fmincon Results!

costFunction.m
- bypasses MATLAB error in which certain values of v,p,h,s0 would cause
ode45 (or any other numerical solver, including Euler's Method) to
evaluate infinite and therefore produce a matrix SX whose size does not
match x_data

costFunctionrad.m
- similar to costFunction.m, but takes in additional arguments
(specifically, probability of survival) to account for radiation
- calls on simulODErad rather than simulODE

eqn0.m and eqn1.m now take an additional parameter d

euler2theta.m
- exact same functionality as euler2.m, but takes in a vector theta=[v;
p; h; si; d] instead of individual parameters as input arguments

euler4.m
- same functionality as euler3.m, but does not take any input arguments;
instead, just change the values for v, p, h, x0, s0, t0, tf, and n in
the file each time it is run

fminconResults**.mat
- See "Optimization Summary.xlsx" for a description of solver (fmincon
or fminsearch), options, and initial values used to obtain each of the
.mat files
- costs{} contains the cost for values of [v; p; h; s0; other
parameters] in theta_solves{}, which were determined by
fmincon/fminsearch from initial values theta_initials

fminconScript.m
- this is a *script*, not a function
- contains options and arguments needed to run fmincon

fminconScriptLoop.m
- this is a *script*, not a function
- similar to fminconScript.m, but loops through different theta_intial
values

LoopThetaInitial.m
- now deprecated - use fminconScriptLoop.m instead

simulODE.m
- now takes in a fifth parameter theta(5)=d

simulODErad.m
- Includes third differential equation f2'(t) to account for senescent
cells as a result of radiation
- x = total tumor cell population
- f0 = fraction of stem cells
- f1 = 1-f0-f2 = fraction of active nonstem cells
- f2 = fraction of senescent cells
- q = rate at which nonstem cells become senescent
- d = rate at which senescent cells die

Untitled.m
- *script*
- takes results (costs{}, theta_initials{}, and theta_solves{}) produced
by fminconScriptLoop.m and creates a summary of results in a workspace
variable called fminconResults** where ** is the name of the run
- Column 2 = index of cost (column 3) and theta_solves values (columns
4-7)

OptimTool.m, data.mat, and filename.mat
- Can be ignored
- Contain random data from non-specific runs