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

View source: R/patch.R

patch_symptoms_testing

R Documentation

Constructor for patch class

Description

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

Usage

patch_symptoms_testing(s_patch, e_patch, i_a_patch, i_p_patch, i_s_patch,
  r_patch, diag_patch, s_false_patch, r_false_patch, birth_rate, death_rate,
  transmission_rate, transmission_rate_pilgrims,
  transmission_rate_pilgrims_and_atrisk, asymptomatic_infectiousness,
  presymptomatic_infectiousness, prop_symptomatic, infection_rate,
  symptom_rate, recovery_rate_asym, recovery_rate_sym, testing_rate,
  test_sensitivity, test_specificity, isolation_period)

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
`diag_patch`	Number of diagnosed individuals in patch
`s_false_patch`	Number of susceptible individuals with false positive test in patch
`r_false_patch`	Number of recovered individuals with false positive test 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
`transmission_rate_pilgrims`	effective contact rate between pilgrims
`transmission_rate_pilgrims_and_atrisk`	effective contact rate between pilgrims and at risk non-pilgrims
`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_asymptomatic to recovered
`recovery_rate_sym`	Rate of moving from I_symptomatic to recovered
`testing_rate`	Proportion of people that are tested
`test_sensitivity`	Sensitivity of tests
`test_specificity`	Specificity of tests
`isolation_period`	Average duration of isolation following positive test

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 ** exposed_diagnosed ** Number of diagnosed exposed individuals in this patch ** infected_asymptomatic ** Number of asymptomatic infected individuals in this patch ** infected_asymptomatic_diagnosed ** Number of diagnosed asymptomatic infected individuals in this patch ** infected_presymptomatic ** Number of presymptomatic infected individuals in this patch ** infected_presymptomatic_diagnosed ** Number of diagnosed presymptomatic infected individuals in this patch ** infected_symptomatic ** Number of symptomatic infected individuals in this patch ** infected_symptomatic_diagnosed ** Number of diagnosed symptomatic infected individuals in this patch ** recovered ** Number of recovered individuals in this patch ** recovered_diagnosed ** Number of diagnosed recovered individuals in this patch ** birth_rate ** Patch-specific birth rate ** death_rate ** Patch-specific death rate ** transmission_rate ** Effective contact rate between non-pilgrims ** transmission_rate_pilgrims ** Effective contact rate between pilgrims ** transmission_rate_pilgrims_and_atrisk ** Effective contact rate between pilgrims and "at risk" non-pilgrims ** 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. ** Testing rate ** Proportion of individuals that are tested. ** Test sensitivity ** Sensitivity of tests. ** Test specificity ** Specificity of tests. ** Isolation period ** Average duration of isolation period in days.