fun_calc_transmission_Africa: calculate the probability of detection for both models

Description Usage Arguments Value

View source: R/transmission_functions.R

Description

calculate the probability of detection for both models

Usage

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fun_calc_transmission_Africa(x, ii, seroout, params, dat, t0_vac_africa,
  dim_year, dim_age, p_prop_3d, P_tot_2d, inc_v3d, pop1, vc2d, varsin_nc,
  polydeg = 5, R0_lookup, model_type)

Arguments

x

glm covariates

ii

indices of glm parameters

seroout

processed serology data

params

estimated parameters for both serology and GLM from either R0 or Foi model

dat

environmental and occurrence data

t0_vac_africa

time of first vaccination for admins in Africa endemic zone

dim_year

years of interest

dim_age

ages of interest

p_prop_3d

prpoprtion of population in array form

P_tot_2d

total population in 2d form

pop1

population data

vc2d

vaccination coverages in 2d form

varsin_nc

covariates in use

polydeg

degree of polynomial, defaults to 5

R0_lookup

table of R0 and infection numbers for each admin

model_type

either "R0" or "Foi"

inc_vc3d

incidence of vaccination in array form

Value

transmission_whole, transmission intensty across Africa endemic zone


mrc-ide/YFestimation documentation built on March 13, 2021, 1:40 p.m.