ModelMeaslesMixing creates a measles epidemiological model with mixing
between different population groups. The model includes vaccination,
quarantine, isolation, and contact tracing mechanisms.
Usage
ModelMeaslesMixing(
vname,
n,
prevalence,
contact_rate,
transmission_rate,
vax_efficacy,
vax_reduction_recovery_rate,
incubation_period,
prodromal_period,
rash_period,
contact_matrix,
hospitalization_rate,
hospitalization_period,
days_undetected,
quarantine_period,
quarantine_willingness,
isolation_willingness,
isolation_period,
prop_vaccinated,
contact_tracing_success_rate = 1,
contact_tracing_days_prior = 4
)Arguments
- vname
String. Name of the virus
- n
Number of individuals in the population.
- prevalence
Double. Initial proportion of individuals with the virus.
- contact_rate
Numeric scalar. Average number of contacts per step.
- transmission_rate
Numeric scalar between 0 and 1. Probability of transmission.
- vax_efficacy
Double. Vaccine efficacy rate.
- vax_reduction_recovery_rate
Double. Vaccine reduction in recovery rate.
- incubation_period
Double. Duration of incubation period.
- prodromal_period
Double. Duration of prodromal period.
- rash_period
Double. Duration of rash period.
- contact_matrix
Matrix of contact rates between individuals.
- hospitalization_rate
Double. Rate of hospitalization.
- hospitalization_period
Double. Period of hospitalization.
- days_undetected
Double. Number of days an infection goes undetected.
- quarantine_period
Integer. Number of days for quarantine.
- quarantine_willingness
Double. Proportion of agents willing to quarantine.
- isolation_willingness
Double. Proportion of agents willing to isolate.
- isolation_period
Integer. Number of days for isolation.
- prop_vaccinated
Double. Proportion of population that is vaccinated.
- contact_tracing_success_rate
Double. Probability of successful contact tracing.
- contact_tracing_days_prior
Integer. Number of days prior to the onset of the infection for which contact tracing is effective.
Value
The
ModelMeaslesMixingfunction returns a model of class epiworld_model.
Details
The contact_matrix is a matrix of contact rates between entities. The
matrix should be of size n x n, where n is the number of entities.
This is a row-stochastic matrix, i.e., the sum of each row should be 1.
The model includes three distinct phases of measles infection: incubation, prodromal, and rash periods. Vaccination provides protection against infection and may reduce recovery time.
The initial_states function allows the user to set the initial state of the model. In particular, the user can specify how many of the non-infected agents have been removed at the beginning of the simulation.
See also
epiworld-methods
Other Models:
ModelDiffNet(),
ModelMeaslesQuarantine(),
ModelSEIR(),
ModelSEIRCONN(),
ModelSEIRD(),
ModelSEIRDCONN(),
ModelSEIRMixing(),
ModelSEIRMixingQuarantine(),
ModelSIR(),
ModelSIRCONN(),
ModelSIRD(),
ModelSIRDCONN(),
ModelSIRLogit(),
ModelSIRMixing(),
ModelSIS(),
ModelSISD(),
ModelSURV(),
epiworld-data
Examples
# Start off creating three entities.
# Individuals will be distributed randomly between the three.
e1 <- entity("Population 1", 3e3, as_proportion = FALSE)
e2 <- entity("Population 2", 3e3, as_proportion = FALSE)
e3 <- entity("Population 3", 3e3, as_proportion = FALSE)
# Row-stochastic matrix (rowsums 1)
cmatrix <- c(
c(0.9, 0.05, 0.05),
c(0.1, 0.8, 0.1),
c(0.1, 0.2, 0.7)
) |> matrix(byrow = TRUE, nrow = 3)
N <- 9e3
measles_model <- ModelMeaslesMixing(
vname = "Measles",
n = N,
prevalence = 1 / N,
contact_rate = 15,
transmission_rate = 0.9,
vax_efficacy = 0.97,
vax_reduction_recovery_rate = 0.8,
incubation_period = 10,
prodromal_period = 3,
rash_period = 7,
contact_matrix = cmatrix,
hospitalization_rate = 0.1,
hospitalization_period = 10,
days_undetected = 2,
quarantine_period = 14,
quarantine_willingness = 0.9,
isolation_willingness = 0.8,
isolation_period = 10,
prop_vaccinated = 0.95,
contact_tracing_success_rate = 0.8,
contact_tracing_days_prior = 4
)
# Adding the entities to the model
measles_model |>
add_entity(e1) |>
add_entity(e2) |>
add_entity(e3)
set.seed(331)
run(measles_model, ndays = 100)
#> _________________________________________________________________________
#> Running the model...
#> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
summary(measles_model)
#> ________________________________________________________________________________
#> ________________________________________________________________________________
#> SIMULATION STUDY
#>
#> Name of the model : Measles with Mixing and Quarantine
#> Population size : 9000
#> Agents' data : (none)
#> Number of entities : 3
#> Days (duration) : 100 (of 100)
#> Number of viruses : 1
#> Last run elapsed t : 120.00ms
#> Last run speed : 7.45 million agents x day / second
#> Rewiring : off
#>
#> Global events:
#> - Update infected individuals (runs daily)
#>
#> Virus(es):
#> - Measles
#>
#> Tool(s):
#> - Vaccine
#>
#> Model parameters:
#> - Contact rate : 15.0000
#> - Contact tracing days prior : 4.0000
#> - Contact tracing success rate : 0.8000
#> - Days undetected : 2.0000
#> - Hospitalization period : 10.0000
#> - Hospitalization rate : 0.1000
#> - Incubation period : 10.0000
#> - Isolation period : 10.0000
#> - Isolation willingness : 0.8000
#> - Prodromal period : 3.0000
#> - Quarantine period : 14.0000
#> - Quarantine willingness : 0.9000
#> - Rash period : 7.0000
#> - Transmission rate : 0.9000
#> - Vaccination rate : 0.9500
#> - Vax efficacy : 0.9700
#> - Vax improved recovery : 0.8000
#>
#> Distribution of the population at time 100:
#> - ( 0) Susceptible : 8999 -> 7172
#> - ( 1) Exposed : 1 -> 405
#> - ( 2) Prodromal : 0 -> 130
#> - ( 3) Rash : 0 -> 45
#> - ( 4) Isolated : 0 -> 5
#> - ( 5) Isolated Recovered : 0 -> 159
#> - ( 6) Detected Hospitalized : 0 -> 15
#> - ( 7) Quarantined Exposed : 0 -> 0
#> - ( 8) Quarantined Susceptible : 0 -> 1
#> - ( 9) Quarantined Prodromal : 0 -> 0
#> - (10) Quarantined Recovered : 0 -> 0
#> - (11) Hospitalized : 0 -> 17
#> - (12) Recovered : 0 -> 1051
#>
#> Transition Probabilities:
#> - Susceptible 1.00 0.00 - - - - - - 0.00 - - - -
#> - Exposed - 0.90 0.10 - - - - 0.00 - 0.00 - - -
#> - Prodromal - - 0.68 0.32 - - - - - - - - -
#> - Rash - - - 0.06 0.08 0.37 0.06 - - - - 0.06 0.38
#> - Isolated - - - - 0.15 0.76 0.09 - - - - - -
#> - Isolated Recovered - - - - - 0.90 - - - - - - 0.10
#> - Detected Hospitalized - - - - - - 0.89 - - - - - 0.11
#> - Quarantined Exposed - 0.02 0.01 - - - - 0.85 - 0.12 - - -
#> - Quarantined Susceptible 0.07 - - - - - - - 0.93 - - - -
#> - Quarantined Prodromal - - 0.04 - 0.46 - - - - 0.50 - - -
#> - Quarantined Recovered - - - - - - - - - - - - -
#> - Hospitalized - - - - - - - - - - - 0.91 0.09
#> - Recovered - - - - - - - - - - - - 1.00
#>