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Fix. Default password should be [] not an empty string
author Daniele Nicolodi <nicolodi@science.unitn.it>
date Wed, 07 Dec 2011 17:29:47 +0100
parents f0afece42f48
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Daniele Nicolodi <nicolodi@science.unitn.it>
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1 % SPCORR calculate Spearman Rank-Order Correlation Coefficient
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Daniele Nicolodi <nicolodi@science.unitn.it>
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2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Daniele Nicolodi <nicolodi@science.unitn.it>
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3 % Description:
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Daniele Nicolodi <nicolodi@science.unitn.it>
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4 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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5 % SPCORR calculates Spearman Rank-Order Correlation Coefficient
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Daniele Nicolodi <nicolodi@science.unitn.it>
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6 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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7 % CALL:
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Daniele Nicolodi <nicolodi@science.unitn.it>
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8 % [rs,pValue,TestRes] = spcorr(y1,y2,alpha)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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9 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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10 % INPUT:
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Daniele Nicolodi <nicolodi@science.unitn.it>
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11 % - y1 and y2 are data series
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Daniele Nicolodi <nicolodi@science.unitn.it>
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12 % - alpha is the significance level. Default 0.05
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Daniele Nicolodi <nicolodi@science.unitn.it>
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13 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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14 % OUTPUT:
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Daniele Nicolodi <nicolodi@science.unitn.it>
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15 % - rs: Spearman rank-order correlation coefficient
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Daniele Nicolodi <nicolodi@science.unitn.it>
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16 % - pValue: Probability associated with the calculated rs in the
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Daniele Nicolodi <nicolodi@science.unitn.it>
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17 % hypothesis that the correlation between y1 and y2 is zero
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Daniele Nicolodi <nicolodi@science.unitn.it>
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18 % - TestRes: True or false on the basis of the test results. The null
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Daniele Nicolodi <nicolodi@science.unitn.it>
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19 % hypothesis for the test is that the two series y1 and y2 are
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Daniele Nicolodi <nicolodi@science.unitn.it>
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20 % uncorrelated.
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Daniele Nicolodi <nicolodi@science.unitn.it>
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21 % TestRes = 0 => Do not reject the null hypothesis at significance
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Daniele Nicolodi <nicolodi@science.unitn.it>
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22 % level alpha. (pValue >= alpha)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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23 % TestRes = 1 => Reject the null hypothesis at significance level
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Daniele Nicolodi <nicolodi@science.unitn.it>
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24 % alpha. (pValue < alpha)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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25 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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26 % NOTE:
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Daniele Nicolodi <nicolodi@science.unitn.it>
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27 % The statistic of Spearman rank-order correlation coefficient is
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Daniele Nicolodi <nicolodi@science.unitn.it>
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28 % well approximated by a Student t distribution. Hypothesis test is
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Daniele Nicolodi <nicolodi@science.unitn.it>
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29 % then based on such statistic.
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Daniele Nicolodi <nicolodi@science.unitn.it>
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30 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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31 % References:
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Daniele Nicolodi <nicolodi@science.unitn.it>
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32 % [1] W. H. Press, S. A. Teukolsky, W. T. Vetterling, B. P. Flannery,
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Daniele Nicolodi <nicolodi@science.unitn.it>
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33 % Numerical Recipes 3rd Edition: The Art of Scientific Computing,
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Daniele Nicolodi <nicolodi@science.unitn.it>
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34 % Cambridge University Press; 3 edition (September 10, 2007)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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35 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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36 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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37 % L Ferraioli 06-12-2010
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Daniele Nicolodi <nicolodi@science.unitn.it>
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38 %
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Daniele Nicolodi <nicolodi@science.unitn.it>
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39 % $Id: spcorr.m,v 1.2 2011/07/06 14:42:26 luigi Exp $
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Daniele Nicolodi <nicolodi@science.unitn.it>
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40 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Daniele Nicolodi <nicolodi@science.unitn.it>
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41 function [rs,pValue,TestRes] = spcorr(y1,y2,alpha)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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42
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Daniele Nicolodi <nicolodi@science.unitn.it>
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43 % check size
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Daniele Nicolodi <nicolodi@science.unitn.it>
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44 if size(y1)~=size(y2)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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45 error('y1 and y2 must have the same size')
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Daniele Nicolodi <nicolodi@science.unitn.it>
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46 end
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47
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Daniele Nicolodi <nicolodi@science.unitn.it>
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48 % check input
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Daniele Nicolodi <nicolodi@science.unitn.it>
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49 if isempty(alpha)
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Daniele Nicolodi <nicolodi@science.unitn.it>
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50 alpha = 0.05;
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Daniele Nicolodi <nicolodi@science.unitn.it>
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51 elseif alpha > 1
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Daniele Nicolodi <nicolodi@science.unitn.it>
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52 alpha = alpha/100;
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53 end
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54
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55
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Daniele Nicolodi <nicolodi@science.unitn.it>
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56 % calculate rank for y1 and y2
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Daniele Nicolodi <nicolodi@science.unitn.it>
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57 [r1,s1] = utils.math.crank(y1);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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58 [r2,s2] = utils.math.crank(y2);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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59
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Daniele Nicolodi <nicolodi@science.unitn.it>
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60 n = numel(y1);
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61
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Daniele Nicolodi <nicolodi@science.unitn.it>
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62 dv = (r1-r2).^2;
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63
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Daniele Nicolodi <nicolodi@science.unitn.it>
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64 dd = sum(dv);
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65
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Daniele Nicolodi <nicolodi@science.unitn.it>
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66 en = n*n*n-n;
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67
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Daniele Nicolodi <nicolodi@science.unitn.it>
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68 sq1 = sqrt(1-s1/en);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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69 sq2 = sqrt(1-s2/en);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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70
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Daniele Nicolodi <nicolodi@science.unitn.it>
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71 % calculate Spearman rank-order correlation coefficient
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Daniele Nicolodi <nicolodi@science.unitn.it>
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72 rs = (1 - 6*(dd + s1/12 + s2/12)/en)/(sq1*sq2);
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73
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Daniele Nicolodi <nicolodi@science.unitn.it>
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74 % transform rs in t which is according Student's distribution with n-2
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Daniele Nicolodi <nicolodi@science.unitn.it>
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75 % degrees of freedom
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Daniele Nicolodi <nicolodi@science.unitn.it>
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76 t = rs*sqrt((n-2)/(1-rs^2));
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77
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Daniele Nicolodi <nicolodi@science.unitn.it>
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78 % Indicated with f(x) the prob. distribution function (Student's t in the
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Daniele Nicolodi <nicolodi@science.unitn.it>
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79 % present caase). The probability Pr(k <= t) is proportional to the
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Daniele Nicolodi <nicolodi@science.unitn.it>
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80 % integral Int_(-t,t)[f(x)dx]. For a Student's distribution such integral
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Daniele Nicolodi <nicolodi@science.unitn.it>
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81 % is represeted by the Beta incomplete function
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Daniele Nicolodi <nicolodi@science.unitn.it>
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82 % Pr(k <= t) = betainc(df/(df+t^2),df/2,1/2,'upper')
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Daniele Nicolodi <nicolodi@science.unitn.it>
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83 % As a consequence Pr(k > t) = 1 - Pr(k <= t) which in Matlab can be
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Daniele Nicolodi <nicolodi@science.unitn.it>
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84 % effectively calculated as
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Daniele Nicolodi <nicolodi@science.unitn.it>
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85 % Pr(k > t) = betainc(df/(df+t^2),df/2,1/2,'lower')
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Daniele Nicolodi <nicolodi@science.unitn.it>
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86 % Which provides the probability of finding a value grater than t if our
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Daniele Nicolodi <nicolodi@science.unitn.it>
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87 % variable k is distributed according to a Student's distribution with df
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Daniele Nicolodi <nicolodi@science.unitn.it>
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88 % degrees of freedom. Such a value represent the required pValue for the
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Daniele Nicolodi <nicolodi@science.unitn.it>
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89 % test in the hypothesis that the two input data series are uncorrelated
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Daniele Nicolodi <nicolodi@science.unitn.it>
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90 fac = (rs+1)*(1-rs);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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91 if fac>0
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Daniele Nicolodi <nicolodi@science.unitn.it>
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92 df = n-2;
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Daniele Nicolodi <nicolodi@science.unitn.it>
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93 pValue = betainc(df/(df+t*t),0.5*df,0.5,'lower');
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Daniele Nicolodi <nicolodi@science.unitn.it>
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94 else
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Daniele Nicolodi <nicolodi@science.unitn.it>
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95 pValue = 0;
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96 end
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Daniele Nicolodi <nicolodi@science.unitn.it>
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97
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Daniele Nicolodi <nicolodi@science.unitn.it>
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98 TestRes = (pValue < alpha);
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Daniele Nicolodi <nicolodi@science.unitn.it>
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99
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Daniele Nicolodi <nicolodi@science.unitn.it>
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100
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101 end