Matlab: mix-up of built-in and external functions - matlab

Question

Matlab (2015a) is behaving weirdly: a number of builtin functions are not responding as expected. For instance, typing
ttest([1 2], [1 2])
results in
Error using size
Dimension argument must be a positive integer scalar within indexing range.
Error in nanstd (line 59)
tile(dim) = size(x,dim);
Error in ttest (line 132)
sdpop = nanstd(x,[],dim);
If I do a which for each of these functions:
which size
which nanstd
which ttest
I get, respetively:
built-in (C:\Program Files\MATLAB\R2015a\toolbox\matlab\elmat\size)
C:\Program Files\MATLAB\R2015a\toolbox\stats\eml\nanstd.m
C:\Program Files\MATLAB\R2015a\toolbox\stats\stats\ttest.m
Each of these files looks fine, except that size.m has each one of its rows commented out.
What could be the problem here?

Answer 1

Perhaps related to your problem:
ttest for R2013a makes the following call:
sdpop = nanstd(x,[],dim);
The helpfile for R2013a version of nanstd states:
Y = nanstd(X,FLAG,DIM) takes the standard deviation along dimension DIM of X.
On the other hand, nanstd in the 2005 nansuite package downloaded off Mathworks file exchange states:
FORMAT: Y = nanstd(X,DIM,FLAG)
Notice how DIM and FLAG are reversed!
If I call R2013a's ttest such that it makes a call to the old, 2005 nansuite function nanstd, Matlab generates an error similar to yours:
Error using size
Dimension argument must be a positive integer scalar within indexing range.
Error in nanmean (line 46)
count = size(x,dim) - sum(nans,dim);
Error in nanstd (line 54)
avg = nanmean(x,dim);
Error in ttest (line 132)
sdpop = nanstd(x,[],dim);
If [] is passed as DIM instead of FLAG, then nanstd's call to size(x, DIM) triggers an error because [] is not a positive integer scalar. If something like this is the cause, the broader question is, what's going on with your Matlab install or setup or downloads or whatever such that you're calling archaic code? Or why is that archaic code even around? I don't know at what point in Matlab's release history that nanstd(x, FLAG, DIM) became supported (instead of simply nanstd(x, DIM))?
Archive: below is my old answer which misdiagnosed your problem
Both of your sample vectors x and y are the same (i.e. [1,2]). The estimated variance of the difference is 0, and all your stats are going to blow up with NaN.
Do the stats step by step, and it will be clear what's going on.
x = [1; 2]; % Data you used in the example.
y = [1; 2]; % Data you used in the example.
z = x - y; % Your call to ttest tests whether this vector is different from zero at a statistically significant level.
Now we do all the stats on z
r.n = length(z);
r.mu = mean(z);
r.standard_error = sqrt(var(z,1) / (r.n-1)); % For your data, this will be zero since z is constant!
r.t = r.mu ./ r.standard_error; % For your data, this will be inf because dividing by zero!
r.df = r.n - 1;
r.pvals(r.t >= 0) = 2 * (1 - tcdf(r.t(r.t>=0), r.df)); % For your data, tcdf returns NaN and this all fails...
r.pvals(r.t < 0) = 2 * tcdf(r.t(r.t<0), r.df);
etc...
This should match a call to
[h, p, ci, stats] = ttest(x-y);