Skip to contents

Get parameters for MOI human model

Source: R/humans_MOI.R
get_config_humans_MOI.Rd

The JSON config file should have 9 entries:

  • stochastic: a boolean value

  • theta: matrix (row major)

  • wf: vector

  • H: vector

  • MOI: matrix (row major)

  • b: scalar

  • c: scalar

  • r: scalar

  • sigma: scalar

For interpretation of the entries, please read setup_humans_MOI.

Usage

get_config_humans_MOI(path)

Arguments

path

a file path to a JSON file

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)
MOI <- matrix(0, nrow = 10, ncol = n)
MOI[1, ] <- H
par <- list(
 "stochastic" = FALSE,
 "theta" = theta,
 "wf" = rep(1, n),
 "H" = H,
 "MOI" = MOI,
 "b" = 0.55,
 "c" = 0.15,
 "r" = 1/200,
 "sigma" = 1
)
toJSON(par, pretty = TRUE)
#> {
#>   "stochastic": [false],
#>   "theta": [
#>     [0.3343, 0.1328, 0.0575, 0.4622, 0.0132],
#>     [0.0129, 0.6613, 0.167, 0.0265, 0.1322],
#>     [0.3156, 0.1031, 0.2141, 0.3636, 0.0036],
#>     [0.1652, 0.1665, 0.4538, 0.1542, 0.0602],
#>     [0.2229, 0.0216, 0.0691, 0.2459, 0.4405],
#>     [0.5604, 0.0019, 0.1993, 0.1353, 0.103]
#>   ],
#>   "wf": [1, 1, 1, 1, 1, 1],
#>   "H": [10, 10, 10, 10, 10, 10],
#>   "MOI": [
#>     [10, 10, 10, 10, 10, 10],
#>     [0, 0, 0, 0, 0, 0],
#>     [0, 0, 0, 0, 0, 0],
#>     [0, 0, 0, 0, 0, 0],
#>     [0, 0, 0, 0, 0, 0],
#>     [0, 0, 0, 0, 0, 0],
#>     [0, 0, 0, 0, 0, 0],
#>     [0, 0, 0, 0, 0, 0],
#>     [0, 0, 0, 0, 0, 0],
#>     [0, 0, 0, 0, 0, 0]
#>   ],
#>   "b": [0.55],
#>   "c": [0.15],
#>   "r": [0.005],
#>   "sigma": [1]
#> }