Yet Another COVID19 Projection

Projection for the next 15 days in several countries using a SEIRQRDP model based on Peng et al. 2020. Code adapted (barely) from matlab E. Cheynet’s code

Source code at github

Argentina

LT <- 5    #1-14 days, latent time in days, incubation period, gamma^(-1)   
QT <- 14  #Quarantine time in days, recovery time, infectious period, delta^(-1)
alpha_guess <- 1.0
beta_guess <- 1.0
gamma_guess <- 1 / LT
delta_guess <- 1 / QT
kappa_guess <- 0.01 #dead rate
lambda_guess <- 0.5 # recover rate
region = "Argentina"
population =  40e6
data<-get_jhu_data(region=region,population = population )
data_fit<-create_fit_data(data,fitted_date = fitted_date,start_date = start_date)
parameters<-c(alpha_guess,beta_guess,gamma_guess,delta_guess,kappa_guess,lambda_guess)
params<-SEIQRDP_fit(parameters,data_fit)
forecast <-15
forecast_data <- SEIQRDP_predict(forecast,params,data_fit,data)
plot<-SEIQRDP_plot(forecast_data,region)
plot

Brazil

region="Brazil"
population=21e7
start_date<-(today()-12) 
fitted_date<-(start_date+10) 
start_date <- start_date %>% format('%m-%d-%Y')
fitted_date <- fitted_date %>% format('%m-%d-%Y')
data<-get_jhu_data(region=region,population = population )
data_fit<-create_fit_data(data,fitted_date = fitted_date,start_date = start_date)
parameters<-c(alpha_guess,beta_guess,gamma_guess,delta_guess,kappa_guess,lambda_guess)
params<-SEIQRDP_fit(parameters,data_fit)
forecast <-15
forecast_data <- SEIQRDP_predict(forecast,params,data_fit,data)
plot<-SEIQRDP_plot(forecast_data,region)
plot

Italy

region ="Italy"
population=61e6
data<-get_jhu_data(region=region,population = population )
data_fit<-create_fit_data(data,fitted_date = fitted_date,start_date = start_date)
parameters<-c(alpha_guess,beta_guess,gamma_guess,delta_guess,kappa_guess,lambda_guess)
params<-SEIQRDP_fit(parameters,data_fit)
forecast <-15
forecast_data <- SEIQRDP_predict(forecast,params,data_fit,data)
plot<-SEIQRDP_plot(forecast_data,region)
plot

Spain

region = "Spain"
population = 46e6
data<-get_jhu_data(region=region,population = population )
data_fit<-create_fit_data(data,fitted_date = fitted_date,start_date = start_date)
parameters<-c(alpha_guess,beta_guess,gamma_guess,delta_guess,kappa_guess,lambda_guess)
params<-SEIQRDP_fit(parameters,data_fit)
forecast <-15
forecast_data <- SEIQRDP_predict(forecast,params,data_fit,data)
plot<-SEIQRDP_plot(forecast_data,region)
plot

Chile

region ="Chile"
population=18e6
data<-get_jhu_data(region=region,population = population )
data_fit<-create_fit_data(data,fitted_date = fitted_date,start_date = start_date)
parameters<-c(alpha_guess,beta_guess,gamma_guess,delta_guess,kappa_guess,lambda_guess)
params<-SEIQRDP_fit(parameters,data_fit)
forecast <-15
forecast_data <- SEIQRDP_predict(forecast,params,data_fit,data)
plot<-SEIQRDP_plot(forecast_data,region)
plot

Korea

region ="Korea, South"
population=60e6
data<-get_jhu_data(region=region,population = population )
data_fit<-create_fit_data(data,fitted_date = fitted_date,start_date = start_date)
parameters<-c(alpha_guess,beta_guess,gamma_guess,delta_guess,kappa_guess,lambda_guess)
params<-SEIQRDP_fit(parameters,data_fit)
forecast <-15
forecast_data <- SEIQRDP_predict(forecast,params,data_fit,data)
plot<-SEIQRDP_plot(forecast_data,region)
plot

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