sutherland_model: Sutherland et al. Model to Estimate Impact of Ending the BCG...

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

Description

Sutherland et al. Model to Estimate Impact of Ending the BCG School Scheme

Usage

sutherland_model(Data = sutherland_data,
  incidence_rates = sutherland_incidence_rates, Rates.Per = 1e+05,
  Cohort.Length = 5, Data.start = 1969,
  Annual.TB.Decrease.Yearly = TB_decrease_as_matrix(sutherland_TB_decrease),
  Percentage.Year.One = NULL, trans_params = sutherland_trans_params(),
  Sym.Lag = 2, update_chains = FALSE)

Arguments

Data	Data used by Sutherland et al. analysis. See sutherland_data.
incidence_rates	A list of Incidence rates (per 100,000) for the BCG vaccinated and unvaccinated population. See sutherland_incidence_rates for details.
Rates.Per	The number of people by which to produce rates, defaults to 100,000 as in Sutherland et al.
Cohort.Length	Numeric, the lengh of time spent in each cohort, defaults to 5 years as in Sutherland et al.
Data.start	Numeric, the year the first data point originates, defaults to 1969 as in Sutherland et al.
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.
Percentage.Year.One	Numeric, the percentage of a generation that occur in the first year. Fitted via, fit_model_to_data.
trans_params	A funciton for estimating the transmission parameters (expected total secondary notifications, the size of the first generation, and the average interval between a primary case and all secondary cases). Defailts to sutherland_trans_params.
Sym.Lag	Numeric, the generation time between infection and symtoms. Must be smaller or equal to the Cohort.Length. Defaults to sutherland_gen_time.
update_chains	Logical, defaults to FALSE. Should the transmission chain model be updated or used as found in Sutherland et al.

Value

A list of tables reproducing the results presented in Sutherland et al. The final table estimates the total number of additional cases from ending the shcheme. In order to provide a complete estimate each 5 year estimate has been multiplied by the cohort length. In addition the primary additional impacts and total secondary notifications arising from each year are also output based on paper revisions.

Examples

sutherland_model(Percentage.Year.One = 0.764)

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