Logrank

Comparing survival curves of two groups using the log rank test

Description

Comparison of two survival curves can be done using a statistical hypothesis test called the log rank test. It is used to test the null hypothesis that there is no difference between the population survival curves (i.e. the probability of an event occurring at any time point is the same for each population). This function use the Kaplan-Meier procedure to estimate the survival function, so it is mandatory to download
KMPLOT (http://www.mathworks.com/matlabcentral/fileexchange/22293).

My profile on LinkedIN http://it.linkedin.com/in/giuseppecardillo

• Required Products: Statistics Toolbox
• MATLAB release: MATLAB 7.6 (R2008a)
• Other requirements: KMPLOT (http://www.mathworks.com/matlabcentral/fileexchange/22293).

[En Bl]

I get this error:
Matrix dimensions must agree.

Error in ==> logrank at 157
    K=find((table12(:,1)<table(c(I),1) & table12(:,1)>=table(J,1)),1,'last');

I debugged it and J=[] .

[Giuseppe Cardillo]

Perhaps, if you email me the data I can understand the error. I think that your input data matrix are in a wrong format.

[En Bl]

Here is the data:
x1 =
3010 1
1733 1
2797 1
334 0
3678 1
3314 1
4378 1
3253 1
1672 0
3709 1
1642 1
3040 1
2827 1
 and x2 =
1955 1
1808 1
2037 1
3136 1
938 0
3497 1
2858 1
3832 1
3256 0
2933 0
5054 1
927 0
3795 0
4155 1
3304 0

sorry for the late reply.

[Giuseppe Cardillo]

I have corrected the bug and uploaded the new version. Anyway, with all these censored data, it is difficult to assess differences....

[En Bl]

Thanks.

[the cyclist]

It seems to me that this function does not work for the case when none of the data are censored. (That shouldn't be a problem, should it?) For example, using only the first columns of your sample x1 and x2:

>> logrank(x1(:,1),x2(:,1))

causes a crash for me.

[Giuseppe Cardillo]

You are partially right. If you use only the first column, the routine crashes because the informations in the second column are mandatory. If you want no censored data:
>> x1(:,2)=0; x2(:,2)=0; logrank(x1,x2);

Anyway, a bug was present but I fixed it and upload the new version.

[the cyclist]

Thanks for the really quick reply. I appreciate it.

However, the program still crashes for me, with the same error, when I try the syntax you suggest. Maybe the version on the File Exchange is not quite the same as yours?

[Giuseppe Cardillo]

At the moment, there is not on FEX the new uploaded file (this takes 1-2 days). If you contact me in private, I'll send you the file as an attach

[J Rey]

 

[J Rey]

Beautiful, thanks for sharing this. If we use your software for a journal purpose, what reference should we use?

[Giuseppe Cardillo]

Thank you for your comment. If you type on matlab "help logrank" you'll find the reference.

[Sven]

Excellent submission - thank you. One note: the outputs to the function [T1,T2] are actually cleared during computation, so an error is thrown if output is requested. To conform a little bit to the MATLAB stats package, I suggest the following changes:

Line one should change to:
function [h,p] = logrank(varargin)

and the end of the function should set h as follows:
h = p<alpha;

The help section could then say:
% Displays:
% Kaplan-Meier plot
% Log-rank statistics
% Outputs:
% H : statistical significance (true if P<ALPHA)
% P : P-value for log-rank test

[Giuseppe Cardillo]

Dear Sven, thank you for your email.
T1 and T2 are cleared because they don't appear in the output. As everybody can see in the figure (without downloading the function) logrank always prints all needed output parameters. Logrank recalls another function that is kmplot: this function can give back T1 (if you want). Anyway this possibility is hidden because usually you are only interested to the plot.

[the cyclist]

I notice that in the call to kmplot [lines 96-97] in current version, the hard-coded value 0.05 is used, even if alpha is specified differently as an input. Is that correct?

[Giuseppe Cardillo]

Yes it is. The 0.05 put in that lines is a dummy variable. Infact, in that lines logrank invokes kmplot to compute needed tables (i didnt want to duplicate code). If you look inside kmplot it is commented that a piece of code id jumped whan invoked by logrank and in that piece of code alpha is used to compute the confidence interval of survival curve (that is useless in logrank).

[sunbb]

Is there a way to retrieve the Hazard ratio from the output of Logrank or Kmplot function?

[Giuseppe Cardillo]

I have just uploaded a new version of KMPLOT and LOGRANK that compute hazard rate and hazard ratio

[Abhijit]

I'm sorry, but using your software I do not get the p-value for the log-rank test that is consistent with the results of either R or Stata (both of which match). For the test data supplied with the function, I get a p-value of 0.0193, whereas you're getting a p-value of 0.01529. The KM curves are the same, but there is apparently something wrong in your logrank computation.

[Nitin]

I also am having trouble with this function.. the p-values are always slightly off (usually a little higher than what I get using other programs)

[the cyclist]

The logrank calculation here is correct. This code applies the Yates correction in the calculation of the z-score. (Line 207 of my version of the code.) I get 0.0193 from this code when I remove the Yates correction.

[Giuseppe Cardillo]

the cyclist is right. He did a perfect explanation