plot_transmission_intensity: calculate and plot the transmission intensity across the...

In mrc-ide/YFestimation: Estimate ecological niche and two transmission models for yellow fever in Africa.

Description

calculate and plot the transmission intensity across the African endemic region

Usage

plot_transmission_intensity(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, R0_lookup, model_type, shp1, shp0, Countries, colours)

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"
shp1	shapefiles at admin 1
shp0	shape files at country level
Countries	list of countries
colours	vector of length 100
inc_vc3d	incidence of vaccination in array form

Value

map of transmission intensity

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