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Get parameters for generalized Ross-Macdonald mosquito model

Source: R/mosquito_RM.R
get_config_mosquito_RM.Rd

The JSON config file should have 8 entries:

  • stochastic: a boolean value

  • f: scalar

  • q: scalar

  • eip: scalar or vector; see time_varying_parameter for valid formats

  • p: scalar or vector; see time_varying_parameter for valid formats

  • psi: matrix

  • nu: scalar

  • M: vector

  • Y: vector

  • Z: vector

For interpretation of the entries, please read setup_mosquito_RM.

Usage

get_config_mosquito_RM(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)
t <- 10 # days to simulate
p <- 5 # number of patches
EIP <-  rep(5, t)
p_surv <- 0.95
psi <- matrix(rexp(p^2), nrow = p, ncol = p)
psi <- psi / rowSums(psi)
par <- list(
 "stochastic" = FALSE,
 "f" = 0.3,
 "q" = 0.9,
 "eip" = EIP,
 "p" = p_surv,
 "psi" = psi,
 "nu" = 20,
 "M" = rep(100, p),
 "Y" = rep(20, p),
 "Z" = rep(5, p)
)
toJSON(par, pretty = TRUE)
#> {
#>   "stochastic": [false],
#>   "f": [0.3],
#>   "q": [0.9],
#>   "eip": [5, 5, 5, 5, 5, 5, 5, 5, 5, 5],
#>   "p": [0.95],
#>   "psi": [
#>     [0.0109, 0.4982, 0.3906, 0.0685, 0.0318],
#>     [0.1154, 0.0884, 0.1007, 0.5189, 0.1766],
#>     [0.3346, 0.1042, 0.1548, 0.1108, 0.2957],
#>     [0.2731, 0.0114, 0.0447, 0.5172, 0.1536],
#>     [0.4365, 0.0609, 0.107, 0.1918, 0.2038]
#>   ],
#>   "nu": [20],
#>   "M": [100, 100, 100, 100, 100],
#>   "Y": [20, 20, 20, 20, 20],
#>   "Z": [5, 5, 5, 5, 5]
#> }