sim_indiv.RdSimulate from simple individual-based model
sim_indiv(max_time = 365, a = 0.3, p = 0.9, mu = -log(p), u = 22, v = 10, g = 10, r = 1/20, b = 1, c = 1, Ih_init = 10, H = 1000, M = 1000, max_infections = 5, migration_matrix = matrix(1), H_auto = FALSE)
| max_time | run simulation for this many days |
|---|---|
| a | human blood feeding rate. The proportion of mosquitoes that feed on humans each day. |
| p | mosquito probability of surviving one day. |
| mu | mosquito instantaneous death rate. mu = -log(p) unless otherwise specified. |
| u | intrinsic incubation period. The number of days from infection to becoming infectious in a human host. |
| v | extrinsic incubation period. The number of days from infection to becoming infectious in a mosquito. |
| g | lag time between human bloodstage infection and production of gametocytes. |
| r | daily recovery rate. |
| b | probability a human becomes infected after being bitten by an infected mosquito. |
| c | probability a mosquito becomes infected after biting an infected human. |
| Ih_init | initial number of infectious humans in each deme. |
| H | human population size in each deme. |
| M | mosquito population size (number of adult female mosquitoes) in each deme. |
| max_infections | maximum number of infections that an individual can hold simultaneously. |
| migration_matrix | matrix giving the probability of migrating from current deme (rows) to new deme (columns). |
| H_auto | if TRUE then human population sizes are chosen automatically based on the migration matrix. In this case the total number of humans is equal to sum(H). |
TODO
# TODO