SEIR_M1: Run SEIR model for Model 1

In lemdt/CovidShinyModel:

Description

Runs the SEIR model using the Model 1 specification. https://docs.google.com/document/d/1CEoKQ1pD1x4yH7GzR3mViWtfVG-4Do8ViZUd4z_t9Ts/edit?usp=sharing

Usage

SEIR_M1(S0, E0, I0, R0, beta.vector, num.days, influx, params)

Arguments

S0	Numeric. Initial number of susceptible individuals.
E0	Numeric. Initial number of exposed individuals.
I0	Numeric. Initial number of infected individuals.
R0	Numeric. Initial number of recovered individuals.
beta.vector	Vector, of beta values to use in the simulation on each day. Should have the same length as num.days.
num.days	Numeric. Number of days to run the simulation.
influx	List. This is hash consisting of a 'day' and an 'influx' number, meant to represent an influx of infections into the region
params	List. This should contain the parameters for running the SEIR, including: - Sigma - Gamma - hosp.delay.time: time between infection and hospitalization - hosp.rate: percent hospitalized out of those infected - hosp.los: hospital length of stay if not admitted to ICU - icu.delay.time: time between hospitalization and ICU admission - icu.rate: percent ICU admitted among those hospitalized - icu.los : average ICU length of stay if not ventilated - vent.delay.time: time between ICU ventilation and being put on a ventilator - vent.rate: percent ventilated among those ICU admitted - vent.los: average time on a ventilator

Details

The simulation ignores births and deaths.

Value

Dataframe, with susceptible counts, exposed counts, infected counts, hospitalization numbers, and recovery numbers.

lemdt/CovidShinyModel documentation built on May 10, 2020, 1:54 p.m.