Simulate genetic data from simple P. falciparum model

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 = 0.1,
  duration_infection = dgeom(1:500, 1/100),
  infectivity = 0.1,
  max_infections = 5,
  H = 1000,
  seed_infections = 100,
  M = 1000,
  mig_matrix = diag(length(M)),
  L = 24,
  mean_oocysts = 2,
  mean_products = 5,
  recomb_prob = 0.1,
  max_time = max(sample_dataframe$time),
  sample_dataframe = data.frame(deme = 1, time = 365, n = 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. Can be a scalar or a vector. If a vector then each value applies over subsequent infections, creating possibility of an exposure-driven immunity model.

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_infections

maximum number of infections that an individual can hold simultaneously.

H

human population size, which is assumed to be 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).

mean_oocysts

the average number of viable oocysts generated from gametocytes upon biting an infective host. The actual number of oocysts is generated from a zero-truncated Poisson distribution with this mean.

mean_products

parasite genotypes are passed from mosquito to host by sampling N times with replacement from the available oocysts products (the available number of products is 4 times the number of oocysts). N is drawn independently for each infection from a zero-truncated Poisson distribution with mean given by mean_products. Hence, large values of this parameter increase the chance of co-transmission of multiple genotypes, while small values increase the chance of picking up just a single genotype.

recomb_prob

the probability of a recombination breakpoint between any sequential pair of loci. Assumed to be the same for all loci.

max_time

number of days in the simulation.

sample_dataframe

a dataframe specifying outputs from the model. Must contain the following three columns:

1. deme: which numbered deme to sample from.

2. time: the day on which samples are taken.

3. n: the number of hosts to randomly sample (without replacement) from the population.

report_progress

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