calculate_r0_rc_fromdata_delay_rcd.RdUses the compartmental model to calculate R0 and Rc using data on incidence and the proportion of imported cases. RCD is accounted for in the calculation of the transmission parameter lambda (but R0 and Rc are the same as in the model without RCD)
calculate_r0_rc_fromdata_delay_rcd(
df,
f = 1/72,
gamma = 1/223,
r = 1/60,
return.all = F,
h.cutoff = 5e-08,
referral = FALSE
)a dataframe containing the data, with one column called h containing the daily incidence and one variable called prop_import containing the proportion of imported cases among new infections. additional optional variables are alpha (effective care), beta (proportion of liver stage cure), rho (reporting rate) and omega (intensity of vector control)
relapse frequency
liver clearance rate
blood clearance rate
if TRUE, also returns delta and I estimates
R0/Rc are not calculated for h values which are strictly inferior to h.cutoff
a boolean indicating if the rcd model includes referral. Default (FALSE) is the model without referral for RCD. This parameter is used only if rcd==TRUE.
A dataframe with 3 additional columns: lambda is the transmission rate,
R0 is the basic reproduction number, Rc is the controlled reproduction number.
If lambda = -2, it means that the parameter combination does not correspond to a positive lambda solution with the model.
If lambda = -3, it means the incidence data contains missing values or infinite values or values below h.cutoff.
If return.all=T, delta and I are also included.
If alpha is not provided in df, alpha=0. If beta is not provided in df, beta=1. If rho is not provided in df, rho=1. If omega is not provided in df, omega=1.