Simulate genetic data from simple P. falciparum model

Source: R/simulation.R

Simulate genetic data from a simple model of P. falciparum epidemiology and genetics.

sim_falciparum(
  a = 0.3,
  p = 0.9,
  mu = -log(p),
  u = 12,
  v = 10,
  g = 10,
  prob_infection = seq(0.1, 0.01, -0.01),
  duration_infection = dgeom(1:500, 1/200),
  infectivity = 1,
  max_innoculations = 5,
  H = 1000,
  seed_infections = 100,
  M = 1000,
  mig_matrix = diag(length(M)),
  L = 24,
  prob_cotransmission = 0.5,
  time_out = 100,
  report_progress = TRUE
)

Arguments

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 blood-stage infection 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 blood-stage infection and production of gametocytes.
prob_infection

probability a human becomes infected after being bitten by an infected mosquito.
duration_infection

vector specifying probability distribution of time (in days) of a malaria episode.
infectivity

probability a mosquito becomes infected after biting an infective human host.
max_innoculations

maximum number of innoculations that an individual can hold simultaneously.
H

human population size, which is assumed the same in every deme.
seed_infections

vector specifying the initial number of infected humans in each deme.
M

vector specifying mosquito population size (strictly the number of adult female mosquitoes) in each deme.
mig_matrix

migration matrix specifing the daily probability of migrating from each deme to each other deme. Migration must be equal in both directions, meaning this matrix must be symmetric.
L

number of loci. The maximum number of loci is 1000, as at higher numbers haplotypes begin to exceed integer representation (2^L).
prob_cotransmission

probability of mosquito transmitting multiple haplotypes to host.
time_out

vector of times (days) at which output is produced.
report_progress

if TRUE then a progress bar is printed to the console during simuation.