patch_symptoms: Constructor for patch class
In sangeetabhatia03/multipatchr: Discrete Time Multi-Patch SEIR Model

View source: R/patch.R

patch_symptoms

R Documentation

Constructor for patch class

Description

Build a patch with seir compartments, including (a/pre-)symptomatic compartments, and patch-specific birth and death rates

Usage

patch_symptoms(s_patch, e_patch, i_a_patch, i_p_patch, i_s_patch, r_patch,
  birth_rate, death_rate, transmission_rate, asymptomatic_infectiousness,
  presymptomatic_infectiousness, prop_symptomatic, infection_rate,
  symptom_rate, recovery_rate_asym, recovery_rate_sym)

Arguments

`s_patch`	Number of susceptible individuals in patch
`e_patch`	Number of exposed individuals in patch
`i_a_patch`	Number of asymptomatic infected individuals in patch
`i_p_patch`	Number of presymptomatic infected individuals in patch
`i_s_patch`	Number of symptomatic infected individuals in patch
`r_patch`	Number of recovered individuals in patch
`birth_rate`	Birth rate for this patch. Number of births per unit time
`death_rate`	Death rate for this patch. Number of deaths per unit time in this patch
`transmission_rate`	effective contact rate
`asymptomatic_infectiousness`	Proportion giving the infectivity of asymptomatic cases relative to symptomatic cases.
`presymptomatic_infectiousness`	Proportion giving the infectivity of presymptomatic cases relative to symptomatic cases.
`prop_symptomatic`	Proportion of cases that are symptomatic.
`infection_rate`	rate of moving from compartment E to I
`symptom_rate`	Rate of moving from I_presymptomatic to I_symptomatic.
`recovery_rate_asym`	Rate of moving from I_asymtpomatic to recovered
`recovery_rate_sym`	Rate of moving from I_symtpomatic to recovered

Value

a list of class patch which has the following items ** susceptible ** Number of susceptibles in this patch ** exposed ** Number of exposed individuals in this patch ** infected_asymptomatic ** Number of asymptomatic infected individuals in this patch ** infected_presymptomatic ** Number of presymptomatic infected individuals in this patch ** infected_symptomatic ** Number of symptomatic infected individuals in this patch ** recovered ** Number of recovered individuals in this patch ** birth_rate ** Patch-specific birth rate ** death_rate ** Patch-specific death rate ** transmission_rate ** Effective contact rate for this patch ** asymptomatic_infectiousness ** Relative infectivity of asymptomatic infected individuals ** presymptomatic_infectiousness ** Relative infectivity of presymptomatic infected individuals ** prop_symptomatic ** Proportion of infections with symptoms ** Infection rate ** Rate at which individuals move from E to I_a or I_p ** Symptom rate ** Rate at which individuals move from I_p to I_s ** Asymptomatic recovery rate ** Rate at which individuals move from I_a to R. ** Symptomatic recovery rate ** Rate at which individuals move from I_s to R.