You should just be able to do that. Make sure all functions are included in the Matlab path and are in their own separate files.

[ MODIFIED to use the terminology 'nested functions'] Hi Sterling, You can define nested functions within other functions as in the following example. function z = xsixth(x) z = xsquare(x).^3; function a = xsquare(b) a = b.^2 end end Here the nested function xsquare is local to the function xsixth, and calling xsquare from the command line results in an error. If for some reason you need the output of (in this example) xsquare, you can either define it as a separate function and no longer a nested function or do something like the following function [z y] = xsixth(x) z = xsquare(x).^3; y = xsquare(x); function a = xsquare(b) a = b.^2 end end with the extra output y pulling out the result.

If the functions are nested, then variables are carried over into all the nested functions and the variable names should turn green to indicate that they are available everywhere (similar to global variables). Make sure your all your end's are in the right place. function GUI Location=[]; function nested1 Location='myFile'; end function nested2 Location='newFile'; end end

If you define a function with output arguments and you then want to get those outputs then of course you will also need to call the function with those output arguments. This is true for every kind of function, including nested functions. function [..] = rodent_trial2(rodent, trial_no) [~,~,out] = fn_all_data(); % you need to call the function with the output arguments!!! idx = out.X>=0 & out.Y>=0; Q1 = out(idx,:); .. %nested function function [X, Y, all_data] = fn_all_data() % if you defined output arguments here. % code all_data = .. whatever end end But I suspect that you were actually attempting to share the data via the parent workspace, perhaps something like this. function [..] = rodent_trial2(rodent, trial_no) all_data = []; % must be defined in the parent workspace before calling nested function! fn_all_data() % no output arguments! idx = all_data.X>=0 & all_data.Y>=0; Q1 = all_data(idx,:); .. %nested function function fn_all_data() % no output arguments! % code all_data = .. whatever end end This is explained here: https://www.mathworks.com/help/matlab/matlab_prog/nested-functions.html#f4-73993

You want to put the nested function inside another function (as the term nested implies) and then call the top-level function. As an example, create the following file, evenodd.m function [even, odd] = evenodd(x) even = evensamples(x); odd = oddsamples(x); function even = evensamples(x) even = x(1:2:end); end function odd = oddsamples(x) odd = x(2:2:end); end end Save the above file evenodd.m in a folder on the MATLAB path and then call >> x = randn(16,1); >> [even,odd] = evenodd(x); Note that evenodd() calls two nested functions evensamples() and oddsamples()

"I do not quite see the need for the 'function nma_project_511()'" There are two main ways to pass extra parameters to functions that are provided to ODE or optimization routines: https://www.mathworks.com/help/matlab/math/parameterizing-functions.html https://www.mathworks.com/help/optim/ug/passing-extra-parameters.html As you can see, using nested functions is one way of parameterizing a function. The author of that code chose to use a nested function (not required, but a design choice). A nested function requires a parent function. Ergo, the function NMA_PROJECT_511() is required to make the code work, otherwise RHS() would not be a nested function. PS: If you have a background in some other languages then you might be used to variables magically being accessible in other workspaces based on very broad and generous scoping rules. MATLAB is not other languages: unless you specifically do something to make it happen (e.g. pass arguments or write a nested function) variables are not accessible in other functions' workspaces.