Posts Tagged With: p-value vs posterior

Excerpts from S. Senn’s Letter on “Replication, p-values and Evidence”

old blogspot typewriter

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I first blogged this letter here. Below the references are some more recent blog links of relevance to this issue. 

 Dear Reader:  I am typing in some excerpts from a letter Stephen Senn shared with me in relation to my April 28, 2012 blogpost.  It is a letter to the editor of Statistics in Medicine  in response to S. Goodman. It contains several important points that get to the issues we’ve been discussing. You can read the full letter here. Sincerely, D. G. Mayo

 STATISTICS IN MEDICINE, LETTER TO THE EDITOR

From: Stephen Senn*

Some years ago, in the pages of this journal, Goodman gave an interesting analysis of ‘replication probabilities’ of p-values. Specifically, he considered the possibility that a given experiment had produced a p-value that indicated ‘significance’ or near significance (he considered the range p=0.10 to 0.001) and then calculated the probability that a study with equal power would produce a significant result at the conventional level of significance of 0.05. He showed, for example, that given an uninformative prior, and (subsequently) a resulting p-value that was exactly 0.05 from the first experiment, the probability of significance in the second experiment was 50 per cent. A more general form of this result is as follows. If the first trial yields p=α then the probability that a second trial will be significant at significance level α (and in the same direction as the first trial) is 0.5. Continue reading

Categories: 4 years ago!, reproducibility, S. Senn, Statistics | Tags: , , , | 3 Comments

Higgs Discovery two years on (1: “Is particle physics bad science?”)

Higgs_cake-s

July 4, 2014 was the two year anniversary of the Higgs boson discovery. As the world was celebrating the “5 sigma!” announcement, and we were reading about the statistical aspects of this major accomplishment, I was aghast to be emailed a letter, purportedly instigated by Bayesian Dennis Lindley, through Tony O’Hagan (to the ISBA). Lindley, according to this letter, wanted to know:

“Are the particle physics community completely wedded to frequentist analysis?  If so, has anyone tried to explain what bad science that is?”

Fairly sure it was a joke, I posted it on my “Rejected Posts” blog for a bit until it checked out [1]. (See O’Hagan’s “Digest and Discussion”) Continue reading

Categories: Bayesian/frequentist, fallacy of non-significance, Higgs, Lindley, Statistics | Tags: , , , , , | 4 Comments

Is Particle Physics Bad Science? (memory lane)

Memory Lane: reblog July 11, 2012 (+ updates at the end). 

I suppose[ed] this was somewhat of a joke from the ISBA, prompted by Dennis Lindley, but as I [now] accord the actual extent of jokiness to be only ~10%, I’m sharing it on the blog [i].  Lindley (according to O’Hagan) wonders why scientists require so high a level of statistical significance before claiming to have evidence of a Higgs boson.  It is asked: “Are the particle physics community completely wedded to frequentist analysis?  If so, has anyone tried to explain what bad science that is?”

Bad science?   I’d really like to understand what these representatives from the ISBA would recommend, if there is even a shred of seriousness here (or is Lindley just peeved that significance levels are getting so much press in connection with so important a discovery in particle physics?)

Well, read the letter and see what you think.

On Jul 10, 2012, at 9:46 PM, ISBA Webmaster wrote:

Dear Bayesians,

A question from Dennis Lindley prompts me to consult this list in search of answers.

We’ve heard a lot about the Higgs boson.  The news reports say that the LHC needed convincing evidence before they would announce that a particle had been found that looks like (in the sense of having some of the right characteristics of) the elusive Higgs boson.  Specifically, the news referred to a confidence interval with 5-sigma limits.

Now this appears to correspond to a frequentist significance test with an extreme significance level.  Five standard deviations, assuming normality, means a p-value of around 0.0000005.  A number of questions spring to mind.

1.  Why such an extreme evidence requirement?  We know from a Bayesian  perspective that this only makes sense if (a) the existence of the Higgs  boson (or some other particle sharing some of its properties) has extremely small prior probability and/or (b) the consequences of erroneously announcing its discovery are dire in the extreme.  Neither seems to be the case, so why  5-sigma?

2.  Rather than ad hoc justification of a p-value, it is of course better to do a proper Bayesian analysis.  Are the particle physics community completely wedded to frequentist analysis?  If so, has anyone tried to explain what bad science that is? Continue reading

Categories: philosophy of science, Statistics | Tags: , , , , , | Leave a comment

P-values as Frequentist Measures

Working on the last two chapters of my book on philosophy of statistical inference, I’m revisiting such topics as weak conditioning, Birnbaum, likelihood principle, etc., and was reading from the Proceedings of the Berkeley Conference in Honor of Jerzy Neyman and Jack Kiefer (1985)[i]. In a paper I had not seen (or had forgotten), Jim Berger “The Frequentist Viewpoint and Conditioning,” writes that the quoting of a P-value “may be felt to be a frequentist procedure by some, since it involves an averaging over the sample space. The reporting of P-values can be given no long-run frequency interpretation [in any of the set-ups generally considered].  A P-value actually lies closer to conditional (Bayesian) measures than to frequentist measures.” (Berger 1985, 23). These views are echoed in Berger’s more recent “Could Fisher,Jeffreys and Neyman Have Agreed on Testing?”(2003). This is at odds with what Fisher, N-P, Cox, Lehmann, etc. have held, and if true, would also seem to entail that a severity assessment had no frequentist interpretation!  The flaw lies in that all-too-common behavioristic, predesignated conception…

Among related posts:

https://errorstatistics.com/2012/04/28/3671/
https://errorstatistics.com/2012/05/10/excerpts-from-s-senns-letter-on-replication-p-values-and-evidence/

 


[i] Also because of Peter Gruenwald’s recent mention of Kiefer’s work, read long ago.

Categories: Statistics | Tags: , , , | Leave a comment

Is Particle Physics Bad Science?

I suppose[ed] this was somewhat of a joke from the ISBA, prompted by Dennis Lindley, but as I [now] accord the actual extent of jokiness to be only ~10%, I’m sharing it on the blog [i].  Lindley (according to O’Hagan) wonders why scientists require so high a level of statistical significance before claiming to have evidence of a Higgs boson.  It is asked: “Are the particle physics community completely wedded to frequentist analysis?  If so, has anyone tried to explain what bad science that is?”

Bad science?   I’d really like to understand what these representatives from the ISBA would recommend, if there is even a shred of seriousness here (or is Lindley just peeved that significance levels are getting so much press in connection with so important a discovery in particle physics?)

Well, read the letter and see what you think.

On Jul 10, 2012, at 9:46 PM, ISBA Webmaster wrote:

Dear Bayesians,

A question from Dennis Lindley prompts me to consult this list in search of answers.

We’ve heard a lot about the Higgs boson.  The news reports say that the LHC needed convincing evidence before they would announce that a particle had been found that looks like (in the sense of having some of the right characteristics of) the elusive Higgs boson.  Specifically, the news referred to a confidence interval with 5-sigma limits.

Now this appears to correspond to a frequentist significance test with an extreme significance level.  Five standard deviations, assuming normality, means a p-value of around 0.0000005.  A number of questions spring to mind.

1.  Why such an extreme evidence requirement?  We know from a Bayesian  perspective that this only makes sense if (a) the existence of the Higgs  boson (or some other particle sharing some of its properties) has extremely small prior probability and/or (b) the consequences of erroneously announcing its discovery are dire in the extreme.  Neither seems to be the case, so why  5-sigma?

2.  Rather than ad hoc justification of a p-value, it is of course better to do a proper Bayesian analysis.  Are the particle physics community completely wedded to frequentist analysis?  If so, has anyone tried to explain what bad science that is? Continue reading

Categories: philosophy of science, Statistics | Tags: , , , , , | 11 Comments

Excerpts from S. Senn’s Letter on “Replication, p-values and Evidence,”

old blogspot typewriterDear Reader:  I am typing in some excerpts from a letter Stephen Senn shared with me in relation to my April 28, 2012 blogpost.  It is a letter to the editor of Statistics in Medicine  in response to S. Goodman. It contains several important points that get to the issues we’ve been discussing, and you may wish to track down the rest of it. Sincerely, D. G. Mayo

Statist. Med. 2002; 21:2437–2444  https://errorstatistics.files.wordpress.com/2013/12/goodman.pdf

 STATISTICS IN MEDICINE, LETTER TO THE EDITOR

A comment on replication, p-values and evidence: S.N. Goodman, Statistics in Medicine 1992; 11:875–879

From: Stephen Senn*

Some years ago, in the pages of this journal, Goodman gave an interesting analysis of ‘replication probabilities’ of p-values. Specifically, he considered the possibility that a given experiment had produced a p-value that indicated ‘significance’ or near significance (he considered the range p=0.10 to 0.001) and then calculated the probability that a study with equal power would produce a significant result at the conventional level of significance of 0.05. He showed, for example, that given an uninformative prior, and (subsequently) a resulting p-value that was exactly 0.05 from the first experiment, the probability of significance in the second experiment was 50 per cent. A more general form of this result is as follows. If the first trial yields p=α then the probability that a second trial will be significant at significance level α (and in the same direction as the first trial) is 0.5. Continue reading

Categories: Statistics | Tags: , , , | 8 Comments

Comedy Hour at the Bayesian Retreat: P-values versus Posteriors

Did you hear the one about the frequentist significance tester when he was shown the nonfrequentist nature of p-values?

JB: I just simulated a long series of tests on a pool of null hypotheses, and I found that among tests with p-values of .05, at least 22%—and typically over 50%—of the null hypotheses are true!

Frequentist Significance Tester: Scratches head: But rejecting the null with a p-value of .05 ensures erroneous rejection no more than 5% of the time!

Raucous laughter ensues!

(Hah, hah,…. I feel I’m back in high school: “So funny, I forgot to laugh!)

The frequentist tester should retort:

Frequentist significance tester: But you assumed 50% of the null hypotheses are true, and  computed P(H0|x) (imagining P(H0)= .5)—and then assumed my p-value should agree with the number you get!

But, our significance tester is not heard from as they move on to the next joke….

Of course it is well-known that for a fixed p-value, with a sufficiently large n, even a statistically significant result can correspond to large posteriors in H0 [i] .  Somewhat more recent work generalizes the result, e.g., J. Berger and Sellke, 1987. Although from their Bayesian perspective, it appears that p-values come up short as measures of evidence, the significance testers balk at the fact that use of the recommended priors allows highly significant results to be interpreted as no evidence against the null — or even evidence for it!   An interesting twist in recent work is to try to “reconcile” the p-value and the posterior e.g., Berger 2003[ii].

The conflict between p-values and Bayesian posteriors considers the two sided  test of the Normal mean, H0: μ = μ0 versus H1: μ ≠ μ0 .

“If n = 50 one can classically ‘reject H0 at significance level p = .05,’ although Pr (H0|x) = .52 (which would actually indicate that the evidence favors H0).” (Berger and Sellke, 1987, p. 113).

If n = 1000, a result statistically significant at the .05 level leads to a posterior to the null of .82!

CHART

Table 1 (modified) from J.O. Berger and T. Selke (1987) “Testing a Point Null Hypothesis,” JASA 82(397) : 113.

Many find the example compelling evidence that the p-value “overstates evidence against a null” because it claims to use an “impartial” or “uninformative”(?) Bayesian prior probability assignment of .5 toH0, the remaining .5 being spread out over the alternative parameter space. Others charge that the problem is not p-values but the high prior (Casella and R.Berger, 1987).  Moreover, the “spiked concentration of belief in the null” is at odds with the prevailing view “we know all nulls are false”.  Note too the conflict with confidence interval reasoning since the value zero (0) lies outside the corresponding confidence interval (Mayo 2005).

But often, as in the opening joke, the prior assignment is claimed to be keeping to the frequentist camp and frequentist error probabilities: it is imagined that we sample randomly from a population of hypotheses, some proportion of which are assumed to be true, 50% is a common number used. We randomly draw a hypothesis and get this particular one, maybe it concerns the mean deflection of light, or perhaps it is an assertion of bioequivalence of two drugs or whatever. The percentage “initially true” (in this urn of nulls) serves as the prior probability for H0. I see this gambit in statistics, psychology, philosophy and elsewhere, and yet it commits a fallacious instantiation of probabilities:

50% of the null hypotheses in a given pool of nulls are true.

This particular null H0 was randomly selected from this urn (and, it may be added, nothing else is known, or the like).

Therefore P(H0 is true) = .5.

It isn’t that one cannot play a carnival game of reaching into an urn of nulls (and one can imagine lots of choices for what to put in the urn), and use a Bernouilli model for the chance of drawing a true hypothesis (assuming we could even tell), but this “generic hypothesis”  is no longer the particular hypothesis one aims to use in computing the probability of data x0 (be it on eclipse data, risk rates, or whatever) under hypothesis H0. [iii]  In any event .5 is not the frequentist probability that the chosen null H0 is true. (Note the selected null would get the benefit of being selected from an urn of nulls where few have been shown false yet: “innocence by association”.)

Yet J. Berger claims his applets are perfectly frequentist, and by adopting his recommended O-priors, we frequentists can become more frequentist (than using our flawed p-values)[iv]. We get what he calls conditional p-values (of a special sort). This is a reason for a coining a different name, e.g.,  frequentist error statistician.

Upshot: Berger and Sellke tell us they will cure  the significance tester’s tendency to exaggerate the evidence against the null  (in two-sided testing) by using some variant on a spiked prior. But the result of their “cure” is that outcomes may too readily be taken as no evidence against, or even evidence for, the null hypothesis, even if it is false.  We actually don’t think we need a cure.  Faced with conflicts between error probabilities and Bayesian posterior probabilities, the error statistician may well conclude that the flaw lies with the latter measure. This is precisely what Fisher argued:

Discussing a test of the hypothesis that the stars are distributed at random, Fisher takes the low p-value (about 1 in 33,000) to “exclude at a high level of significance any theory involving a random distribution” (Fisher, 1956, page 42). Even if one were to imagine that H0 had an extremely high prior probability, Fisher continues—never minding “what such a statement of probability a priori could possibly mean”—the resulting high posteriori probability to H0, he thinks, would only show that “reluctance to accept a hypothesis strongly contradicted by a test of significance” (44) . . . “is not capable of finding expression in any calculation of probability a posteriori” (43). Sampling theorists do not deny there is ever a legitimate frequentist prior probability distribution for a statistical hypothesis: one may consider hypotheses about such distributions and subject them to probative tests. Indeed, Fisher says,  if one were to consider the claim about the a priori probability to be itself a hypothesis, it would be rejected by the data!


[i] A result my late colleague I.J. wanted me to call the Jeffreys-Good-Lindley Paradox).

[ii] An applet is available at http://www.stat.duke.edu/∼berger

[iii] Bayesian philosophers, e.g., Achinstein, allow this does not yield a frequentist prior, but he claims it yields an acceptable prior for the epistemic  probabilist (e.g., See Error and Inference 2010).

[iv]Does this remind you of how the Bayesian is said to become more subjective by using the Berger O-Bayesian prior? See Berger deconstruction.

References & Related articles

Berger, J. O.  (2003). “Could Fisher, Jeffreys and Neyman have Agreed on Testing?” Statistical Science 18: 1-12.

Berger, J. O. and Sellke, T.  (1987). “Testing a point null hypothesis: The irreconcilability of p values and evidence,” (with discussion). J. Amer. Statist. Assoc. 82: 112–139.

Cassella G. and Berger, R..  (1987). “Reconciling Bayesian and Frequentist Evidence in the One-sided Testing Problem,” (with discussion). J. Amer. Statist. Assoc. 82 106–111, 123–139.

Fisher, R. A., (1956) Statistical Methods and Scientific Inference, Edinburgh: Oliver and Boyd.

Jeffreys, (1939) Theory of Probability, Oxford: Oxford University Press.

Mayo, D. (2003), Comment on J. O. Berger’s “Could Fisher,Jeffreys and Neyman Have Agreed on Testing?”Statistical Science 18, 19-24.

Mayo, D. (2004). “An Error-Statistical Philosophy of Evidence,” in M. Taper and S. Lele (eds.) The Nature of Scientific Evidence: Statistical, Philosophical and Empirical Considerations. Chicago: University of Chicago Press: 79-118.

Mayo, D.G. and Cox, D. R. (2006) “Frequentists Statistics as a Theory of Inductive Inference,” Optimality: The Second Erich L. Lehmann Symposium (ed. J. Rojo), Lecture Notes-Monograph series, Institute of Mathematical Statistics (IMS), Vol. 49: 77-97.

Mayo, D. and Kruse, M. (2001). “Principles of Inference and Their Consequences,” in D. Cornfield and J. Williamson (eds.) Foundations of Bayesianism. Dordrecht: Kluwer Academic Publishes: 381-403.

Mayo, D. and Spanos, A. (2011) “Error Statistics” in Philosophy of Statistics , Handbook of Philosophy of Science Volume 7 Philosophy of Statistics, (General editors: Dov M. Gabbay, Paul Thagard and John Woods; Volume eds. Prasanta S. Bandyopadhyay and Malcolm R. Forster.) Elsevier: 1-46.
Categories: Statistics | Tags: , , , , , | 53 Comments

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