Date  File  Comment by  Comment  Rating 

10 Oct 2014  Logrank Comparing survival curves of two groups using the log rank test  Giuseppe Cardillo  Thank you Jacob.


30 Sep 2014  Four parameters logistic regression  There and back again Fit data points with a four points logistic regression or interpolate data.  Giuseppe Cardillo  I don't know. I should see your data points 

15 May 2014  Variable Precision Integer Arithmetic Arithmetic with integers of fully arbitrary size. Arrays and vectors of vpi numbers are supported.  Giuseppe Cardillo  Dear John,
if N<2047
Regards 

03 Apr 2014  MyFisher23 A very compact routine for Fisher's exact test on 2x3 contingency table  Giuseppe Cardillo  For negative values, gammaln would return INF so that table is not added to computation. Maybe in previous version of gammaln this is not allowed and it calls error. So rows in Tables matrix with negative values must be erased before to give it to gammaln.


03 Apr 2014  MyFisher23 A very compact routine for Fisher's exact test on 2x3 contingency table  Giuseppe Cardillo  try to add this line before line 108


03 Apr 2014  MyFisher23 A very compact routine for Fisher's exact test on 2x3 contingency table  Giuseppe Cardillo  I checked but on my pc the version is the same and the result is 2x3 matrix Fisher's exact test: 540 tables were evaluated


12 Feb 2014  MyFisher33 A very compact routine to compute Fisher's exact test on a 3x3 matrix  Giuseppe Cardillo  in my PC version it is correct. Bah! I uploaded it again 

12 Feb 2014  MyFisher23 A very compact routine for Fisher's exact test on 2x3 contingency table  Giuseppe Cardillo  Sorry, but it doesn't crash! myfisher23([ 6 6 9 ; 7 7 9])


07 Jan 2014  CODIS Combined DNA Index System: a GUI tool for forensic paternity lawsuit  Giuseppe Cardillo  If you want a flowchart explaining how the code works, it is long as a book and anyway the code is heavly commented so you can look at it. If you want a flowchart explaining how using GUI, I'm surprised because it is very intuitive for Forensic Genetist and there are several demos.
That's all 

28 Nov 2013  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  the Equal Error Rate (EER) is the point on the ROC curve that corresponds to have an equal probability of missclassifying a positive or negative sample. This point is obtained by intersecting the ROC curve with a diagonal of the unit square.


27 Nov 2013  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  Simply... I don't know 

31 Aug 2013  MyBarnard A very compact and fast routine for Barnard's exact test on 2x2 matrix  Giuseppe Cardillo  I dont know. I didnt read the original papers. Maybe now computation power is higher and more accurate and precise 

08 Aug 2013  MyFriedman Friedman test for non parametric two way ANalysis Of VAriance  Giuseppe Cardillo  Sorry, but you should ask this to a statistics...I'm a biochemist that wrote a script using the algorithm of Fisher's least significant difference method (Conover WJ, Practical Nonparametric Statistics (3rd edition). Wiley 1999).


13 Jun 2013  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  I have just uploaded a new roc version. You can set the verbose flag and so you will have not plots and results summary, but only the rocout structure 

05 Jun 2013  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  to be honest, I haven't. I run on R2012a and it works. Maybe you haven't curvefit toolbox 

07 May 2013  Clinical Test Performance The test calculate the performance of a clinical test based on the Bayes theorem  Giuseppe Cardillo  Noam, the message you get is from a previous version of roc.m routine and not from partest.m. When you have a test, using roc curve analysis you can choose a cutoff point (the point above/below which the test is positive) to obtain the max sensitivity or the max specificity or the max cost effective or the max efficiency or the max positive predictive value...and this choosing depends on your specific problem. Actually, I erased partest invoking from roc to simplify the code. Anyway, Partest asks whether you want to input the true prevalence of a disease or not. Partest uses the Bayes'es Theorem and the true prevalence is needed to correctly apply it 

07 May 2013  Five parameters logistic regression  There and back again Fit data points with a five points logistic regression or interpolate data.  Giuseppe Cardillo  this is not true!
slope=(y(end)y(1))/(x(end)x(1)); and so slope can be positive or negative. Moreover, in the starting points vector: st_=[min(y) sign(slope) x(Idx) max(y) 1]; sign(slope) is 1 or +1. So your comment is completely wrong! 

29 Apr 2013  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  As I previously wrote, the main paper you have to read is Hanley JA, McNeil BJ. The Meaning and Use of the Area under a Receiver Operating Characteristic (ROC) Curve. Radiology. 1982 Apr;143(1):2936.
Adding a costant will not affect results. 

12 Apr 2013  HolmSidak ttest HolmSidak ttest for multiple comparisons  Giuseppe Cardillo  I don't agree. If you are so able to write a script, it would not to be so difficult to write 1 line of code to obtain an output struct. You can modify my script as you want: it is open source. 

11 Apr 2013  CODIS Combined DNA Index System: a GUI tool for forensic paternity lawsuit  Giuseppe Cardillo  simply do this:


02 Apr 2013  Four parameters logistic regression  There and back again Fit data points with a four points logistic regression or interpolate data.  Giuseppe Cardillo  sorry, I did an error when I created the zip file. I'm uploading the correct version 

27 Mar 2013  Odds Compute odds and risk ratio on 2x2 matrix  Giuseppe Cardillo  Look well the matrix you gave to odds!


13 Mar 2013  MannWhitneyWilcoxon test MannWhitneyWilcoxon non parametric test for two unpaired groups.  Giuseppe Cardillo  The results are exactly equal: ranksum gives a 2tailed pvalue and mwwtest gives a 1tailed pvalue. If you need a 2tailed pvalue simply multiply 1tailed pvalue by 2 (or, viceversa, divide 2tailed pvalue by 2 if you need 1tailed pvalue).


06 Feb 2013  MyRegression A simple function on LS linear regression with many informative outputs  Giuseppe Cardillo  Why people always talk before read? Robert Did you read "Description" and "Updates" sections before posting your comments? 

25 Jan 2013  MyFriedman Friedman test for non parametric two way ANalysis Of VAriance  Giuseppe Cardillo  This is becaming a private lesson of statistic... I should claim my name on the paper....


23 Jan 2013  MyFriedman Friedman test for non parametric two way ANalysis Of VAriance  Giuseppe Cardillo  So you can't use any statistical test because they require real number and not probabilities... 

23 Jan 2013  MyFriedman Friedman test for non parametric two way ANalysis Of VAriance  Giuseppe Cardillo  I think it is correct. If you want to test if classifiers are in agreement or not you have to use Fleiss'es test. 

23 Jan 2013  MyFriedman Friedman test for non parametric two way ANalysis Of VAriance  Giuseppe Cardillo  yes you are right. Look well if you need Friedman or Fleiss test. 

21 Jan 2013  Wilcoxon test non parametric Wilcoxon test for two paired samples  Giuseppe Cardillo  if you type: wilcoxon it will works showing the example. in the other cases you have to write:
where n1...ni are the values of the first vector and m2...mi are the values of the second vector. 

21 Jan 2013  Wilcoxon test non parametric Wilcoxon test for two paired samples  Giuseppe Cardillo  Madi, I wrote Wilcoxon to manage two vectors and not a matrix.


21 Jan 2013  MyFriedman Friedman test for non parametric two way ANalysis Of VAriance  Giuseppe Cardillo  Madi, SPSS seems to use something like the Bonferroni's correction. When the number of comparisons is very high the Bonferroni's correction is too much conservative (is very difficult to have a statistical difference) 

21 Jan 2013  MyFisher33 A very compact routine to compute Fisher's exact test on a 3x3 matrix  Giuseppe Cardillo  Thank you. If you need fisher onto 2x3 matrix it is on FEX: http://www.mathworks.com/matlabcentral/fileexchange/15399 In any case, you can use Myfisher that it is able to manage any kind of matrix


03 Jan 2013  Superformula generator 2d generator of superformula plot  Giuseppe Cardillo  yes you are right. It was among first functions I wrote. I fixed the bug and upload the new version. 

06 Dec 2012  Wilcoxon test non parametric Wilcoxon test for two paired samples  Giuseppe Cardillo  No it is not normal: ther is a bug on row 152.
I've just upload the correct version


14 Nov 2012  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  By definition, the efficiency is the fraction of subjects that are correctly classified.


08 Jul 2012  MannWhitneyWilcoxon test MannWhitneyWilcoxon non parametric test for two unpaired groups.  Giuseppe Cardillo  1) if you have to compare more than 2 groups mwwtest is not the test for you...you should use the KruskalWallis test. Or if you have "repeated measures" of the same group in different moments you should use the Friedman's test. 2) the concept of the mwwtest is that if the medians are equals the ranks will distribute equally in both groups and they will have a mean equal to n1*n2/2 (and so you can use Zscore...). The acceptance is the same of the Student's ttest because T (or U) is asintotically normally distributed. The magnitude of T is not the only parameter....if you two very large samples sizes also mean(T) will be very large... 

08 Jul 2012  MannWhitneyWilcoxon test MannWhitneyWilcoxon non parametric test for two unpaired groups.  Giuseppe Cardillo  There are two way to compute T: I setup that described by Stanton Glantz in "Primer of biostatistics". U is related to T by a subtraction factor. Zscore is the same because it is (Tmean(T))/std(T): if you use the other computational method, mean(T) and std(T) change of course. This means that both methods are equivalent. To reply to your question I have to put off a basically error that everybody do. The question median(1)>median(2) have to be asked BEFORE performing test, during experimental design project. An example: you discover a new diuretic drug. You want to demonstrate that group 1 treated by drug has a median value or urine (mL/24h) higher than group 2 treated by placebo. So you ask to mwwtest if median(1)>median(2). Of course you could decide to treat group 2 by drug: the result of mwwtest will be the same.
Anyway, don't tell me that you don't know how to ask matlab to compute medians.... 

28 Jun 2012  Fleiss'es kappa Compute the Fleiss'es kappa for multiple raters  Giuseppe Cardillo  no you are right 

22 Jun 2012  Fleiss'es kappa Compute the Fleiss'es kappa for multiple raters  Giuseppe Cardillo  Of course, no. Pj is function of Kj and K1=K2 if and only if sum(x.*(mx)) are equal (m is the numbers of raters). 

18 May 2012  MannWhitneyWilcoxon test MannWhitneyWilcoxon non parametric test for two unpaired groups.  Giuseppe Cardillo  if you like it...


10 May 2012  Logrank Comparing survival curves of two groups using the log rank test  Giuseppe Cardillo  Thank you Jan.


29 Mar 2012  KMPlot Plot the KaplanMeier estimation of the survival function  Giuseppe Cardillo  usually you dont exaclty know when a subject really is censored (in example: a patient died between to followup points or a patient that decided to not present himself to followup). So the best "graphical" choice is to divide the space between to points in to N+1 segments (where N is the censored data between T1 and T2) and to plot a cross for each segments. 

12 Mar 2012  MyFriedman Friedman test for non parametric two way ANalysis Of VAriance  Giuseppe Cardillo  The posthoc is a nonparametric equivalent to Fisher's least significant difference method (Conover WJ, Practical Nonparametric Statistics (3rd edition). Wiley 1999).


07 Mar 2012  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  @Jorge Amaral
so there is not error. If you want contact me by email and we'll try to better understand and to solve 

04 Feb 2012  Logrank Comparing survival curves of two groups using the log rank test  Giuseppe Cardillo  the cyclist is right. He did a perfect explanation 

17 Jan 2012  Fisherâ€™s Exact Test Hypergeometric cumulative distribution (left, right and twotailed) including permutation testing.  Giuseppe Cardillo  I compared your function with the mine using this matrix:
Using Myfisher22(x), the function written by me, the result was:
Using your
??? Maximum variable size allowed by the program is exceeded. Error in ==> fexact>tri2sqind at 325
Same results reducing the complexity to
When I tried on x=[7 12; 8 2].*1000 the pc looped and after 15 minutes I switched it off. Finally I tried it on x=[7 12; 8 2].*100
So before to write "Other implementations on the file exchange are reportedly buggy and are far too slow for problems I'm working on."
Regards 

17 Jan 2012  MyFisher the definitive function for the Fisher's exact and conditional test for any RxC matrix  Giuseppe Cardillo  pvalue=1chi2cdf(chi2,df) 

27 Dec 2011  MyFisher the definitive function for the Fisher's exact and conditional test for any RxC matrix  Giuseppe Cardillo  Considering that chi square is an approximation of Fisher's test, in my opinion it is completely useless to have chi square pvalue. Anyway, if you want, you can simply set up it using this code:


05 Dec 2011  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  this is a problem caused by using a new syntax of matlab that is not supported by your version. Simply do this:


16 Nov 2011  ROCout=roc(varargin) compute a ROC curve  Giuseppe Cardillo  this error shows that something doesnt work on rocdata and so you have not x in your workspace. Now I have changed and uploaded a new version of roc so, if you call roc without arguments, it will run the demo by itself. If you dont want to wait for the FEX updating simply change in the code the default.value in this way default.values = {[165 1;140 1;154 1;139 1;134 1;154 1;120 1;133 1;150 1;... 146 1;140 1;114 1;128 1;131 1;116 1;128 1;122 1;129 1;145 1;117 1;140 1;... 149 1;116 1;147 1;125 1;149 1;129 1;157 1;144 1;123 1;107 1;129 1;152 1;... 164 1;134 1;120 1;148 1;151 1;149 1;138 1;159 1;169 1;137 1;151 1;141 1;... 145 1;135 1;135 1;153 1;125 1;159 1;148 1;142 1;130 1;111 1;140 1;136 1;... 142 1;139 1;137 1;187 1;154 1;151 1;149 1;148 1;157 1;159 1;143 1;124 1;... 141 1;114 1;136 1;110 1;129 1;145 1;132 1;125 1;149 1;146 1;138 1;151 1;... 147 1;154 1;147 1;158 1;156 1;156 1;128 1;151 1;138 1;193 1;131 1;127 1;... 129 1;120 1;159 1;147 1;159 1;156 1;143 1;149 1;160 1;126 1;136 1;150 1;... 136 1;151 1;140 1;145 1;140 1;134 1;140 1;138 1;144 1;140 1;140 1;159 0;... 136 0;149 0;156 0;191 0;169 0;194 0;182 0;163 0;152 0;145 0;176 0;122 0;... 141 0;172 0;162 0;165 0;184 0;239 0;178 0;178 0;164 0;185 0;154 0;164 0;... 140 0;207 0;214 0;165 0;183 0;218 0;142 0;161 0;168 0;181 0;162 0;166 0;... 150 0;205 0;163 0;166 0;176 0;],0,0.05,1}; 
