Iv been writing a program which is to examine a function of CD = f(Re,Ma,Alpha,X1,X2) with the aim being to reduce this to a function relating Fuel Burn = f(X1,X2). Iv written the program fine and provided I give it values for X1 and X2 I get reasonable results but I dont want to define them as the aim is to use the function in an optimisation routine (to optimise X1 and X2). Is there a way of setting Matlab to ignore the missing data and give me a result in these terms?
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I am not sure I understand what you want. If you want a routine that takes your function f(X1,X2) as an input and finds the best (X1,X2) numerically, you could use fminsearch or a solver from Optimization Toolbox. You write x = [X1,X2], meaning you pass a function f(x) that depends on one vector argument x. For details, see the documentation for fminsearch or the Optimization Toolbox documentation.
However, if you are looking for a symbolic solution, then as Walter said, you need Symbolic Math Toolbox.
MATLAB mathematical toolbox documentation