Description Usage Arguments Value
View source: R/diagnostic_functions.R
calculate and plot the transmission intensity across the African endemic region
1 2 3 | 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)
|
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 |
map of transmission intensity
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