sutherland_trans_params: Estimate Transmission chain parameters using Sutherland et...

In seabbs/AssessBCGPolicyChange: Assess the Evidence Used to Motivate the 2005 Change in BCG Vaccination Policy

Description

Estimate Transmission chain parameters using Sutherland et al.s Approach

Usage

  sutherland_trans_params(Annual.TB.Decrease.Yearly = TB_decrease_as_matrix(sutherland_TB_decrease),
  Sym.Lag = sutherland_gen_time, Sutherland = TRUE, Repro.No = NULL,
  Cohort.Length = 5, update_chains = FALSE)

Arguments

Annual.TB.Decrease.Yearly	Matrix of average yearly decreases in TB with each column representing an age group (15-19, 20-24, 25-29). Row names must be the year, starting from Data.start. Defaults to using sutherland_TB_decrease.
Sym.Lag	Numeric, the generation time between infection and symtoms. Must be smaller or equal to the Cohort.Length. Defaults to sutherland_gen_time.
Sutherland	Logical, defaults to TRUE. Whether or not to use Sutherland et al.'s assumption for estimating the basic reproduction number.
Repro.No	If Sutherland is FALSE sets the basic reproduction number used to estimate the transmission chain parameters.
Cohort.Length	Numeric, the lengh of time spent in each cohort, defaults to 5 years as in Sutherland et al.
update_chains	Logical, defaults to FALSE. Should the transmission chain model be updated or used as found in Sutherland et al.

Value

A dlist containing the expected total secondary notifications (Expected.Total.Sec.Note), the size of the first generation (Size.First.Gen) and the average interval to all secondary cases (Avg.Int.All.Sec).

Examples

# Orginal model
sutherland_trans_params()

# Updated model
sutherland_trans_params(update_chains = TRUE)

seabbs/AssessBCGPolicyChange documentation built on Dec. 24, 2019, 11:56 a.m.