Undefined function or variable 'lgamma'.

Hello experts,

as the title says I have a problem with this undefined 'lgamma'.

I'm trying to run an ANCOVA using the function aoctool() but it stops and throws me that error.

Below I post the entire message:

Undefined function or variable 'lgamma'.

Error in betapdf (line 60)
                  + lgamma (a + b) - lgamma (a) - lgamma (b));

Error in betainv (line 87)
    h     = (betacdf (y_old, a, b) - x) ./ betapdf (y_old, a, b);

Error in finv (line 58)
  inv(k) = ((1 ./ betainv (1 - x(k), n/2, m/2) - 1) * n / m);

Error in aoctool>getyvalues (line 777)
      crit = sqrt(df1 * finv(1-alpha/bonf, df1, df2));

Error in aoctool (line 335)
        [newy, ~, ycov] = getyvalues(allx, allgrps, model, stats, ud);
 

I'm working on MATLAB R2018b.

Is this related with a MATLAB issue or (most likely) it's just me erroneously defining the ANCOVA variables?

Thank you for your help!

Marco

[Adam Danz]

I'm aware of a gamma function but not a function named lgamma.

It is a variable name? Did the function come from some other source outside of Matlab?

[Star Strider]

You need to Contact Support .

I opened betapdf.m in the MATLAB editor, and the last line of the function is 58. That line contains a betaln call, and there are no gamma function calls of any kind in the entire function. (I am using R2020b.)

[NMarco]

@Adam Danz , @Star Strider thank you for your feedback.

The lgamma is from a internal MATLAB code, that's why I'm concerned about this error.

I will contact the support, I guess..

Thanks anyway!

Answer 1

[Walter Roberson]

I see relevant discussion at https://github.com/wichmann-lab/psignifit/issues/4 . The implications there are that you are picking up a third-party toolbox version of finv that is invoking a third-party betainv that is invoking a third-party betapdf that is asking for lgamma that has not been part of MATLAB for a number of years.

The fix would be to move those that third-party finv (and related) out of your MATLAB path.

By the way, the Mathworks long gamma function is gammaln() these days, and is part of basic MATLAB.

[NMarco]

Thank you for your reply.

I explored where the finv and betainv and betapdf were located and all of them were part of SPM12 software (for brain imaging analysis).

>> which finv
C:\Users\me\Desktop\MATLAB\R2018b_windows\spm12\spm12\external\fieldtrip\external\stats\finv.m
>> which betainv
C:\Users\me\Desktop\MATLAB\R2018b_windows\spm12\spm12\external\fieldtrip\external\stats\betainv.m
>> which betapdf
C:\Users\me\Desktop\MATLAB\R2018b_windows\spm12\spm12\external\fieldtrip\external\stats\betapdf.m

Because right now I don't need to use SPM software, I removed that specific folder from the path

rmpath C:\Users\me\Desktop\MATLAB\R2018b_windows\spm12\spm12\external\fieldtrip\external\stats

And now everything works fine.

I really appreciate your help!

[Qiuxia Wu]

I got the same issue when I use pTFCE within Matlab2020b. The problem is, I need to use SPM12, is there anything I could do to fix it?

[NMarco]

Cannot you use one before or after the other? Like, use SPM and than make calculations using pTFE upon removing that folder from the path.

[Walter Roberson]

https://miplab.epfl.ch/BrainHack/Practice/Utilities/spm12/external/fieldtrip/external/stats/ shows that lgamma.m is defined in the external/fieldtrip/external/stats directory that is installed with SPM12.