PfMOI.Setup: Initialize PfMOI MODULE
In smitdave/MASH: MASH (Modular Analysis and Simulation for Human Health)

Description Usage Arguments Value

Generate a list of parameters PfMOI_PAR in Human and public methods in Human for PfSI infection model; also defines public methods in MicroMosquitoFemale for PfMOI infection model.

PfMOI.Setup(overwrite = TRUE, interaction = FALSE, InteractionPf = 0,
  MosyMaxI = 1L, HumanMaxI = 1L, Pf_c = 0.15, Pf_b = 0.55,
  DurationPf = 200, LatentPf = 10, FeverPf = 0.3, mnFeverPf = 10,
  vrFeverPf = 0.1, TreatPf = 0.5, mnTreatPf = 3,
  mnChemoprophylaxisPf = 32, PEProtectPf = 0.99, peBlockPf = 1,
  mnPEPf = 270, vrPEPf = 50, GSProtectPf = 1, gsBlockPf = 0.9,
  mnGSPf = 180, vrGSPf = 20, rdtSensPf = 0.9, rdtSpecPf = 0.1,
  lmSensPf = 0.9, lmSpecPf = 0.1)

`overwrite`	overwrite existing methods and fields?
`interaction`	independent clearance or pathogen interaction model for calculating infection clearance waiting times (if `FALSE` use `PfMOI_ttClearPf_Independent`, if `TRUE` use `PfMOI_ttClearPf_Interaction`)
`InteractionPf`	if using pathogen interaction model of clearance this parameter control strength of interaction 0: no interaction (reduces to independent clearance) <0: facilitation against host immune system (slower clearance rate than independent queueing) 0<: competition for host resources (faster clearance rate than independent queueing) See https://doi.org/10.1186/1475-2875-8-87 for details of queueing model with pathogen interaction.
`MosyMaxI`	maximum number of clonal variants passed in single mosquito to human transmission event (set to `-1L` for unlimited)
`HumanMaxI`	maximum number of clonal variants passed in single human to mosquito transmission event (set to `-1L` for unlimited)
`Pf_c`	infected human to mosquito transmission efficiency
`Pf_b`	infected mosquito to human transmission efficiency
`DurationPf`	duration of infection (assuming clonal variants are cleared independently)
`LatentPf`	latency (How many days after the infectious bite does the infection start?)
`FeverPf`	probability of fever
`mnFeverPf`	mean of timing of fever incident relative to start of PfMOI infection (log-normally distributed, mean on natural scale)
`vrFeverPf`	standard deviation of timing of fever incident relative to start of PfMOI infection (log-normally distributed, standard deviation on natural scale)
`TreatPf`	probability of treatment after fever incident
`mnTreatPf`	average waiting time from fever to treatment (exponentially distributed)
`mnChemoprophylaxisPf`	constant period of proteection from chemoprophylaxis
`PEProtectPf`	proportion protected by PE vaccination (probability vaccination successful)
`peBlockPf`	proportion of infections blocked by PE vaccination
`mnPEPf`	mean duration of protection from PE vaccination
`vrPEPf`	standard deviation of protection from PE vaccination
`GSProtectPf`	proportion protected by GS vaccination (probability vaccination successful)
`gsBlockPf`	proportion of infections blocked by GS vaccination
`mnGSPf`	mean duration of protection from GS vaccination
`vrGSPf`	standard deviation of protection from GS vaccination
`rdtSensPf`	RDT sensitivity
`rdtSpecPf`	RDT specificity
`lmSensPf`	Light Microscopy sensitivity
`lmSpecPf`	Light Microscopy specificity