Files in smitdave/MASH

MASH (Modular Analysis and Simulation for Human Health)

.Rbuildignore

.gitignore

DESCRIPTION

MASH.Rproj

NAMESPACE

R/.gitignore

R/AQUA-Macro-EL4P.R R/AQUA-Macro-Emerge.R R/AQUA-Micro-EL4P-Calibrate.R R/AQUA-Micro-EL4P-Methods.R R/AQUA-Micro-EL4P-Setup.R R/AQUA-Micro-Emerge-Methods.R R/AQUA-Micro-Emerge-Setup.R R/AQUA-Structures.R R/AQUA-Utilities.R R/DEPRECATED/AQUA-Micro-Queues.R R/DEPRECATED/MICRO-Site-RiskList.R R/DEPRECATED/MICRO-Tile-Parameters.R R/DEPRECATED/MOSQUITO-Mosquito-Class.R R/DEPRECATED/PATHOGEN-PfMOI-Class.R R/DEPRECATED/PATHOGEN-PfSI-Class.R R/DEPRECATED/test_MICRO_structures.R R/DEPRECATED/test_MOSQUITO.R R/HUMANS-Human-Class.R R/HUMANS-HumanPop-Class.R R/HUMANS-HumanPop-Parameters.R R/MACRO-Human-Biting.R R/MACRO-Human-Setup.R R/MACRO-Human-Travel.R R/MACRO-MosquitoPop-Class.R R/MACRO-MosquitoPop-Methods.R R/MACRO-MosquitoPop-Parameters.R R/MACRO-Patch-Class.R R/MACRO-Patch-Parameters.R R/MACRO-Tile-Class.R R/MACRO-Tile-Methods.R R/MACRO-Tile-Parameters.R R/MASH-Utilities.R R/MASH.R R/MBITES-Auxiliary.R R/MBITES-BRO-Bouts.R R/MBITES-BRO-Cohort-Setup.R R/MBITES-BRO-Cohort.R R/MBITES-BRO-Energetics.R R/MBITES-BRO-HostEncounter.R R/MBITES-BRO-Parameters.R R/MBITES-BRO-Setup.R R/MBITES-BRO-Survival.R R/MBITES-ChooseHost.R R/MBITES-Cohort-Setup.R R/MBITES-Energetics.R R/MBITES-Parameters.R R/MBITES-Setup.R R/MBITES-Survival.R R/MBITES-Utility.R R/MICRO-Human-ActivitySpace.R R/MICRO-Human-Setup.R R/MICRO-Landscape-Class.R R/MICRO-Landscape-Parameters.R R/MICRO-Landscape-Utilities.R R/MICRO-Site-Class.R R/MICRO-Tile-Class.R R/MICRO-Tile-Methods.R R/MOSQUITO-Mosquito-Class.R R/MOSQUITO-MosquitoPop-Class.R R/MOSQUITO-MosquitoPop-Methods.R R/MOSQUITO-MosquitoPop-Setup.R R/PATHOGEN-PfMOI-Methods.R R/PATHOGEN-PfMOI-Parameters.R R/PATHOGEN-PfMOI-Setup.R R/PATHOGEN-PfMOI-SimBite.R R/PATHOGEN-PfSI-Methods.R R/PATHOGEN-PfSI-Parameters.R R/PATHOGEN-PfSI-Setup.R R/PATHOGEN-PfSI-SimBite.R R/PATHOGEN-PfSI-Utilities.R R/PROTOTYPE/MACRO-Patch-Class.R R/PROTOTYPE/MACRO-Tile-Class.R R/PROTOTYPE/MOSQUITO-MacroRM-Class.R R/PROTOTYPE/MOSQUITO-MacroRM-Methods.R R/PROTOTYPE/MOSQUITO-MacroRM-Parameters.R R/PROTOTYPE/MOSQUITO-MacroRM-Setup.R R/QUEUEING-ParametricDistribution.R R/QUEUEING-QueueODE.R R/RcppExports.R R/RcppR6.R R/SEARCH-MicroKernel-Generate.R R/SEARCH-MicroKernel-Methods.R R/SEARCH-MicroKernel-Setup.R R/SEARCH-MicroKernel-Utility.R R/pkgname.R R/zzz.R README.md Test-MACRO-Emerge.R Test-MICRO-EL4P.R Test-MICRO-Emerge.R Test-PATHOGEN-PfMOI.R Test-PATHOGEN-PfSI.R

_pkgdown.yml

docs/articles/Conventions.html

docs/articles/Human-EventQueue.html

docs/articles/HumanEventQueue.html

docs/articles/LandscapeAnalysis.html

docs/articles/MACRO-Example.html

docs/articles/MACRO-Example_files/figure-html/unnamed-chunk-4-1.png

docs/articles/MACRO-LandscapeAnalysis.html

docs/articles/MACRO-SpatialDynamics.html

docs/articles/PathogenPfLOME.html

docs/articles/PathogenPfMOI.html

docs/articles/ToDo.html

docs/articles/index.html

docs/articles/test.R

docs/articles/test.html

docs/articles/test_files/figure-html/unnamed-chunk-1-1.png

docs/articles/test_files/figure-html/unnamed-chunk-1-2.png

docs/authors.html

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/reference/AquaticSite.html

docs/reference/FeedingSite.html

docs/reference/Human.html

docs/reference/HumanEventQ.html

docs/reference/HumanPop.Parameters.html

docs/reference/HumanPop.html

docs/reference/HumanPop_get_PfMOI_history.html

docs/reference/HumanPop_set_PfMOI_PAR.html

docs/reference/HumanPop_set_PfSI_PAR.html

docs/reference/HumanPop_set_humanPfMOI.html

docs/reference/HumanPop_set_humanPfSI.html

docs/reference/Human_get_PfMOI_PAR.html

docs/reference/Human_get_PfSI_PAR.html

docs/reference/Human_get_humanPfMOI.html

docs/reference/Human_get_humanPfSI.html

docs/reference/Human_set_PfMOI_PAR.html

docs/reference/Human_set_PfSI_PAR.html

docs/reference/Human_set_humanPfMOI.html

docs/reference/Human_set_humanPfSI.html

docs/reference/Landscape.Aqua.Parameters.html

docs/reference/Landscape.Feeding.Parameters.html

docs/reference/Landscape.Parameters.html

docs/reference/Landscape.html

docs/reference/MACRO.Humans.Setup.html

docs/reference/MACRO.MosquitoPop.Parameters.html

docs/reference/MACRO.Patch.Emerge.Setup.html

docs/reference/MACRO.Patch.Parameters.html

docs/reference/MACRO.PatchPf.Setup.html

docs/reference/MACRO.Tile.Parameters.html

docs/reference/MASH-package.html

docs/reference/MBITES.Parameters.html

docs/reference/MICRO.Aqua.Setup.html

docs/reference/MICRO.Emerge.Setup.html

docs/reference/MICRO.Humans.Setup.html

docs/reference/MICRO.Tile.Parameters.html

docs/reference/MacroHumanPop_get_patchID.html

docs/reference/MacroHumanPop_set_patchID.html

docs/reference/MacroHuman_add2Q_Bites.html

docs/reference/MacroHuman_add2Q_returnHome.html

docs/reference/MacroHuman_add2Q_takeTrip.html

docs/reference/MacroHuman_event_returnHome.html

docs/reference/MacroHuman_event_takeTrip.html

docs/reference/MacroHuman_expectedBites.html

docs/reference/MacroHuman_get_MosquitoPointer.html

docs/reference/MacroHuman_get_PatchesPointer.html

docs/reference/MacroHuman_get_TilePointer.html

docs/reference/MacroHuman_get_location.html

docs/reference/MacroHuman_get_myEIR.html

docs/reference/MacroHuman_get_patchID.html

docs/reference/MacroHuman_get_travel.html

docs/reference/MacroHuman_get_travelHistoryHuman.html

docs/reference/MacroHuman_get_travelHistoryHumanPop.html

docs/reference/MacroHuman_go_Patch.html

docs/reference/MacroHuman_init_travel.html

docs/reference/MacroHuman_json_travelHistory.html

docs/reference/MacroHuman_queueInfectiousBites.html

docs/reference/MacroHuman_returnHome.html

docs/reference/MacroHuman_set_MosquitoPointer.html

docs/reference/MacroHuman_set_PatchesPointer.html

docs/reference/MacroHuman_set_TilePointer.html

docs/reference/MacroHuman_set_location.html

docs/reference/MacroHuman_set_myEIR.html

docs/reference/MacroHuman_set_patchID.html

docs/reference/MacroHuman_set_travel.html

docs/reference/MacroHuman_sumKappa.html

docs/reference/MacroHuman_takeTrip.html

docs/reference/MacroHuman_track_travel.html

docs/reference/MacroHuman_updateKappa.html

docs/reference/MacroMosquitoPop.html

docs/reference/MacroPatch.html

docs/reference/MacroPatchPf.html

docs/reference/MacroTile.html

docs/reference/MbitesBRO.Setup.html

docs/reference/MbitesBRO_getWTS.html

docs/reference/MbitesBRO_timingExponential.html

docs/reference/MbitesGeneric.Setup.html

docs/reference/MbitesGeneric_FemaleBout.html

docs/reference/MbitesGeneric_isActive.html

docs/reference/MbitesGeneric_isAlive.html

docs/reference/MicroKernel_DistanceMat.html

docs/reference/MicroKernel_KernelsPlot.html

docs/reference/MicroKernel_PowerKernel.html

docs/reference/MicroKernel_SampleMvOb.html

docs/reference/MicroKernel_exactAll.html

docs/reference/MicroKernel_exactMvOb.html

docs/reference/MicroKernel_moveMe_BRO.html

docs/reference/MicroKernel_moveMe_BROM.html

docs/reference/MicroKernel_moveMe_FULL.html

docs/reference/MicroKernel_moveMe_Male.html

docs/reference/MicroKernel_prSort.html

docs/reference/MicroMosquito.html

docs/reference/MicroMosquitoFemale.html

docs/reference/MicroMosquitoMale.html

docs/reference/MicroMosquitoPop.html

docs/reference/MicroSite.html

docs/reference/MicroTile.html

docs/reference/MosquitoFemaleHistory.html

docs/reference/MosquitoMaleHistory.html

docs/reference/PfMOI.Parameters.html

docs/reference/PfMOI.Setup.html

docs/reference/PfMOI_increment_PfID.html

docs/reference/PfMOI_ttClearPf.html

docs/reference/PfMOI_ttFeverPf.html

docs/reference/PfMOI_ttGSWanePf.html

docs/reference/PfMOI_ttInfectionPf.html

docs/reference/PfMOI_ttPEWanePf.html

docs/reference/PfMOI_ttSusceptiblePf.html

docs/reference/PfMOI_ttTreatPf.html

docs/reference/PfSI.Parameters.html

docs/reference/PfSI.Setup.html

docs/reference/PfSI_increment_PfID.html

docs/reference/PfSI_ttClearPf.html

docs/reference/PfSI_ttFeverPf.html

docs/reference/PfSI_ttGSWanePf.html

docs/reference/PfSI_ttInfectionPf.html

docs/reference/PfSI_ttPEWanePf.html

docs/reference/PfSI_ttSusceptiblePf.html

docs/reference/PfSI_ttTreatPf.html

docs/reference/SEARCH.MicroKernel.Setup.html

docs/reference/SimBitePfMOI.Setup.html

docs/reference/SimBitePfMOI.html

docs/reference/SimBitePfSI.Setup.html

docs/reference/SimBite_MeanBites.html

docs/reference/SimBite_WaitingTime.html

docs/reference/add2Q_SimBitePfMOI.html

docs/reference/add2Q_endPfMOI.html

docs/reference/add2Q_endPfSI.html

docs/reference/add2Q_endprophylaxisPfMOI.html

docs/reference/add2Q_endprophylaxisPfSI.html

docs/reference/add2Q_feverPfMOI.html

docs/reference/add2Q_feverPfSI.html

docs/reference/add2Q_gsvaccinatePfMOI.html

docs/reference/add2Q_gsvaccinatePfSI.html

docs/reference/add2Q_gswanePfMOI.html

docs/reference/add2Q_gswanePfSI.html

docs/reference/add2Q_infectHumanPfMOI.html

docs/reference/add2Q_infectHumanPfSI.html

docs/reference/add2Q_pevaccinatePfMOI.html

docs/reference/add2Q_pevaccinatePfSI.html

docs/reference/add2Q_pewanePfMOI.html

docs/reference/add2Q_pewanePfSI.html

docs/reference/add2Q_treatPfMOI.html

docs/reference/add2Q_treatPfSI.html

docs/reference/addCohort_MacroEmerge.html

docs/reference/addCohort_MicroEmerge.html

docs/reference/add_MicroEggQ.html

docs/reference/add_MicroImagoQ.html

docs/reference/add_riskList.html

docs/reference/allocEggQ.html

docs/reference/allocImagoQ.html

docs/reference/betaRootA.html

docs/reference/betaRootB.html

docs/reference/clear_MicroEggQ.html

docs/reference/clear_MicroImagoQ.html

docs/reference/emergingAdults_MacroEmerge.html

docs/reference/emergingAdults_MicroEmerge.html

docs/reference/empty_MicroEggQ.html

docs/reference/empty_MicroImagoQ.html

docs/reference/endPfMOI.html

docs/reference/endPfSI.html

docs/reference/endprophylaxisPfMOI.html

docs/reference/endprophylaxisPfSI.html

docs/reference/event_SimBitePfMOI.html

docs/reference/event_endPfMOI.html

docs/reference/event_endPfSI.html

docs/reference/event_endprophylaxisPfMOI.html

docs/reference/event_endprophylaxisPfSI.html

docs/reference/event_feverPfMOI.html

docs/reference/event_feverPfSI.html

docs/reference/event_gsvaccinatePfMOI.html

docs/reference/event_gsvaccinatePfSI.html

docs/reference/event_gswanePfMOI.html

docs/reference/event_gswanePfSI.html

docs/reference/event_infectHumanPfMOI.html

docs/reference/event_infectHumanPfSI.html

docs/reference/event_pevaccinatePfMOI.html

docs/reference/event_pevaccinatePfSI.html

docs/reference/event_pewanePfMOI.html

docs/reference/event_pewanePfSI.html

docs/reference/event_treatPfMOI.html

docs/reference/event_treatPfSI.html

docs/reference/extend_MicroEggQ.html

docs/reference/extend_MicroImagoQ.html

docs/reference/extend_PatchesImagoQ.html

docs/reference/extend_riskList.html

docs/reference/feverPfMOI.html

docs/reference/feverPfSI.html

docs/reference/full_MicroEggQ.html

docs/reference/full_MicroImagoQ.html

docs/reference/gammaRates.html

docs/reference/getEIP_MacroMosquitoPop.html

docs/reference/get_MicroEggQ.html

docs/reference/get_MicroHumanPop_FemalePopPointer.html

docs/reference/get_MicroHumanPop_LandscapePointer.html

docs/reference/get_MicroHumanPop_TilePointer.html

docs/reference/get_MicroHuman_ActivitySpace.html

docs/reference/get_MicroHuman_FemalePopPointer.html

docs/reference/get_MicroHuman_LandscapePointer.html

docs/reference/get_MicroHuman_TilePointer.html

docs/reference/get_MicroImagoQ.html

docs/reference/get_MicroKernel_movement_Male.html

docs/reference/get_MicroKernel_movement_bro.html

docs/reference/get_MicroKernel_movement_brom.html

docs/reference/get_MicroKernel_movement_full.html

docs/reference/get_MicroLambda.html

docs/reference/get_PatchPf.html

docs/reference/get_PatchesEggQ.html

docs/reference/get_PatchesImagoQ.html

docs/reference/get_season.html

docs/reference/gsvaccinatePfMOI.html

docs/reference/gsvaccinatePfSI.html

docs/reference/gswanePfMOI.html

docs/reference/gswanePfSI.html

docs/reference/humanPfMOI.html

docs/reference/humanPfSI.html

docs/reference/index.html

docs/reference/infectHumanPfMOI.html

docs/reference/infectHumanPfSI.html

docs/reference/infectiousBite_PfMOI.html

docs/reference/infectiousBite_PfSI.html

docs/reference/init.mbitesEnergetics.html

docs/reference/init_MACRO_PfSI.html

docs/reference/init_MICRO_PfMOI.html

docs/reference/init_MICRO_PfSI.html

docs/reference/init_MacroTile_PfSI.html

docs/reference/init_MicroHumanPop_ActivitySpace.html

docs/reference/init_MicroHuman_ActivitySpace.html

docs/reference/init_PfMOI.html

docs/reference/init_PfSI.html

docs/reference/init_riskList.html

docs/reference/layEggs_MacroMosquitoPop.html

docs/reference/lmTest_PfMOI.html

docs/reference/lmTest_PfSI.html

docs/reference/makeLambda_Macro.html

docs/reference/makeLambda_Micro.html

docs/reference/manage_PatchesImagoQ.html

docs/reference/mosquitoPfMOI.html

docs/reference/mosquitoPfSI.html

docs/reference/newEgg.html

docs/reference/newImago.html

docs/reference/oneDay_MacroEmerge.html

docs/reference/oneDay_MicroEmerge.html

docs/reference/oneDay_MicroEmergeSite.html

docs/reference/oneDay_RM.html

docs/reference/pevaccinatePfMOI.html

docs/reference/pevaccinatePfSI.html

docs/reference/pewanePfMOI.html

docs/reference/pewanePfSI.html

docs/reference/plot_PfSI.html

docs/reference/plot_PfsiOneTrajectory.html

docs/reference/pointsClustered.html

docs/reference/pointsLattice.html

docs/reference/pointsOverdispersed.html

docs/reference/pointsPoisson.html

docs/reference/probeHost_PfMOI.html

docs/reference/probeHost_PfSI.html

docs/reference/queueBitesNegBinom_SimBitePfSI.html

docs/reference/queueBites_SimBitePfMOI.html

docs/reference/queueVaccination_SimBitePfMOI.html

docs/reference/rdtTest_PfMOI.html

docs/reference/rdtTest_PfSI.html

docs/reference/set_MicroEggQ.html

docs/reference/set_MicroHumanPop_FemalePopPointer.html

docs/reference/set_MicroHumanPop_LandscapePointer.html

docs/reference/set_MicroHumanPop_TilePointer.html

docs/reference/set_MicroHuman_ActivitySpace.html

docs/reference/set_MicroHuman_FemalePopPointer.html

docs/reference/set_MicroHuman_LandscapePointer.html

docs/reference/set_MicroHuman_TilePointer.html

docs/reference/set_MicroImagoQ.html

docs/reference/set_MicroLambda.html

docs/reference/set_PatchPf.html

docs/reference/set_PatchesEggQ.html

docs/reference/set_PatchesImagoQ.html

docs/reference/set_season.html

docs/reference/simMacro.html

docs/reference/sim_MicroHumanPop_ActivitySpace.html

docs/reference/sim_MicroHuman_ActivitySpace.html

docs/reference/siteAges.html

docs/reference/sitePops.html

docs/reference/track_MicroEggQ.html

docs/reference/track_MicroImagoQ.html

docs/reference/treatPfMOI.html

docs/reference/treatPfSI.html

docs/reference/ttClearPfMOI.html

docs/reference/ttFeverPfMOI.html

docs/reference/ttInfectPfMOI.html

docs/reference/ttSusceptiblePfMOI.html

docs/reference/ttTreatPfMOI.html

docs/reference/util_List2Df.html

docs/reference/util_PfSIHistory.html

docs/reference/util_PfSISlice.html

docs/reference/util_PfSIoneHistory.html

docs/reference/zero_MicroEggQ.html

docs/reference/zero_MicroImagoQ.html

inst/AQUA-EL4P.yml

inst/AQUA-EggQ.yml

inst/AQUA-ImagoQ.yml

inst/HUMANS-EventQ.yml

inst/HUMANS-History.yml

inst/MICRO-RiskQ.yml

inst/MOSQUITO-History.yml

inst/PATHOGEN-PfMOI.yml

inst/PATHOGEN-PfSI.yml

inst/RcppR6.yml

inst/include/MASH.h

inst/include/MASH/AQUA-EL4P.hpp

inst/include/MASH/AQUA-EggQ.hpp

inst/include/MASH/AQUA-ImagoQ.hpp

inst/include/MASH/HUMANS-EventQ.hpp

inst/include/MASH/HUMANS-History.hpp

inst/include/MASH/MICRO-MatingQ.hpp

inst/include/MASH/MICRO-RiskQ.hpp

inst/include/MASH/MOSQUITO-History.hpp

inst/include/MASH/PATHOGEN-PfMOI.hpp

inst/include/MASH/PATHOGEN-PfSI.hpp

inst/include/MASH/RcppR6_post.hpp

inst/include/MASH/RcppR6_pre.hpp

inst/include/MASH/RcppR6_support.hpp

man/AquaEmergeLambdaPlot_utility.Rd man/AquaticSite.Rd man/EL4P.Landscape.Fit.Rd man/EL4P.Mesh.Fit.Rd man/EL4P.Parameters.Rd man/EL4P.Rd man/EggQ.Rd man/FeedingSite.Rd man/HistoryGeneric.Rd man/HistoryTravel.Rd man/Human.Rd man/HumanEventQ.Rd man/HumanPop.Parameters.Rd man/HumanPop.Rd man/HumanPop_get_PfMOI_PAR.Rd man/HumanPop_get_PfMOI_history.Rd man/HumanPop_get_PfSI_PAR.Rd man/HumanPop_get_PfSI_history.Rd man/HumanPop_set_PfMOI_PAR.Rd man/HumanPop_set_PfSI_PAR.Rd man/HumanPop_set_humanPfMOI.Rd man/HumanPop_set_humanPfSI.Rd man/Human_get_PfMOI_PAR.Rd man/Human_get_PfSI_PAR.Rd man/Human_set_humanPfMOI.Rd man/Human_set_humanPfSI.Rd man/ImagoQ.Rd man/K2psi_MicroEL4P.Rd man/Landscape.Aqua.Parameters.Rd man/Landscape.Feeding.Parameters.Rd man/Landscape.Parameters.Rd man/Landscape.Rd man/MACRO.Humans.Setup.Rd man/MACRO.MosquitoPop.Parameters.Rd man/MACRO.Patch.Emerge.Setup.Rd man/MACRO.Patch.Parameters.Rd man/MACRO.Tile.Parameters.Rd man/MASH-package.Rd man/MBITES.BRO.Cohort.Setup.Rd man/MBITES.BRO.Parameters.Rd man/MBITES.BRO.Setup.Rd man/MBITES.Cohort.Setup.Rd man/MBITES.FULL.Parameters.Rd man/MBITES.Generic.Setup.Rd man/MICRO.EL4P.Setup.Rd man/MICRO.Emerge.Setup.Rd man/MICRO.Humans.Setup.Rd man/MacroHumanPop_get_patchID.Rd man/MacroHumanPop_set_patchID.Rd man/MacroHuman_add2Q_Bites.Rd man/MacroHuman_add2Q_returnHome.Rd man/MacroHuman_add2Q_takeTrip.Rd man/MacroHuman_event_returnHome.Rd man/MacroHuman_event_takeTrip.Rd man/MacroHuman_expectedBites.Rd man/MacroHuman_get_MosquitoPointer.Rd man/MacroHuman_get_PatchesPointer.Rd man/MacroHuman_get_TilePointer.Rd man/MacroHuman_get_location.Rd man/MacroHuman_get_myEIR.Rd man/MacroHuman_get_patchID.Rd man/MacroHuman_get_travel.Rd man/MacroHuman_get_travelHistoryHuman.Rd man/MacroHuman_get_travelHistoryHumanPop.Rd man/MacroHuman_go_Patch.Rd man/MacroHuman_init_travel.Rd man/MacroHuman_json_travelHistory.Rd man/MacroHuman_queueInfectiousBites.Rd man/MacroHuman_returnHome.Rd man/MacroHuman_set_MosquitoPointer.Rd man/MacroHuman_set_PatchesPointer.Rd man/MacroHuman_set_TilePointer.Rd man/MacroHuman_set_location.Rd man/MacroHuman_set_myEIR.Rd man/MacroHuman_set_patchID.Rd man/MacroHuman_set_travel.Rd man/MacroHuman_sumKappa_PfMOI.Rd man/MacroHuman_sumKappa_PfSI.Rd man/MacroHuman_takeTrip.Rd man/MacroHuman_updateKappa.Rd man/MacroMosquitoPop.Rd man/MacroPatch.Rd man/MacroTile.Rd man/MbitesBRO_timingExponential.Rd man/MbitesGeneric_isActive.Rd man/MbitesGeneric_isAlive.Rd man/MicroKernelPlot_utility.Rd man/MicroKernel_DistanceMat.Rd man/MicroKernel_PowerKernel.Rd man/MicroKernel_SampleMvOb_MicroMosquitoPopFemale.Rd man/MicroKernel_exactAll.Rd man/MicroKernel_exactMvOb.Rd man/MicroKernel_moveMe_BRO.Rd man/MicroKernel_moveMe_BROM.Rd man/MicroKernel_moveMe_FULL.Rd man/MicroKernel_moveMe_Male.Rd man/MicroKernel_prSort.Rd man/MicroLandscapePlot_utility.Rd man/MicroMosquitoFemale.Rd man/MicroMosquitoMale.Rd man/MicroMosquitoPop.Setup.Rd man/MicroMosquitoPopFemale_clear_pop.Rd man/MicroMosquitoPopFemale_extend_pop.Rd man/MicroMosquitoPopFemale_push_pop.Rd man/MicroMosquitoPopFemale_update_nullPop.Rd man/MicroMosquitoPopFemale_update_pop.Rd man/MicroMosquitoPopFemale_which_alive.Rd man/MicroTile.Rd man/MosquitoFemaleHistory.Rd man/PfMOI.Parameters.Rd man/PfMOI.Setup.Rd man/PfMOI_increment_PfID.Rd man/PfMOI_ttClearPf_Independent.Rd man/PfMOI_ttClearPf_Interaction.Rd man/PfMOI_ttFeverPf.Rd man/PfMOI_ttGSWanePf.Rd man/PfMOI_ttInfectionPf.Rd man/PfMOI_ttPEWanePf.Rd man/PfMOI_ttSusceptiblePf.Rd man/PfMOI_ttTreatPf.Rd man/PfSI.Parameters.Rd man/PfSI.Setup.Rd man/PfSI_increment_PfID.Rd man/PfSI_ttClearPf.Rd man/PfSI_ttFeverPf.Rd man/PfSI_ttGSWanePf.Rd man/PfSI_ttInfectionPf.Rd man/PfSI_ttPEWanePf.Rd man/PfSI_ttSusceptiblePf.Rd man/PfSI_ttTreatPf.Rd man/RiskQ.Rd man/SEARCH.MicroKernel.Setup.Rd man/SimBitePfMOI.Rd man/SimBitePfMOI.Setup.Rd man/SimBitePfSI.Setup.Rd man/SimBite_MeanBites.Rd man/SimBite_WaitingTime.Rd man/add2Q_SimBitePfMOI.Rd man/add2Q_endPfMOI.Rd man/add2Q_endPfSI.Rd man/add2Q_endprophylaxisPfMOI.Rd man/add2Q_endprophylaxisPfSI.Rd man/add2Q_feverPfMOI.Rd man/add2Q_feverPfSI.Rd man/add2Q_gsvaccinatePfMOI.Rd man/add2Q_gsvaccinatePfSI.Rd man/add2Q_gswanePfMOI.Rd man/add2Q_gswanePfSI.Rd man/add2Q_infectHumanPfMOI.Rd man/add2Q_infectHumanPfSI.Rd man/add2Q_pevaccinatePfMOI.Rd man/add2Q_pevaccinatePfSI.Rd man/add2Q_pewanePfMOI.Rd man/add2Q_pewanePfSI.Rd man/add2Q_treatPfMOI.Rd man/add2Q_treatPfSI.Rd man/addCohort_MacroEmerge.Rd man/addCohort_MicroEL4P.Rd man/addCohort_MicroEL4PSite.Rd man/addCohort_MicroEmerge.Rd man/addCohort_MicroEmergeSite.Rd man/allocEggQ.Rd man/allocImagoQ.Rd man/betaRootA.Rd man/betaRootB.Rd man/calcLambda_MicroEL4P.Rd man/calculateBionomics_utility.Rd man/colLuminosity_utility.Rd man/emergingAdults_MacroEmerge.Rd man/endPfMOI.Rd man/endPfSI.Rd man/endprophylaxisPfMOI.Rd man/endprophylaxisPfSI.Rd man/event_SimBitePfMOI.Rd man/event_endPfMOI.Rd man/event_endPfSI.Rd man/event_endprophylaxisPfMOI.Rd man/event_endprophylaxisPfSI.Rd man/event_feverPfMOI.Rd man/event_feverPfSI.Rd man/event_gsvaccinatePfMOI.Rd man/event_gsvaccinatePfSI.Rd man/event_gswanePfMOI.Rd man/event_gswanePfSI.Rd man/event_infectHumanPfMOI.Rd man/event_infectHumanPfSI.Rd man/event_pevaccinatePfMOI.Rd man/event_pevaccinatePfSI.Rd man/event_pewanePfMOI.Rd man/event_pewanePfSI.Rd man/event_treatPfMOI.Rd man/event_treatPfSI.Rd man/extend_PatchesImagoQ.Rd man/feeding_PfMOI.Rd man/feeding_PfSI.Rd man/feverPfMOI.Rd man/feverPfSI.Rd man/gammaRates.Rd man/getEIP_MacroMosquitoPop.Rd man/get_MicroHumanPop_FemalePopPointer.Rd man/get_MicroHumanPop_LandscapePointer.Rd man/get_MicroHumanPop_TilePointer.Rd man/get_MicroHuman_ActivitySpace.Rd man/get_MicroHuman_FemalePopPointer.Rd man/get_MicroHuman_LandscapePointer.Rd man/get_MicroHuman_TilePointer.Rd man/get_MicroKernel_movement_BRO.Rd man/get_MicroKernel_movement_BROM.Rd man/get_MicroKernel_movement_FULL.Rd man/get_MicroKernel_movement_Male.Rd man/get_PatchesEggQ.Rd man/get_PatchesImagoQ.Rd man/get_lambda_MicroEmerge.Rd man/get_season.Rd man/ggColOffset_utility.Rd man/ggCol_utility.Rd man/gsvaccinatePfMOI.Rd man/gsvaccinatePfSI.Rd man/gswanePfMOI.Rd man/gswanePfSI.Rd man/humanPfMOI.Rd man/humanPfSI.Rd man/importMicroMosquitoHistory_utility.Rd man/infectHumanPfMOI.Rd man/infectHumanPfSI.Rd man/infectiousBite_PfMOI.Rd man/infectiousBite_PfSI.Rd man/init_MACRO_PfMOI.Rd man/init_MACRO_PfSI.Rd man/init_MICRO_PfMOI.Rd man/init_MICRO_PfSI.Rd man/init_MacroTile_PfMOI.Rd man/init_MacroTile_PfSI.Rd man/init_MicroHumanPop_ActivitySpace.Rd man/init_MicroHuman_ActivitySpace.Rd man/init_Pathogens_MicroMosquitoFemale_PfMOI.Rd man/init_Pathogens_MicroMosquitoFemale_PfSI.Rd man/init_Pathogens_MicroMosquitoPopFemale_PfMOI.Rd man/init_Pathogens_MicroMosquitoPopFemale_PfSI.Rd man/layEggs_MacroMosquitoPop.Rd man/lmTest_PfMOI.Rd man/lmTest_PfSI.Rd man/makeLambda_Macro.Rd man/makeLambda_MicroEmerge.Rd man/manage_PatchesImagoQ.Rd man/mbitesBRO_BloodMeal.Rd man/mbitesBRO_boutB.Rd man/mbitesBRO_boutO.Rd man/mbitesBRO_boutR.Rd man/mbitesBRO_cohort_humanEncounter.Rd man/mbitesBRO_cohort_oneMosquito_MBITES.Rd man/mbitesBRO_cohort_simCohort.Rd man/mbitesBRO_get_MySiteType.Rd man/mbitesBRO_get_WTS.Rd man/mbitesBRO_get_restHaz.Rd man/mbitesBRO_get_surviveFlightProb.Rd man/mbitesBRO_humanEncounter.Rd man/mbitesBRO_landingSpot.Rd man/mbitesBRO_layEggs_EL4P.Rd man/mbitesBRO_layEggs_Emerge.Rd man/mbitesBRO_zooEncounter.Rd man/mbitesBro_Pop_MBITES.Rd man/mbitesBro_enterHouse.Rd man/mbitesBro_newSpot.Rd man/mbitesBro_oneBout.Rd man/mbitesBro_oneMosquito_MBITES.Rd man/mbitesCohort_chooseHost.Rd man/mbitesGeneric_chooseHost.Rd man/mbitesGeneric_pEnergySurvival.Rd man/mbitesGeneric_pOverFeed.Rd man/mbitesGeneric_pReFeed.Rd man/mbitesGeneric_pSenesce.Rd man/mbitesGeneric_pSugarBout.Rd man/mbitesGeneric_pTatter.Rd man/mbitesGeneric_rBatchSizeBms.Rd man/mbitesGeneric_rBatchSizeNorm.Rd man/mbitesGeneric_rBloodMealSize.Rd man/mbitesGeneric_rEggMaturationTimeNorm.Rd man/mbitesGeneric_rEggMaturationTimeOff.Rd man/mbitesGeneric_rTatterSize.Rd man/mbitesGeneric_surviveFlight.Rd man/mbitesGeneric_surviveResting.Rd man/meshK_MicroEL4P.Rd man/mosquitoPfMOI.Rd man/mosquitoPfSI.Rd man/newEgg.Rd man/newImago.Rd man/oneDay_MacroEmerge.Rd man/oneDay_RM.Rd man/oneStep_MicroEL4P.Rd man/oneStep_MicroEL4PSite.Rd man/oneStep_MicroEmerge.Rd man/oneStep_MicroEmergeSite.Rd man/ovipositionEq_oneHistory_utility.Rd man/ovipositionEq_utility.Rd man/pevaccinatePfMOI.Rd man/pevaccinatePfSI.Rd man/pewanePfMOI.Rd man/pewanePfSI.Rd man/plot_PfSI.Rd man/plot_PfSIOneTrajectory.Rd man/pointsClustered.Rd man/pointsLattice.Rd man/pointsOverdispersed.Rd man/pointsPoisson.Rd man/probeHost_PfMOI.Rd man/probeHost_PfSI.Rd man/probeHost_SimBitePfMOI.Rd man/probing_PfMOI.Rd man/probing_PfSI.Rd man/psi2K_cf_MicroEL4P.Rd man/psi2K_plot_MicroEL4P.Rd man/psiFit_MicroEL4P.Rd man/queueBitesNegBinom_SimBitePfSI.Rd man/queueBites_SimBitePfMOI.Rd man/queueVaccination_SimBitePfMOI.Rd man/rdtTest_PfMOI.Rd man/rdtTest_PfSI.Rd man/run2eq_MicroEL4P.Rd man/sampleIx_utility.Rd man/set_FemalePop_MicroTile.Rd man/set_MicroHumanPop_FemalePopPointer.Rd man/set_MicroHumanPop_LandscapePointer.Rd man/set_MicroHumanPop_TilePointer.Rd man/set_MicroHuman_ActivitySpace.Rd man/set_MicroHuman_FemalePopPointer.Rd man/set_MicroHuman_LandscapePointer.Rd man/set_MicroHuman_TilePointer.Rd man/set_PatchesEggQ.Rd man/set_PatchesImagoQ.Rd man/set_lambda_MicroEmerge.Rd man/set_season.Rd man/simMICRO_oneStep.Rd man/simMacro.Rd man/sim_MicroHumanPop_ActivitySpace.Rd man/sim_MicroHuman_ActivitySpace.Rd man/siteAges.Rd man/sitePops.Rd man/treatPfMOI.Rd man/treatPfSI.Rd man/updateLandscape_MicroEL4P.Rd man/util_List2Df.Rd man/util_PfSIHistory.Rd man/util_PfSISlice.Rd man/util_PfSIoneHistory.Rd

src/.gitignore

src/Makevars

src/Makevars.win

src/PATHOGEN-PfSI-Utilities.cpp

src/RcppExports.cpp

src/RcppR6.cpp

vignettes/Conventions.Rmd vignettes/HumanEventQueue.Rmd vignettes/MACRO-Example.Rmd vignettes/MACRO-LandscapeAnalysis.Rmd vignettes/MACRO-SpatialDynamics.Rmd vignettes/PathogenPfLOME.Rmd vignettes/PathogenPfMOI.Rmd vignettes/ToDo.Rmd vignettes/test.R vignettes/test.Rmd

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