Final ODE Model

costFunction.m, costFuncionrad.m
- new function naming convention: x(t) = total population, f0(t) =
fraction of stem cells (species 0), f2(t) = fraction of senescent cells
(species 2) *note: f1(t) = 1 - f0(t) - f2(t)
- ode45 now solves a system of three differential equations as specified
in simulODE, and therefore takes three initial conditions as inputs:
x(0), f0(0), and f2(0)
- f2(0) = 0 if no radiation treatment is given
- f2(0) = 1 - probability of survival *note: this necessitates an
additional input argument (Ps) to costFunctionrad.m
- ode45 now outputs a three column matrix XF0F2 = [x(t); f0(t); f2(t)]
- note: theta is now in a different order that I think better reflects
their importance: p, h, f0_i, v, d1, d2, r.  *f0_i = f0(0)
- both costFunction and costFunctionrad now call the same simulODE.m
function (simulODErad is now deprecated)

costFunctionLoop.m and costFunctionradLoop.m calculate the costs of
4,459,000 different parameter (theta) values. In other words, it is a
brute force optimization. The idea is to better understand how the
parameter values affect cost by noticing patterns (i.e. plot the cost on
the y-axis against the index of the cost calculated on the x-axis). Then
take the best costs and further refine through fminsearch/fmincon

euler2theta.m
- needs fixing still
- now takes all 7 parameters, but the differential equations eqn0, eqn1,
and the yet-to-be-created eqn2 have not been updated to reflect the
final ode model

euler4.m
- as this file is solely used as a test-bed, the changes are not worth
documenting and can be ignored

euler5.m
- reflects final ODE model
- takes all the parameters as one argument theta
- the file contains all three differential equations (i.e. it uses
internal functions)

simulODE.m
- updated to reflect final ODE model

simulODErad.m
- now deprecated