Simulation of a compartmental infectious disease transmission model with 3 types of hosts and intervention

This model allows for the simulation of an ID with 3 types of hosts. Groups are assumed to be children, adults and elderly. Intervention can be applied to any of the groups for a certain duration.

simulate_idcontrolmultigroup_ode(
  Sc = 1000,
  Ic = 0,
  Sa = 1000,
  Ia = 1,
  Se = 1000,
  Ie = 0,
  bcc = 3e-04,
  bca = 1e-04,
  bce = 1e-04,
  bac = 1e-04,
  baa = 3e-04,
  bae = 1e-04,
  bec = 1e-04,
  bea = 1e-04,
  bee = 3e-04,
  gc = 0.1,
  ga = 0.1,
  ge = 0.1,
  wc = 0,
  wa = 0,
  we = 0,
  mc = 0.001,
  ma = 0.01,
  me = 0.1,
  f1 = 0,
  T1_start = 50,
  T1_end = 150,
  f2 = 0,
  T2_start = 50,
  T2_end = 150,
  f3 = 0,
  T3_start = 50,
  T3_end = 150,
  tmax = 600
)

Arguments

Sc

: initial number of susceptible children : numeric

Ic

: initial number of infected children : numeric

Sa

: initial number of susceptible adults : numeric

Ia

: initial number of infected adults : numeric

Se

: initial number of susceptible elderly : numeric

Ie

: initial number of infected elderly : numeric

bcc

: rate of transmission to susceptible child from infected child : numeric

bca

: rate of transmission to susceptible child from infected adult : numeric

bce

: rate of transmission to susceptible child from infected elderly : numeric

bac

: rate of transmission to susceptible adult from infected child : numeric

baa

: rate of transmission to susceptible adult from infected adult : numeric

bae

: rate of transmission to susceptible adult from infected elderly : numeric

bec

: rate of transmission to susceptible elderly from infected child : numeric

bea

: rate of transmission to susceptible elderly from infected adult : numeric

bee

: rate of transmission to susceptible elderly from infected elderly : numeric

gc

: rate at which infected children recover or die : numeric

ga

: rate at which infected adults recover or die : numeric

ge

: rate at which infected elderly recover or die : numeric

wc

: rate at which immunity in children wanes : numeric

wa

: rate at which immunity in adults wanes : numeric

we

: rate at which immunity in elderly wanes : numeric

mc

: fraction of infected children who die : numeric

ma

: fraction of infected adults who die : numeric

me

: fraction of infected elderly who die : numeric

f1

: strength of intervention applied to children, between 0 and 1 : numeric

T1_start

: start of intervention applied to children : numeric

T1_end

: end of intervention applied to children : numeric

f2

: strength of intervention applied to adults, between 0 and 1 : numeric

T2_start

: start of intervention applied to adults : numeric

T2_end

: end of intervention applied to adults : numeric

f3

: strength of intervention applied to elderly, between 0 and 1 : numeric

T3_start

: start of intervention applied to elderly : numeric

T3_end

: end of intervention applied to elderly : numeric

tmax

: maximum simulation time : numeric

Value

This function returns the simulation result as obtained from a call to the deSolve ode solver.

Details

A compartmental ID model with several states/compartments is simulated as a set of ordinary differential equations. The function returns the output from the odesolver as a matrix, with one column per compartment/variable. The first column is time. The model implement basic processes of infection, recovery and death. Waning immunity is also implemented. Control is applied, which reduces transmission by the indicated proportion, during times tstart and tend. Control can be applied at different levels to the different groups.

Warning

This function does not perform any error checking. So if you try to do something nonsensical (e.g. any negative values or fractions > 1), the code will likely abort with an error message.

Author

Andreas Handel

Examples

  # To run the simulation with default parameters just call the function:
  result <- simulate_idcontrolmultigroup_ode()