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comoOdeCpp

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This package implements CoMo Consortium's COVID-19 transmission model in Rcpp. comoOdeCpp is designed to work with CoMo COVID-19 app

by Ricardo Aguas, Sompob Saralamba, Bo Gao

Install

install.packages("devtools")
library("devtools")
install_github("ocelhay/comoOdeCpp", subdir="comoOdeCpp")

Usage:

Add library("comoOdeCpp") at the beginning of your script, or require("comoOdeCpp") if you are writing a package

Examples use with ode function:

covidOdeCpp_reset()
out0 <- ode(y = Y, times = times, func = covidOdeCpp, parms = parameters,
            input=vectors0, A=A,
            contact_home=contact_home, contact_school=contact_school,
            contact_work=contact_work, contact_other=contact_other,
            popbirth_col2=popbirth[,2], popstruc_col2=popstruc[,2],
            ageing=ageing,
            ifr_col2=ifr[,2], ihr_col2=ihr[,2], mort_col=mort)


covidOdeCpp_reset()
out0 <- ode(y = Y, times = times, method = "euler", hini = 0.05, func = covidOdeCpp, parms = parameters,
            input=vectors0, A=A,
            contact_home=contact_home, contact_school=contact_school,
            contact_work=contact_work, contact_other=contact_other,
            popbirth_col2=popbirth[,2], popstruc_col2=popstruc[,2],
            ageing=ageing,
            ifr_col2=ifr[,2], ihr_col2=ihr[,2], mort_col=mort)
)

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