state_symptoms_testing: Constructor for state class

In sangeetabhatia03/multipatchr: Discrete Time Multi-Patch SEIR Model

Constructor for state class

Description

Build a state, which is a collection of patches where each patch has SEIR compartments, with the addition of asymptomatic, pre-symptomatic and symptomatic compartments, and patch-specific birth and death rates.

Usage

state_symptoms_testing(s_patches, e_patches, i_a_patches, i_p_patches,
  i_s_patches, r_patches, diag_patches, s_false_patches, r_false_patches,
  birth_rates, death_rates, transmission_rates, transmission_rates_pilgrims,
  transmission_rates_pilgrims_and_atrisk, asymptomatic_infectiousness,
  presymptomatic_infectiousness, prop_symptomatic, infection_rates,
  symptom_rates, recovery_rates_asym, recovery_rates_sym, testing_rates,
  test_sensitivity, test_specificity, isolation_period, movement_rate)

Arguments

s_patches	Vector of number of susceptibles in each patch,
e_patches	Vector of number of exposed in each patch
i_a_patches	Vector of number of asymptomatic infected in each patch
i_p_patches	Vector of number of pre-symptomatic infected in each patch
i_s_patches	Vector of number of symptomatic infected in each patch
r_patches	Vector of number of recovered in each patch
diag_patches	Vector of number of diagnosed (true diagnosis) in each patch
s_false_patches	Vector of number of susceptibles in patch with false positive test result.
r_false_patches	Vector of number of recovered in patch with false positive test result.
birth_rates	patch-specific birth rates
death_rates	patch-specific death rates
transmission_rates	Vector of patch-specific transmission rate
transmission_rates_pilgrims	Vector of transmission rate between pilgrims
transmission_rates_pilgrims_and_atrisk	Vector of transmission rate between pilgrims and "at risk" non-pilgrims
asymptomatic_infectiousness	Vector of proportions that give the infectivity of asymptomatic cases relative to symptomatic cases.
presymptomatic_infectiousness	Vector of proportions that give the infectivity of presymptomatic cases relative to symptomatic cases.
prop_symptomatic	Vector of patch-specific proportion of cases that are symptomatic
infection_rates	Vector of patch-specific infection rate
symptom_rates	Vector of patch-specific rate at which pre-symptomatic infections develop symptoms
recovery_rates_asym	Vector of patch-specific recovery rate for asymptomatic infections
recovery_rates_sym	Vector of patch-specific recovery rate for symptomatic infections
testing_rates	Vector of patch-specific testing rates
test_sensitivity	Vector of patch-specific test sensitivity
test_specificity	Vector of patch-specific test specificity
isolation_period	Vector of patch-specific mean duration of isolation following positive test
movement_rate	M rate of movement between patches is defined the rate matrix M where m[i, j] is the rate of movement from i to j conditional on moving out of i per unit time. Must be n X n matrix where is the number of patches i.e, max of lengths of all input vectors s_patches, e_patches, i_patches, r_patches, birth_rates, and death_rates.

Value

List with class 'state'. Each element of 'state' is a list of class 'patch'. In addition, 'state' contains a 'movement_rate' which is a non-negative matrix of rates of movement between patches.

Author(s)

Jack Wardle

See Also

[patch()]

sangeetabhatia03/multipatchr documentation built on Aug. 13, 2024, 4:05 p.m.