Solve SquIP

This function solves the model SquIP using deSolve::ode. It is a wrapper around the derivatives function dSquIP. It does the following:

• N — set a value for the truncation parameter, if no value was passed

• y — set up the the initial values vector as a named vector

• times — set up a mesh over the independent variable \(a\) (age, in days)

• parms — set up a named vector with the parameter values

After solving the equations, it parses the outputs, and returns the values of the dependent variables by name. The wrapper

Usage

solve_SquIP(
  h,
  F_a,
  bday = 0,
  r = 1/200,
  rho = 0.2,
  sigma = 1/365,
  xi = 1/365,
  eta = 1/25,
  mu = 0,
  H = 1000,
  Amax = 730,
  da = 1,
  N = NULL
)

Arguments

h

the force of infection

F_a

a trace function

bday

the cohort birthday

r

the clearance rate for a simple infection

rho

the fraction of incident cases that gets treted

sigma

treatment rate for infected individuals

xi

background drug taking

eta

loss of chemoprotection

mu

population death rate

H

cohort size

Amax

The maximum runtime (in days)

da

The output interval (in days)

N

truncation parameter (maximum MoI): if NULL, then set by rule

Value

a named list of parsed outputs

Parased Outputs

After solving the equations, the solutions are parsed and returned as a named list:

• age — the ages at which the dependent variables were output

• S — Susceptible, a vector

• P — Chemoprotected, a vector

• Ii — Infected \(\times\) MoI, a matrix

• H — Cohort population size

• m_1 — The hybrid variable \(m_1\), mean MoI

• m_2 — The hybrid variable \(m_2\), the second moment of the MoI

• m1— The mean MoI, computed from Ii

• m2— The second moment of the MoI, computed from Ii

• x — The prevalence of infection: \(x = (H-P-S)/H\)

• F_r — The rate of natural clearance: \(r I_1\)

• N — The truncation parameter

• out — The matrix returned by deSolve

See also

SquIP