GI.seminr: Calculates the intrinsic, forward and backward generation...

In davidchampredon/gitest: Generation intervals

Description

Calculates the intrinsic, forward and backward generation interval distributions for SEmInR epidemic model. The SEmInR model is an epidemiological model that compartments individuals by stages of infections: S for susceptible, E for exposed (infected but not yet infectious), I infectious and R for individuals removed from the model (following recovery and immunity, deaths, etc.). In order to have realistic residency distributions in compartments E and I, these compartments are artificially sub-divided into m for E, and n for I. It is not straightforward to calculate the generation interval distributions for a SEmInR model. This function numericaly solves the three generation interval distributions (intrinsic, backward and forward ones, see [1] for theoretical framework).

Usage

GI.seminr(latent_mean, infectious_mean, R0, nE, nI, cal.times.fwdbck, horizon,
  dt = 0.1, I.init = 1e-05)

Arguments

latent_mean	Numeric. The mean duration of the latent period (in 'E' compartments)
infectious_mean	Numeric. The mean duration of the infectious period (in 'I' compartments)
R0	Numeric. The basic reproduction number
nE	Integer Number of E compatments
nI	Integer. Number of I compatments
cal.times.fwdbck	Numeric vector. Times where the backward and forward generation interval distributions will be calculated
horizon	Numeric. Time until which the simultion is run. User must make sure it is beyond the end of the epidemic, else the calculation of generation interval distributions may be wrong!
I.init	Integer. Initial proportion of infectious individuals. Default value at 1
pop_size	Integer. Constant population size. Default value at 1E4

Value

Returns a named list.

• intrinsic: Intrinsic generation interval distribution. List composed of two elements: tsi, the time since infection vector and density the associated vector of densities.

• fwd: Forward generation interval distribution. List composed of cal.times.fwdbck elements, each one representing the densities of the forward generation interval distribution at the requested calendar times.

• bck: Backward generation interval distribution. List composed of cal.times.fwdbck elements, each one representing the densities of the backward generation interval distribution at the requested calendar times.

• fwd.mean: Mean of the forward generation interval distribution. List composed of cal.times.fwdbck elements, each one representing the mean of the forward generation interval distribution at the requested calendar times.

• bck.mean: Mean of the backward generation interval distribution. List composed of cal.times.fwdbck elements, each one representing the mean of the backward generation interval distribution at the requested calendar times.

• incidence: Incidence modeled from the SEmInR model.

• susceptible: Time series of the number of susceptible individuals modeled from the SEmInR model.

References

[1] Champredon D, Dushoff J. Intrinsic and realized generation intervals in infectious-disease transmission. Proceedings of the Royal Society B: Biological Sciences 2015; 282: 20152026.

davidchampredon/gitest documentation built on May 14, 2019, 5:13 p.m.