Function reference • comomodels

All functions

InterventionParameters-class: An S4 object representing the InterventionParameters,

R0(): Calculates basic reproduction number

initial_conditions(<SEIRD>) transmission_parameters(<SEIRD>) `initial_conditions<-`(<SEIRD>) `transmission_parameters<-`(<SEIRD>) run(<SEIRD>) R0(<SEIRD>) ode_structure_diagram(<SEIRD>): An S4 object representing the SEIRD.

initial_conditions(<SEIRDAge>) `initial_conditions<-`(<SEIRDAge>) transmission_parameters(<SEIRDAge>) `transmission_parameters<-`(<SEIRDAge>) run(<SEIRDAge>) R0(<SEIRDAge>) ode_structure_diagram(<SEIRDAge>): An S4 object representing the SEIRDAge.

initial_conditions(<SEIRDNPIAge>) `initial_conditions<-`(<SEIRDNPIAge>) transmission_parameters(<SEIRDNPIAge>) `transmission_parameters<-`(<SEIRDNPIAge>) interventions(<SEIRDNPIAge>) `interventions<-`(<SEIRDNPIAge>) run(<SEIRDNPIAge>) R0(<SEIRDNPIAge>) ode_structure_diagram(<SEIRDNPIAge>): Defines an age-structured SEIR model with non-pharmaceutical interventions (NPIs) which influence social contact

initial_conditions(<SEIRDV>) transmission_parameters(<SEIRDV>) `initial_conditions<-`(<SEIRDV>) `transmission_parameters<-`(<SEIRDV>) intervention_parameters(<SEIRDV>) `intervention_parameters<-`(<SEIRDV>) run(<SEIRDV>): An S4 object representing the SEIRDV.

initial_conditions(<SEIRDVAge>) `initial_conditions<-`(<SEIRDVAge>) transmission_parameters(<SEIRDVAge>) `transmission_parameters<-`(<SEIRDVAge>) interventions(<SEIRDVAge>) `interventions<-`(<SEIRDVAge>) run(<SEIRDVAge>): An S4 object representing the SEIRDVAge.

initial_conditions(<SEIRD_BD>) transmission_parameters(<SEIRD_BD>) `initial_conditions<-`(<SEIRD_BD>) `transmission_parameters<-`(<SEIRD_BD>) run(<SEIRD_BD>) R0(<SEIRD_BD>) ode_structure_diagram(<SEIRD_BD>): An S4 object representing the SEIRD_BD model.

initial_conditions(<SEIRD_CT>) transmission_parameters(<SEIRD_CT>) `initial_conditions<-`(<SEIRD_CT>) `transmission_parameters<-`(<SEIRD_CT>) run(<SEIRD_CT>) R0(<SEIRD_CT>) ode_structure_diagram(<SEIRD_CT>): An S4 object representing the SEIRD_CT.

initial_conditions(<SEIRD_RU>) initial_cases_deaths(<SEIRD_RU>) transmission_parameters(<SEIRD_RU>) contact_rates(<SEIRD_RU>) country_demog(<SEIRD_RU>) fraction_rural(<SEIRD_RU>) `initial_conditions<-`(<SEIRD_RU>) `transmission_parameters<-`(<SEIRD_RU>) `contact_rates<-`(<SEIRD_RU>) `country_demog<-`(<SEIRD_RU>) run(<SEIRD_RU>) R0(<SEIRD_RU>) ode_structure_diagram(<SEIRD_RU>): An S4 object representing the SEIRD_RU.

initial_conditions(<SEIaImIsRD>) transmission_parameters(<SEIaImIsRD>) `initial_conditions<-`(<SEIaImIsRD>) `transmission_parameters<-`(<SEIaImIsRD>) run(<SEIaImIsRD>) R0(<SEIaImIsRD>) ode_structure_diagram(<SEIaImIsRD>): An S4 object representing the SEIaImIsRD.

initial_conditions(<SEmIRD>) transmission_parameters(<SEmIRD>) `initial_conditions<-`(<SEmIRD>) `transmission_parameters<-`(<SEmIRD>) run(<SEmIRD>) R0(<SEmIRD>) ode_structure_diagram(<SEmIRD>): An S4 object representing the SEmIRD.

SimulationParameters-class: An S4 object representing the SimulationParameters.

agedemographics_by_country: agedemographics_by_country

check(): Checks that the format of the InterventionParameters is correct: only whole intervals are allowed; intervals do not overlap; no backwards intervals.

contact_all_rural: contact_all_rural

contact_all_urban: contact_all_urban

contact_home: contact_home

contact_other: contact_other

`contact_rates<-`(): Setter method for contact matrices, or contact rates directly, for urban and rural communities in the SEIRD_RU model. Matrices must be of type double. NOTE: if inputting matrices, you MUST assign fraction_rural first, and you must input full age demographics, i.e. you cannot only provide the fraction of the population that is rural!

contact_rates(): Retrieves contact rates of SEIR model.

contact_school: contact_school

contact_work: contact_work

country_codetoname: country_codetoname

`country_demog<-`(): Setter method for demographic data for urban and rural communities in the SEIR model. If inputting demographic vectors, both vectors together must sum to 1.

country_demog(): Retrieves age demographics, if provided, of SEIR model.

covid_transmission_parameters(): Returns transmission parameter values for gamma, mu, kappa and R0 given a specific variant

fraction_rural(): Retrieves fraction of the population that lives in a rural environment of SEIR model.

infection_fatality_ratio: infection_fatality_ratio

initial_cases_deaths(): Retrieves initial cases and deaths of SEIRD_RU model.

`initial_conditions<-`(): Set initial conditions of a class within comomodels package.

initial_conditions(): Retrieves initial conditions of a class within comomodels package

`intervention_parameters<-`(): Set intervention parameters of the SEIRV or SEIRDAge model.

intervention_parameters(): Retrieves intervention parameters of SEIRDV or SEIRDAge_interventions model.

intervention_protocol(): Creates protocols for the interventions using parameters of the model; used in the 'run' method of compartmental model with interventions.

`interventions<-`(): Setter method for intervention of the age-structured SEIRV model.

interventions(): Retrieves interventions of age-structured SEIRDV model.

ode_structure_diagram(): Plots model structure for a model object

percentrural_by_country: percentrural_by_country

population: population

run(): Solves ODEs for a given model

stack_intervention_coverages(): Creates stacks of interventions using parameters of the model; used in the 'run' method of compartmental model with interventions.

tanh_coverage_smoother(): Smoother function for the curve of the interventions. Used to avoid breaks in the ode solver of compartmental models with non-smooth interventions.

`transmission_parameters<-`(): Set transmission parameters for a class within comomodels package

transmission_parameters(): Retrieves transmission parameters of a class within comomodels package