method: Set Human-stage PfSI Object |
| ImagoQ | MICRO Imago Queue |
| importMicroMosquitoHistory_utility | M-BITES Utility: Import JSON Mosquito Histories |
| infectHumanPfMOI | PfMOI 'Human' Event: PfMOI Infection Event |
| infectHumanPfSI | PfSI 'Human' Event: PfSI Infection Event |
| infectiousBite_PfMOI | PfMOI 'Human' Method: Infectious Bite on Human |
| infectiousBite_PfSI | PfSI 'Human' Method: Infectious Bite on Human |
| init_MACRO_PfMOI | PfMOI 'HumanPop' Method: Initialize MACRO PfMOI Infections |
| init_MACRO_PfSI | PfSI 'HumanPop' Method: Initialize MACRO PfSI Infections |
| init_MacroTile_PfMOI | MACRO PfMOI 'MacroTile' Method: Initialize MACRO PfMOI... |
| init_MacroTile_PfSI | MACRO PfSI 'MacroTile' Method: Initialize MACRO PfSI... |
| init_MicroHuman_ActivitySpace | MICRO 'Human' Method: Initialize Activity Space |
| init_MicroHumanPop_ActivitySpace | MICRO 'HumanPop' Method: Initialize Activity Space |
| init_MICRO_PfMOI | PfMOI 'HumanPop' Method: Initialize MICRO PfMOI Infections |
| init_MICRO_PfSI | PfSI 'HumanPop' Method: Initialize MICRO PfSI Infections |
| init_Pathogens_MicroMosquitoFemale_PfMOI | PfMOI Helper Code for Pathogen Initialization in... |
| init_Pathogens_MicroMosquitoFemale_PfSI | PfSI Helper Code for Pathogen Initialization in... |
| init_Pathogens_MicroMosquitoPopFemale_PfMOI | PfMOI Helper Code for Pathogen Initialization in... |
| init_Pathogens_MicroMosquitoPopFemale_PfSI | PfSI Helper Code for Pathogen Initialization in... |
| K2psi_MicroEL4P | Convert K and Regression Coefficient into Psi |
| Landscape | MICRO Landscape Class Definition |
| Landscape.Aqua.Parameters | MICRO: Generate Parameters for 'Landscape' 'AquaticSite' |
| Landscape.Feeding.Parameters | MICRO: Generate Parameters for 'Landscape' 'FeedingSite' |
| Landscape.Parameters | MICRO: Generate Parameters for 'Landscape' Object |
| layEggs_MacroMosquitoPop | 'MacroMosquitoPop' layEggs |
| lmTest_PfMOI | PfMOI 'Human' Method: Light Microscopy Test |
| lmTest_PfSI | PfSI 'Human' Method: PfSI Light Microscopy Test |
| MacroHuman_add2Q_Bites | MACRO 'Human' Method: add2Q_Bites |
| MacroHuman_add2Q_returnHome | add2Q_returnHome |
| MacroHuman_add2Q_takeTrip | add2Q_takeTrip |
| MacroHuman_event_returnHome | event_returnHome |
| MacroHuman_event_takeTrip | event_takeTrip |
| MacroHuman_expectedBites | MACRO 'Human' Method: expectedBites |
| MacroHuman_get_location | MACRO: Get 'Human' location |
| MacroHuman_get_MosquitoPointer | Get 'Human' 'MacroMosquitoPop' Pointer |
| MacroHuman_get_myEIR | Get 'Human' myEIR |
| MacroHuman_get_PatchesPointer | Get 'Human' 'MacroPatch' Pointer |
| MacroHuman_get_patchID | Get 'Human' patchID |
| MacroHuman_get_TilePointer | Get 'Human' 'MacroTile' Pointer |
| MacroHuman_get_travel | Get 'Human' travel |
| MacroHuman_get_travelHistoryHuman | Return 'Human' Travel History |
| MacroHuman_get_travelHistoryHumanPop | Return 'HumanPop' Travel History |
| MacroHuman_go_Patch | Set 'Human' go_Patch |
| MacroHuman_init_travel | MACRO 'Human' Method: Initialize Travel |
| MacroHuman_json_travelHistory | Write 'HumanPop' Travel History to JSON |
| MacroHumanPop_get_patchID | MACRO 'HumanPop' Method: Get all patchID |
| MacroHumanPop_set_patchID | MACRO 'HumanPop' Method: Set all patchID |
| MacroHuman_queueInfectiousBites | MACRO 'HumanPop' Method: queueInfectiousBites |
| MacroHuman_returnHome | returnHome |
| MacroHuman_set_location | MACRO: Set 'Human' location |
| MacroHuman_set_MosquitoPointer | Set 'Human' 'MacroMosquitoPop' Pointer |
| MacroHuman_set_myEIR | Set 'Human' myEIR |
| MacroHuman_set_PatchesPointer | Set 'Human' 'MacroPatch' Pointer |
| MacroHuman_set_patchID | Set 'Human' patchID |
| MacroHuman_set_TilePointer | Set 'Human' 'MacroTile' Pointer |
| MacroHuman_set_travel | Set 'Human' travel |
| MACRO.Humans.Setup | MACRO: Initialize Additional Methods & Fields in 'Human' and... |
| MacroHuman_sumKappa_PfMOI | MACRO: Update 'Human' PfMOI kappa For a Patch |
| MacroHuman_sumKappa_PfSI | MACRO: Update 'Human' PfSI kappa For a Patch |
| MacroHuman_takeTrip | takeTrip |
| MacroHuman_updateKappa | MACRO: Update 'HumanPop' kappa For all Patches |
| MacroMosquitoPop | MACRO Mosquito Population Class Definition |
| MACRO.MosquitoPop.Parameters | Initialize MosquitoPop Parameters for 'MacroMosquitoPop' |
| MacroPatch | MACRO Patch Class Definition |
| MACRO.Patch.Emerge.Setup | Initialize Additional Methods & Fields in 'MacroPatch' for... |
| MACRO.Patch.Parameters | Initialize MACRO Patch Parameters for 'MacroPatch' |
| MacroTile | MACRO Tile Class Definition |
| MACRO.Tile.Parameters | Initialize MACRO Tile Parameters for 'MacroTile' |
| makeLambda_Macro | MACRO: Generate Seasonal Emergence (Lambda) for 'Emerge'... |
| makeLambda_MicroEmerge | MICRO: Generate Seasonal Emergence (Lambda) for 'Emerge'... |
| manage_PatchesImagoQ | Manage 'MacroPatch' ImagoQ (Emerging Adults Queue) |
| MASH-package | MASH (Modular Analysis and Simulation for Human Health) |
| mbitesBRO_BloodMeal | MBITES-BRO: Bloodmeal Energetics for 'MicroMosquitoFemale' |
| mbitesBRO_boutB | MBITES-BRO: Blood Feeding Bout 'MicroMosquitoFemale' |
| mbitesBRO_boutO | MBITES-BRO: Egg Laying Bout 'MicroMosquitoFemale' |
| mbitesBRO_boutR | MBITES-BRO: Post-Prandial Resting Bout 'MicroMosquitoFemale' |
| mbitesBRO_cohort_humanEncounter | MBITES-BRO-Cohort: Human Host Encounter for... |
| mbitesBRO_cohort_oneMosquito_MBITES | MBITES-BRO-Cohort: Run Simulation for 'MicroMosquitoFemale' |
| MBITES.BRO.Cohort.Setup | MBITES-BRO-Cohort: Initialize Additional Methods & Fields in... |
| mbitesBRO_cohort_simCohort | MBITES-BRO-Cohort: Human Host Encounter for... |
| mbitesBro_enterHouse | MBITES-BRO: Attempt to Enter a House for... |
| mbitesBRO_get_MySiteType | MBITES-BRO: Return Site Type 'MicroMosquitoFemale' |
| mbitesBRO_get_restHaz | MBITES-BRO: Get Resting Hazards for 'MicroMosquitoFemale' |
| mbitesBRO_get_surviveFlightProb | MBITES-BRO: Get Baseline Survival Probability for... |
| mbitesBRO_get_WTS | MBITES-BRO: Return Landing Spot Weights for... |
| mbitesBRO_humanEncounter | MBITES-BRO: Human Host Encounter for 'MicroMosquitoFemale' |
| mbitesBRO_landingSpot | MBITES-BRO: Land After Flight 'MicroMosquitoFemale' |
| mbitesBRO_layEggs_EL4P | MBITES-BRO: Lay Eggs for 'EL4P' 'MicroMosquitoFemale' |
| mbitesBRO_layEggs_Emerge | MBITES-BRO: Lay Eggs for 'Emerge' 'MicroMosquitoFemale' |
| mbitesBro_newSpot | MBITES-BRO: Generate New Landing Spot for... |
| mbitesBro_oneBout | MBITES-BRO: One Bout 'MicroMosquitoFemale' |
| mbitesBro_oneMosquito_MBITES | MBITES-BRO: Run Simulation for 'MicroMosquitoFemale' |
| MBITES.BRO.Parameters | Generate Parameters for M-BITES 'BRO' Module |
| mbitesBro_Pop_MBITES | MBITES-BRO: Run Simulation for 'MicroMosquitoPopFemale' |
| MBITES.BRO.Setup | MBITES-BRO: Initialize Additional Methods & Fields in... |
| MbitesBRO_timingExponential | MBITES-BRO: Exponential Timing for 'MicroMosquitoFemale' |
| mbitesBRO_zooEncounter | MBITES-BRO: Non-Human Host Encounter for... |
| mbitesCohort_chooseHost | MBITES-Cohort: Host Choosing for 'MicroMosquitoFemale' |
| MBITES.Cohort.Setup | Initialize Cohort Methods for M-BITES |
| MBITES.FULL.Parameters | Generate Parameters for M-BITES 'Full' Module |
| mbitesGeneric_chooseHost | MBITES-Generic: Host Choosing for 'MicroMosquitoFemale' |
| MbitesGeneric_isActive | MBITES-Generic: Active Check for 'MicroMosquitoFemale' and... |
| MbitesGeneric_isAlive | MBITES-Generic: Alive Check for 'MicroMosquitoFemale' and... |
| mbitesGeneric_pEnergySurvival | MBITES-Generic: Probability of Death due to Energy Reserves... |
| mbitesGeneric_pOverFeed | MBITES-Generic: Probaility of Overfeeding due to Bloodmeal... |
| mbitesGeneric_pReFeed | MBITES-Generic: Probaility to re-enter Blood Feeding Cycle... |
| mbitesGeneric_pSenesce | MBITES-Generic: Probability of Death due to Senescence for... |
| mbitesGeneric_pSugarBout | MBITES-Generic: Probability to Queue Sugar Bout due to Energy... |
| mbitesGeneric_pTatter | MBITES-Generic: Probability of Death due to Wing Tattering... |
| mbitesGeneric_rBatchSizeBms | MBITES-Generic: Egg Batch Size due to Bloodmeal Size for... |
| mbitesGeneric_rBatchSizeNorm | MBITES-Generic: Draw Normally-distributed Egg Batch Size for... |
| mbitesGeneric_rBloodMealSize | MBITES-Generic: Draw Bloodmeal Size for 'MicroMosquitoFemale' |
| mbitesGeneric_rEggMaturationTimeNorm | MBITES-Generic: Normally-distributed Egg Maturation Time for... |
| mbitesGeneric_rEggMaturationTimeOff | MBITES-Generic: No Egg Maturation Time for... |
| mbitesGeneric_rTatterSize | MBITES-Generic: Wing Tattering for 'MicroMosquitoFemale' |
| MBITES.Generic.Setup | Initialize Generic Methods for M-BITES |
| mbitesGeneric_surviveFlight | MBITES-Generic: Flight Survival for 'MicroMosquitoFemale' |
| mbitesGeneric_surviveResting | MBITES-Generic: Resting Survival for 'MicroMosquitoFemale' |
| meshK_MicroEL4P | Fit Psi on Mesh of K Values |
| MICRO.EL4P.Setup | Initialize EL4P Aquatic Ecology Module |
| MICRO.Emerge.Setup | Initialize Emerge Aquatic Ecology Module |
| MICRO.Humans.Setup | MICRO: Initialize Additional Methods & Fields in 'Human' and... |
| MicroKernel_DistanceMat | MICRO Search Kernels: Calculate Euclidean Distance Matrix |
| MicroKernel_exactAll | MICRO Search Kernels: Exact Movement Object Between All Point... |
| MicroKernel_exactMvOb | MICRO Search Kernels: Exact Movement Object Between Two Point... |
| MicroKernel_moveMe_BRO | MICRO Search Kernels: 'MicroMosquitoFemale' Movement Function... |
| MicroKernel_moveMe_BROM | MICRO Search Kernels: 'MicroMosquitoFemale' Movement Function... |
| MicroKernel_moveMe_FULL | MICRO Search Kernels: 'MicroMosquitoFemale' Movement Function... |
| MicroKernel_moveMe_Male | MICRO Search Kernels: 'MicroMosquitoMale' Movement Function... |
| MicroKernelPlot_utility | MICRO Search Kernels: Plot Kernel Functions |
| MicroKernel_PowerKernel | MICRO Search Kernels: Calculate Power Kernel |
| MicroKernel_prSort | MICRO Search Kernels: Sort ID and Probabilities |
| MicroKernel_SampleMvOb_MicroMosquitoPopFemale | MICRO Search Kernels: 'MicroMosquito' Sample MvOb |
| MicroLandscapePlot_utility | Plot a MICRO Landscape |
| MicroMosquitoFemale | MICRO Female Mosquito Class Definition |
| MicroMosquitoMale | MICRO 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.Setup | Setup MICRO Mosquito Population & M-BITES Module for a... |
| MicroTile | MICRO Tile Class Definition |
| MosquitoFemaleHistory | Mosquito Female History Class |
| mosquitoPfMOI | PfMOI Mosquito Stage Pathogen Class |
| mosquitoPfSI | PfSI Mosquito Stage Pathogen Class |
| newEgg | Empty Egg Batch Slot for EggQ |
| newImago | Generate a ImagoQ Slot |
| oneDay_MacroEmerge | Get 'MacroPatch' Seasonal Emergence |
| oneDay_RM | MACRO 'MacroMosquitoPop' Method: oneDay_RM |
| oneStep_MicroEL4P | MICRO 'Landscape' Method: EL4P One Day Dynamics |
| oneStep_MicroEL4PSite | MICRO 'AquaticSite' Method: EL4P One Day Dynamics |
| oneStep_MicroEmerge | MICRO 'Landscape' Method: Emerge One Day Dynamics |
| oneStep_MicroEmergeSite | MICRO 'AquaticSite' Method: Emerge One Day Dynamics |
| ovipositionEq_oneHistory_utility | M-BITES Utility: Calculate Counts of Oviposition at... |
| ovipositionEq_utility | M-BITES Utility: Calculate Empirical Probability of... |
| pevaccinatePfMOI | PfMOI 'Human' Event: PfMOI PE Vaccination Event |
| pevaccinatePfSI | PfSI 'Human' Event: PfSI PE Vaccination Event |
| pewanePfMOI | PfMOI 'Human' Event: PfMOI PE Waning Protection Event |
| pewanePfSI | PfSI 'Human' Event: PfSI PE Waning Protection Event |
| PfMOI_increment_PfID | PfMOI 'HumanPop' Method: Increment PfID |
| PfMOI.Parameters | Initialize PfMOI Module Parameters |
| PfMOI.Setup | Initialize PfMOI MODULE |
| PfMOI_ttClearPf_Independent | PfMOI 'Human' Method: Duration of Infection |
| PfMOI_ttClearPf_Interaction | PfMOI 'Human' Method: Duration of Infection with Pathogen... |
| PfMOI_ttFeverPf | PfMOI 'Human' Method: Timing of Fever Incident |
| PfMOI_ttGSWanePf | PfMOI 'Human' Method: Duration of protection by GS... |
| PfMOI_ttInfectionPf | PfMOI 'Human' Method: Duration of Latency |
| PfMOI_ttPEWanePf | PfMOI 'Human' Method: Duration of protection by PE... |
| PfMOI_ttSusceptiblePf | PfMOI 'Human' Method: Duration of Protection from... |
| PfMOI_ttTreatPf | PfMOI 'Human' Method: Timing of Treatment |
| PfSI_increment_PfID | PfSI 'HumanPop' Method: Increment PfID |
| PfSI.Parameters | Initialize PfSI Module Parameters |
| PfSI.Setup | Initialize PfSI MODULE |
| PfSI_ttClearPf | PfSI 'Human' Method: Duration of Infection |
| PfSI_ttFeverPf | PfSI 'Human' Method: Timing of Fever Incident |
| PfSI_ttGSWanePf | PfSI 'Human' Method: Duration of protection by GS Vaccination |
| PfSI_ttInfectionPf | PfSI 'Human' Method: Duration of Latency |
| PfSI_ttPEWanePf | PfSI 'Human' Method: Duration of protection by PE Vaccination |
| PfSI_ttSusceptiblePf | PfSI 'Human' Method: Duration of Protection from... |
| PfSI_ttTreatPf | PfSI 'Human' Method: Timing of Treatment |
| plot_PfSI | plot_PfSI |
| plot_PfSIOneTrajectory | plot_PfSI_oneTrajectory |
| pointsClustered | Generate Matern Clustering Point Pattern for Landscape Sites |
| pointsLattice | Generate Regular Grid (Lattice) Point Pattern for Landscape... |
| pointsOverdispersed | Generate Overdispersed (SSI) Point Pattern for Landscape... |
| pointsPoisson | Generate Poisson Point Pattern for Landscape Sites |
| probeHost_PfMOI | PfMOI 'Human' Method: Host Probing |
| probeHost_PfSI | PfSI 'Human' Method: Host Probing |
| probeHost_SimBitePfMOI | PfMOI 'Human' Method: Simulated Host Probing |
| probing_PfMOI | PfMOI 'MicroMosquitoFemale' Method: Host Probing |
| probing_PfSI | PfSI 'MicroMosquitoFemale' Method: Host Probing |
| psi2K_cf_MicroEL4P | Regress K on Psi and Return Coefficients |
| psi2K_plot_MicroEL4P | Plot Regression of K on Psi |
| psiFit_MicroEL4P | Objective Function for Fitting Psi |
| queueBitesNegBinom_SimBitePfSI | PfSI SimBite 'HumanPop' Method: Generate Negative Binomial... |
| queueBites_SimBitePfMOI | PfMOI SimBite 'HumanPop' Method: Queue SimBites for... |
| queueVaccination_SimBitePfMOI | PfMOI SimBite 'HumanPop' Method: Queue Vaccination for... |
| rdtTest_PfMOI | PfMOI 'Human' Method: Rapid Diagnostic Test |
| rdtTest_PfSI | PfSI 'Human' Method: PfSI Rapid Diagnostic Test |
| RiskQ | MICRO Risk Queue |
| run2eq_MicroEL4P | Run a Single Aquatic Population to Equilibrium |
| sampleIx_utility | Sample Indices |
| SEARCH.MicroKernel.Setup | MICRO Search Kernels: Initialize Additional Methods & Fields... |
| set_FemalePop_MicroTile | MICRO 'MicroTile': Re-initialize 'MicroMosquitoPopFemale' |
| set_lambda_MicroEmerge | MICRO 'AquaticSite' Method: Set Lambda |
| set_MicroHuman_ActivitySpace | MICRO: Set 'Human' ActivitySpace |
| set_MicroHuman_FemalePopPointer | MICRO: Set 'Human' 'MicroMosquitoPopFemale' Pointer |
| set_MicroHuman_LandscapePointer | MICRO: Set 'Human' 'Landscape' Pointer |
| set_MicroHumanPop_FemalePopPointer | MICRO: Set 'HumanPop' 'MicroMosquitoPopFemale' Pointer |
| set_MicroHumanPop_LandscapePointer | MICRO: Set 'HumanPop' 'Landscape' Pointer |
| set_MicroHumanPop_TilePointer | MICRO: Set 'HumanPop' 'MicroTile' Pointer |
| set_MicroHuman_TilePointer | MICRO: Set 'Human' 'MicroTile' Pointer |
| set_PatchesEggQ | Set 'MacroPatch' EggQ (Egg Batches) |
| set_PatchesImagoQ | Set 'MacroPatch' ImagoQ (Emerging Adults Queue) |
| set_season | Set 'MacroPatch' Seasonal Emergence |
| SimBite_MeanBites | Simulate Biting Process from Population Mean Number of Bites |
| SimBitePfMOI | PfMOI SimBite 'Human' Event: PfMOI Simulated Bite Event |
| SimBitePfMOI.Setup | Initialize SimBite PfMOI Module |
| SimBitePfSI.Setup | Initialize SimBite PfSI Module |
| SimBite_WaitingTime | Simulate Biting Process from Population Mean Waiting Time... |
| simMacro | MACRO 'MacroTile' Simulate MACRO Dynamics |
| sim_MicroHuman_ActivitySpace | MICRO 'Human' Method: Initialize Activity Space |
| sim_MicroHumanPop_ActivitySpace | MICRO 'HumanPop' Method: Simulate Activity Space |
| simMICRO_oneStep | MICRO 'MicroTile': Run Simulation one Time Step |
| siteAges | Generate Ages for 'HumanPop' |
| sitePops | Generate Site Sizes for 'HumanPop' |
| treatPfMOI | PfMOI 'Human' Event: PfMOI Treatment Event |
| treatPfSI | PfSI 'Human' Event: PfSI Treatment Event |
| updateLandscape_MicroEL4P | Update 'Landscape' and 'AquaticSite' after Fitting EL4P... |
| util_List2Df | Utility: Convert List to Data Frame |
| util_PfSIHistory | PfSI: Calculate State Space Occupancy Vector |
| util_PfSIoneHistory | PfSI: Write One Human History |
| util_PfSISlice | PfSI: Empty Occupancy Vector |
