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I have been playing with DistributionFitTest as a means of testing how normal some data sets I have. I've been working with some simulated data sets so I can try and understand what's going on. From the documentation it seems DistributionFitTest returns a $p$-value by default, which according to the documentation

A small $p$-value suggests that it is unlikely that the data came from dist.

Firstly, how is "small" defined?

From my limited understanding of $p$-values, it seems that if the resultant $p$-value is $< 0.05$ then one can say it is unlikely that the data belongs to the proposed distribution. Again, from my understanding this $0.05$ threshold should be considered as a hard line, so $p = 0.04999$ should be rejected while $p = 0.05000$ is accepted.

As for my "simulations" I did a simple test to find out how $p$-values are distributed for multiple data sets which are generated from the dame distribution. I use the "KolmogorovSmirnov" option as the K-S test seems to be the standard approach used.

ManypValue = 
Table[
        NormalData = RandomVariate[NormalDistribution[0, 1], 1000];
        pValue = DistributionFitTest[NormalData, NormalDistribution[\[Mu], \[Sigma]], "KolmogorovSmirnov"],
        {i, 1, 512}
    ];
    
Histogram[ManypValue, "FreedmanDiaconis", "PDF",Frame->True, FrameLabel->{"p-Value","PDF"}]

The result is a uniform or box distribution which goes between $0$ and $1$, so I understand this to mean that there is a $5\%$ chance of a dataset which is normal being identified as non-normal -- on the basis of this $p>0.05$ threshold: enter image description here

Finally, are there any other methods in Mathematica as a means of testing whether data belongs to a distribution?

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  • $\begingroup$ This question seems related: mathematica.stackexchange.com/questions/86304/… $\endgroup$
    – user27119
    Oct 9, 2020 at 19:22
  • $\begingroup$ What you describe is the "popular" but wrong interpretation of a P-value. From en.wikipedia.org/wiki/P-value: "...the p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct." It is NOT the likelihood that the null hypothesis is wrong because it is constructed under the assumption that the null hypothesis is true. And there is no law about 0.05. Would you follow a rule base on absolutely no knowledge of the subject matter or consequences of a wrong decision? $\endgroup$
    – JimB
    Oct 13, 2020 at 3:03
  • $\begingroup$ See stats.stackexchange.com/questions/46856/…. $\endgroup$
    – JimB
    Oct 13, 2020 at 3:05
  • $\begingroup$ Thanks JimB. I was worried I was falling into this trap. There is indeed a whole article on the misunderstanding of $p$-values: en.wikipedia.org/wiki/Misuse_of_p-values. The stats SE link you said is helpful. But now I don't understand the "point" of the DistributionFitTest function -- or at least the results it provides. If I want to have some measure of how normal my data is, how can DistributionFitTest help me? $\endgroup$
    – user27119
    Oct 13, 2020 at 12:09
  • 2
    $\begingroup$ Also, to reinforce: the p<0.05 value is a completely arbitrary value for "statistical significance". There is nothing magic about it. Different disciplines have different accepted values for "statistical significance" based upon "p-values" (all largely arbitrary convention). The links provided are very useful. $\endgroup$
    – flyingmind
    Oct 14, 2020 at 8:51

1 Answer 1

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If you want to see "how normal" your data appears to be, you first need to decide on a metric (or metrics) that characterize the departures from normality that are important to you. You also really need to know what values of those metrics imply "non-normality".

I'd argue that many folks don't know they need to consider both the kind of metric and the size of that metric. But lets suspend disbelief and consider what the Kolmogorov-Smirnov assumes for you.

First the metric used is the maximum distance between the hypothesized cumulative distribution function and the empirical cumulative distribution function from the sample data. In Mathematica one can run the following to test for normality (and that is not a specific normal distribution but any normal distribution):

SeedRandom[12345]; 
n = 20;
data = RandomVariate[NormalDistribution[0, 1], n];
h = DistributionFitTest[data, NormalDistribution[μ, σ], "HypothesisTestData"];
h["TestDataTable", {"KolmogorovSmirnov"}]

KS test results

So the maximum distance between the empirical distribution of the sample and the hypothesized normal distribution with the same mean and standard deviation is 0.155088.

If that were the "true" value from a humongous sample, would that be considered a large value? Large enough to jettison the assumption of normality? I don't know. I don't know physics, chemistry, engineering, and a whole sort of applied fields but it is certainly up to the subject matter expert to make that decision and different fields will certainly different assessments which also depend on specific objectives.

And to thrown in more complexity, the value observed will be dependent on sample size (i.e., the size of your budget to collect samples which not scientifically related to the research objective).

Now hypothesis testing comes into play. The P-value of 0.242247 states that if the sample came from a normal distribution, then 24.2247% of the time one would observe a larger maximum distance than what was observed. (The P-value is NOT the probability that the hypothesized distribution is true.) The OP mentions Misuse of P-values which is a good read along with the statement from the American Statistical Association.

To duplicate what DistributionFitTest does when testing for normality and find where the largest deviation from the cumulative normal distribution exists, one can execute the following:

(* Sample mean and standard deviation *)
xbar = Mean[data];
(* Note we need to "adjust" the definition of the sample standard deviation *)
sd = StandardDeviation[data]*Sqrt[(n - 1)/n];

(* CDF of normal distribution with same sample mean and sample standard deviation *)
F[x_] := CDF[NormalDistribution[xbar, sd], x]

(* Calculate KS statistic *)
data = Sort[data];
ks1 = Table[{data[[j]], j/n, j/n - F[data[[j]]]}, {j, n}];
ks2 = Table[{data[[j]], (j - 1)/n, F[data[[j]]] - (j - 1)/n}, {j, n}];
ks12 = Join[ks1, ks2];
ks = Select[ks12, #[[3]] == Max[ks12[[All, 3]]] &][[1]]
(* {-0.633614, 11/20, 0.155088} *)

We see the same value for the KS statistic: 0.155088.

(* Plot results *)
Show[Plot[{CDF[EmpiricalDistribution[data], x],
    CDF[NormalDistribution[xbar, sd], x]}, {x, -3, 3},
  AxesOrigin -> {-3, 0}, Frame -> True, 
  FrameLabel -> {"", "Cumulative probability"},
  PlotLegends -> {"Empirical distribution", 
    "Normal distribution with same\nsample mean and std. dev."}],
 ListPlot[{{ks[[1]], ks[[2]]}, {ks[[1]], F[ks[[1]]]}}, Joined -> True, PlotStyle -> Red]]

Empirical and hypothesized cdfs

The red line segment shows where the maximum difference occurs.

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  • $\begingroup$ Excellent answer as always, I appreciate the effort. So what you are saying is: the cut off at which I accept or discard a data set as being normal, $p < \alpha$ needs to be decided on the basis of my problem? And this convention of $\alpha = 0.05$ is really a statement that most people don't have a good understanding of their problem? $\endgroup$
    – user27119
    Oct 14, 2020 at 1:25
  • $\begingroup$ The answer to the first question in the comment is Yes. Why should a statistical procedure which intrinsically knows nothing of your subject matter be all that would be needed to make a decision? For example, suppose the data is sampled from a non-normal distribution. The P-value will tend to be smaller the more money you spend on sampling. And are there consequences for a wrong decision? How can one make an intelligent decision without knowing the consequences? For the second question I would say "Yes" if the term "most people" was changed to "many people". $\endgroup$
    – JimB
    Oct 14, 2020 at 3:43
  • $\begingroup$ P-values are just fine. They just don't supply all of the information one needs to make an informed and justified decision. $\endgroup$
    – JimB
    Oct 14, 2020 at 3:44

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