ode tests in julia

ode_test1.jl

using DifferentialEquations
using ParameterizedFunctions
using DataFrames


type OneCmtOral{T} <: DEDataArray{T}
    x::Array{T,1}
    KA::T
    CL::T
    V::T
end

function onecmtoral(t, u, du)
  du[1] = -u.KA*u[1]
  du[2] =  u.KA*u[1] - u[2]*(u.CL/u.V)
end

# try changing the overall drug clearance to 3x
function affect!(integrator)
  for c in user_cache(integrator)
    c.CL = c.CL*3.0
  end
end

const tstop1 = [10.]

function condition(t,u,integrator) # Event when event_f(t,u) == 0
   t in tstop1
end

cb = DiscreteCallback(condition, affect!, (true, true))
u0 = OneCmtOral([200.0;0.0], 1.0, 1.3, 12.3)
tspan = (0.0,20.0)
prob = ODEProblem(onecmtoral,u0,tspan)


function sim(prob, cb, tstops)
  # saveat does not seem to be working?
  #solve(prob, callback = cb, tstops = [10.], saveat=0.25)
  #solve(prob, callback = cb, tstops = [10.], saveat=collect([0.:0.25:12.]))
  # stop where the discrete condition occurs to make sure the changes happen
  solve(prob, callback = cb, tstops = tstops)
end

function get_params(sol)
  CL = zeros(length(sol))
  V = zeros(length(sol))
  pred = zeros(length(sol))
  for s in 1:length(sol)
    CL[s] = sol[s].CL
    V[s] = sol[s].V
    pred[s] = sol[s][2]
  end

  DataFrame(CL = CL, V = V, TIME = sol.t, pred = pred )
end

sol = sim(prob, cb, tstop1)

@time res = get_params(sim(prob, cb, tstop1))