The JSON config file should have 8 entries:
stochastic: a boolean value
theta: matrix (row major)
wf: vector
H: vector
SIR: matrix (row major)
b: scalar
c: scalar
gamma: scalar
For interpretation of the entries, please read setup_humans_SIR.
Value
a named list
Examples
# to see an example of proper JSON input, run the following
library(jsonlite)
n <- 6 # number of human population strata
p <- 5 # number of patches
theta <- matrix(rexp(n*p), nrow = n, ncol = p)
theta <- theta / rowSums(theta)
H <- rep(10, n)
SIR <- matrix(0, nrow = n, ncol = 3)
SIR[, 1] <- H
par <- list(
"stochastic" = FALSE,
"theta" = theta,
"wf" = rep(1, n),
"H" = H,
"SIR" = SIR,
"b" = 0.55,
"c" = 0.15,
"gamma" = 1/7
)
toJSON(par, pretty = TRUE)
#> {
#> "stochastic": [false],
#> "theta": [
#> [0.1675, 0.2697, 0.2, 0.2614, 0.1014],
#> [0.0778, 0.5656, 0.1881, 0.1361, 0.0325],
#> [0.019, 0.2514, 0.1755, 0.3766, 0.1775],
#> [0.1063, 0.064, 0.6656, 0.0711, 0.0931],
#> [0.2622, 0.0796, 0.0912, 0.4596, 0.1074],
#> [0.1893, 0.1131, 0.0709, 0.1661, 0.4606]
#> ],
#> "wf": [1, 1, 1, 1, 1, 1],
#> "H": [10, 10, 10, 10, 10, 10],
#> "SIR": [
#> [10, 0, 0],
#> [10, 0, 0],
#> [10, 0, 0],
#> [10, 0, 0],
#> [10, 0, 0],
#> [10, 0, 0]
#> ],
#> "b": [0.55],
#> "c": [0.15],
#> "gamma": [0.1429]
#> }