Statistics

“Intentions” is the new code word for “error probabilities”: Allan Birnbaum’s Birthday

Posted on May 27, 2015 by Mayo
27 May 1923-1 July 1976

27 May 1923-1 July 1976

Today is Allan Birnbaum’s Birthday. Birnbaum’s (1962) classic “On the Foundations of Statistical Inference,” in Breakthroughs in Statistics (volume I 1993), concerns a principle that remains at the heart of today’s controversies in statistics–even if it isn’t obvious at first: the Likelihood Principle (LP) (also called the strong likelihood Principle SLP, to distinguish it from the weak LP [1]). According to the LP/SLP, given the statistical model, the information from the data are fully contained in the likelihood ratio. Thus, properties of the sampling distribution of the test statistic vanish (as I put it in my slides from my last post)! But error probabilities are all properties of the sampling distribution. Thus, embracing the LP (SLP) blocks our error statistician’s direct ways of taking into account “biasing selection effects” (slide #10).

Intentions is a New Code Word: Where, then, is all the information regarding your trying and trying again, stopping when the data look good, cherry picking, barn hunting and data dredging? For likelihoodists and other probabilists who hold the LP/SLP, it is ephemeral information locked in your head reflecting your “intentions”!  “Intentions” is a code word for “error probabilities” in foundational discussions, as in “who would want to take intentions into account?” (Replace “intentions” (or the “researcher’s intentions”) with “error probabilities” (or the method’s error probabilities”) and you get a more accurate picture.) Keep this deciphering tool firmly in mind as you read criticisms of methods that take error probabilities into account[2]. For error statisticians, this information reflects real and crucial properties of your inference procedure.

Continue reading →

Categories: Birnbaum, Birnbaum Brakes, frequentist/Bayesian, Likelihood Principle, phil/history of stat, Statistics | 48 Comments

From our “Philosophy of Statistics” session: APS 2015 convention

Posted on May 24, 2015 by Mayo
aps_2015_logo_cropped-1

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“The Philosophy of Statistics: Bayesianism, Frequentism and the Nature of Inference,” at the 2015 American Psychological Society (APS) Annual Convention in NYC, May 23, 2015:

 

D. Mayo: “Error Statistical Control: Forfeit at your Peril” 

 

S. Senn: “‘Repligate’: reproducibility in statistical studies. What does it mean and in what sense does it matter?”

 

A. Gelman: “The statistical crisis in science” (this is not his exact presentation, but he focussed on some of these slides)

 

For more details see this post.

Categories: Bayesian/frequentist, Error Statistics, P-values, reforming the reformers, reproducibility, S. Senn, Statistics | 10 Comments

Stephen Senn: Double Jeopardy?: Judge Jeffreys Upholds the Law (sequel to the pathetic P-value)

Posted on May 9, 2015 by Mayo
S. Senn

S. Senn

Stephen Senn
Head of Competence Center for Methodology and Statistics (CCMS)
Luxembourg Institute of Health

Double Jeopardy?: Judge Jeffreys Upholds the Law

“But this could be dealt with in a rough empirical way by taking twice the standard error as a criterion for possible genuineness and three times the standard error for definite acceptance”. Harold Jeffreys(1) (p386)

This is the second of two posts on P-values. In the first, The Pathetic P-Value, I considered the relation of P-values to Laplace’s Bayesian formulation of induction, pointing out that that P-values, whilst they had a very different interpretation, were numerically very similar to a type of Bayesian posterior probability. In this one, I consider their relation or lack of it, to Harold Jeffreys’s radically different approach to significance testing. (An excellent account of the development of Jeffreys’s thought is given by Howie(2), which I recommend highly.)

The story starts with Cambridge philosopher CD Broad (1887-1971), who in 1918 pointed to a difficulty with Laplace’s Law of Succession. Broad considers the problem of drawing counters from an urn containing n counters and supposes that all m drawn had been observed to be white. He now considers two very different questions, which have two very different probabilities and writes:

C.D. Broad quoteNote that in the case that only one counter remains we have n = m + 1 and the two probabilities are the same. However, if n > m+1 they are not the same and in particular if m is large but n is much larger, the first probability can approach 1 whilst the second remains small.

The practical implication of this just because Bayesian induction implies that a large sequence of successes (and no failures) supports belief that the next trial will be a success, it does not follow that one should believe that all future trials will be so. This distinction is often misunderstood. This is The Economist getting it wrong in September 2000

The canonical example is to imagine that a precocious newborn observes his first sunset, and wonders whether the sun will rise again or not. He assigns equal prior probabilities to both possible outcomes, and represents this by placing one white and one black marble into a bag. The following day, when the sun rises, the child places another white marble in the bag. The probability that a marble plucked randomly from the bag will be white (ie, the child’s degree of belief in future sunrises) has thus gone from a half to two-thirds. After sunrise the next day, the child adds another white marble, and the probability (and thus the degree of belief) goes from two-thirds to three-quarters. And so on. Gradually, the initial belief that the sun is just as likely as not to rise each morning is modified to become a near-certainty that the sun will always rise.

See Dicing with Death(3) (pp76-78).

The practical relevance of this is that scientific laws cannot be established by Laplacian induction. Jeffreys (1891-1989) puts it thus

Thus I may have seen 1 in 1000 of the ‘animals with feathers’ in England; on Laplace’s theory the probability of the proposition, ‘all animals with feathers have beaks’, would be about 1/1000. This does not correspond to my state of belief or anybody else’s. (P128)

Continue reading →

Categories: Jeffreys, P-values, reforming the reformers, Statistics, Stephen Senn | 42 Comments

Spurious Correlations: Death by getting tangled in bedsheets and the consumption of cheese! (Aris Spanos)

Posted on May 4, 2015 by Mayo
Spanos

Spanos

These days, there are so many dubious assertions about alleged correlations between two variables that an entire website: Spurious Correlation (Tyler Vigen) is devoted to exposing (and creating*) them! A classic problem is that the means of variables X and Y may both be trending in the order data are observed, invalidating the assumption that their means are constant. In my initial study with Aris Spanos on misspecification testing, the X and Y means were trending in much the same way I imagine a lot of the examples on this site are––like the one on the number of people who die by becoming tangled in their bedsheets and the per capita consumption of cheese in the U.S.

The annual data for 2000-2009 are: xt: per capita consumption of cheese (U.S.) : x = (29.8, 30.1, 30.5, 30.6, 31.3, 31.7, 32.6, 33.1, 32.7, 32.8); yt: Number of people who died by becoming tangled in their bedsheets: y = (327, 456, 509, 497, 596, 573, 661, 741, 809, 717)

I asked Aris Spanos to have a look, and it took him no time to identify the main problem. He was good enough to write up a short note which I’ve pasted as slides.

spurious-correlation-updated-4-1024

Aris Spanos

Wilson E. Schmidt Professor of Economics
Department of Economics, Virginia Tech

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*The site says that the server attempts to generate a new correlation every 60 seconds.

Categories: misspecification testing, Spanos, Statistics, Testing Assumptions | 14 Comments

96% Error in “Expert” Testimony Based on Probability of Hair Matches: It’s all Junk!

Posted on April 30, 2015 by Mayo

Objectivity 1: Will the Real Junk Science Please Stand Up?Imagine. The New York Times reported a few days ago that the FBI erroneously identified criminals 96% of the time based on probability assessments using forensic hair samples (up until 2000). Sometimes the hair wasn’t even human, it might have come from a dog, a cat or a fur coat!  I posted on  the unreliability of hair forensics a few years ago.  The forensics of bite marks aren’t much better.[i] John Byrd, forensic analyst and reader of this blog had commented at the time that: “At the root of it is the tradition of hiring non-scientists into the technical positions in the labs. They tended to be agents. That explains a lot about misinterpretation of the weight of evidence and the inability to explain the import of lab findings in court.” DNA is supposed to cure all that. So is it? I don’t know, but apparently the FBI “has agreed to provide free DNA testing where there is either a court order or a request for testing by the prosecution.”[ii] See the FBI report.

Here’s the op-ed from the New York Times from April 27, 2015:

“Junk Science at the FBI”

The odds were 10-million-to-one, the prosecution said, against hair strands found at the scene of a 1978 murder of a Washington, D.C., taxi driver belonging to anyone but Santae Tribble. Based largely on this compelling statistic, drawn from the testimony of an analyst with the Federal Bureau of Investigation, Mr. Tribble, 17 at the time, was convicted of the crime and sentenced to 20 years to life.

But the hair did not belong to Mr. Tribble. Some of it wasn’t even human. In 2012, a judge vacated Mr. Tribble’s conviction and dismissed the charges against him when DNA testing showed there was no match between the hair samples, and that one strand had come from a dog.

Mr. Tribble’s case — along with the exoneration of two other men who served decades in prison based on faulty hair-sample analysis — spurred the F.B.I. to conduct a sweeping post-conviction review of 2,500 cases in which its hair-sample lab reported a match.

The preliminary results of that review, which Spencer Hsu of The Washington Post reported last week, are breathtaking: out of 268 criminal cases nationwide between 1985 and 1999, the bureau’s “elite” forensic hair-sample analysts testified wrongly in favor of the prosecution, in 257, or 96 percent of the time. Thirty-two defendants in those cases were sentenced to death; 14 have since been executed or died in prison.Forensic Hair red

The agency is continuing to review the rest of the cases from the pre-DNA era. The Justice Department is working with the Innocence Project and the National Association of Criminal Defense Lawyers to notify the defendants in those cases that they may have grounds for an appeal. It cannot, however, address the thousands of additional cases where potentially flawed testimony came from one of the 500 to 1,000 state or local analysts trained by the F.B.I. Peter Neufeld, co-founder of the Innocence Project, rightly called this a “complete disaster.”

Law enforcement agencies have long known of the dubious value of hair-sample analysis. A 2009 report by the National Research Council found “no scientific support” and “no uniform standards” for the method’s use in positively identifying a suspect. At best, hair-sample analysis can rule out a suspect, or identify a wide class of people with similar characteristics.

Yet until DNA testing became commonplace in the late 1990s, forensic analysts testified confidently to the near-certainty of matches between hair found at crime scenes and samples taken from defendants. The F.B.I. did not even have written standards on how analysts should testify about their findings until 2012.

Continue reading →

Categories: evidence-based policy, junk science, PhilStat Law, Statistics | 3 Comments

3 YEARS AGO (APRIL 2012): MEMORY LANE

Posted on April 27, 2015 by Mayo
3 years ago...

* 3 years ago…

MONTHLY MEMORY LANE: 3 years ago: March 2012. I mark in red three posts that seem most apt for general background on key issues in this blog* (Posts that are part of a “unit” or a group of “U-Phils” count as one.) This new feature, appearing the last week of each month, began at the blog’s 3-year anniversary in Sept, 2014.

*excluding those recently reblogged.

April 2012

Contributions from readers in relation to published papers

Two book reviews of Error and the Growth of Experimental Knowledge (EGEK 1996)-counted as 1 unit

Categories: 3-year memory lane, Statistics | Tags: | Leave a comment

“Statistical Concepts in Their Relation to Reality” by E.S. Pearson

Posted on April 24, 2015 by Mayo

To complete the last post, here’s Pearson’s portion of the “triad” 

E.S.Pearson on Gate

E.S.Pearson on Gate (sketch by D. Mayo)

“Statistical Concepts in Their Relation to Reality“

by E.S. PEARSON (1955)

SUMMARY: This paper contains a reply to some criticisms made by Sir Ronald Fisher in his recent article on “Scientific Methods and Scientific Induction”.

Controversies in the field of mathematical statistics seem largely to have arisen because statisticians have been unable to agree upon how theory is to provide, in terms of probability statements, the numerical measures most helpful to those who have to draw conclusions from observational data.  We are concerned here with the ways in which mathematical theory may be put, as it were, into gear with the common processes of rational thought, and there seems no reason to suppose that there is one best way in which this can be done.  If, therefore, Sir Ronald Fisher recapitulates and enlarges on his views upon statistical methods and scientific induction we can all only be grateful, but when he takes this opportunity to criticize the work of others through misapprehension of their views as he has done in his recent contribution to this Journal (Fisher 1955), it is impossible to leave him altogether unanswered.

In the first place it seems unfortunate that much of Fisher’s criticism of Neyman and Pearson’s approach to the testing of statistical hypotheses should be built upon a “penetrating observation” ascribed to Professor G.A. Barnard, the assumption involved in which happens to be historically incorrect.  There was no question of a difference in point of view having “originated” when Neyman “reinterpreted” Fisher’s early work on tests of significance “in terms of that technological and commercial apparatus which is known as an acceptance procedure”.  There was no sudden descent upon British soil of Russian ideas regarding the function of science in relation to technology and to five-year plans.  It was really much simpler–or worse.  The original heresy, as we shall see, was a Pearson one!

TO CONTINUE READING E.S. PEARSON’S PAPER CLICK HERE.

Categories: E.S. Pearson, phil/history of stat, Statistics | Tags: , , | Leave a comment

NEYMAN: “Note on an Article by Sir Ronald Fisher” (3 uses for power, Fisher’s fiducial argument)

Posted on April 22, 2015 by Mayo

Note on an Article by Sir Ronald Fisher

By Jerzy Neyman (1956)

Summary

(1) FISHER’S allegation that, contrary to some passages in the introduction and on the cover of the book by Wald, this book does not really deal with experimental design is unfounded. In actual fact, the book is permeated with problems of experimentation.  (2) Without consideration of hypotheses alternative to the one under test and without the study of probabilities of the two kinds, no purely probabilistic theory of tests is possible.  (3) The conceptual fallacy of the notion of fiducial distribution rests upon the lack of recognition that valid probability statements about random variables usually cease to be valid if the random variables are replaced by their particular values.  The notorious multitude of “paradoxes” of fiducial theory is a consequence of this oversight.  (4)  The idea of a “cost function for faulty judgments” appears to be due to Laplace, followed by Gauss.

1. Introduction

In a recent article (Fisher, 1955), Sir Ronald Fisher delivered an attack on a a substantial part of the research workers in mathematical statistics. My name is mentioned more frequently than any other and is accompanied by the more expressive invectives. Of the scientific questions raised by Fisher many were sufficiently discussed before (Neyman and Pearson, 1933; Neyman, 1937; Neyman, 1952). In the present note only the following points will be considered: (i) Fisher’s attack on the concept of errors of the second kind; (ii) Fisher’s reference to my objections to fiducial probability; (iii) Fisher’s reference to the origin of the concept of loss function and, before all, (iv) Fisher’s attack on Abraham Wald.

THIS SHORT (5 page) NOTE IS NEYMAN’S PORTION OF WHAT I CALL THE “TRIAD”. LET ME POINT YOU TO THE TOP HALF OF p. 291, AND THE DISCUSSION OF FIDUCIAL INFERENCE ON p. 292 HERE.

 

Categories: Fisher, Neyman, phil/history of stat, Statistics | Tags: , , | 2 Comments

Neyman: Distinguishing tests of statistical hypotheses and tests of significance might have been a lapse of someone’s pen

Posted on April 18, 2015 by Mayo
neyman

Neyman, drawn by ?

“Tests of Statistical Hypotheses and Their Use in Studies of Natural Phenomena” by Jerzy Neyman

ABSTRACT. Contrary to ideas suggested by the title of the conference at which the present paper was presented, the author is not aware of a conceptual difference between a “test of a statistical hypothesis” and a “test of significance” and uses these terms interchangeably. A study of any serious substantive problem involves a sequence of incidents at which one is forced to pause and consider what to do next. In an effort to reduce the frequency of misdirected activities one uses statistical tests. The procedure is illustrated on two examples: (i) Le Cam’s (and associates’) study of immunotherapy of cancer and (ii) a socio-economic experiment relating to low-income homeownership problems.

I hadn’t posted this paper of Neyman’s before, so here’s something for your weekend reading:  “Tests of Statistical Hypotheses and Their Use in Studies of Natural Phenomena.”  I recommend, especially, the example on home ownership. Here are two snippets:

1. INTRODUCTION

The title of the present session involves an element that appears mysterious to me. This element is the apparent distinction between tests of statistical hypotheses, on the one hand, and tests of significance, on the other. If this is not a lapse of someone’s pen, then I hope to learn the conceptual distinction. Continue reading →

Categories: Error Statistics, Neyman, Statistics | Tags: | 18 Comments

A. Spanos: Jerzy Neyman and his Enduring Legacy

Posted on April 16, 2015 by Mayo

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A Statistical Model as a Chance Mechanism
Aris Spanos 

Today is the birthday of Jerzy Neyman (April 16, 1894 – August 5, 1981). Neyman was a Polish/American statistician[i] who spent most of his professional career at the University of California, Berkeley. Neyman is best known in statistics for his pioneering contributions in framing the Neyman-Pearson (N-P) optimal theory of hypothesis testing and his theory of Confidence Intervals. (This article was first posted here.)

Neyman: 16 April

Neyman: 16 April 1894 – 5 Aug 1981

One of Neyman’s most remarkable, but least recognized, achievements was his adapting of Fisher’s (1922) notion of a statistical model to render it pertinent for  non-random samples. Fisher’s original parametric statistical model Mθ(x) was based on the idea of ‘a hypothetical infinite population’, chosen so as to ensure that the observed data x0:=(x1,x2,…,xn) can be viewed as a ‘truly representative sample’ from that ‘population’:

photoSmall

Fisher and Neyman

“The postulate of randomness thus resolves itself into the question, Of what population is this a random sample? (ibid., p. 313), underscoring that: the adequacy of our choice may be tested a posteriori.’’ (p. 314)

In cases where data x0 come from sample surveys or it can be viewed as a typical realization of a random sample X:=(X1,X2,…,Xn), i.e. Independent and Identically Distributed (IID) random variables, the ‘population’ metaphor can be helpful in adding some intuitive appeal to the inductive dimension of statistical inference, because one can imagine using a subset of a population (the sample) to draw inferences pertaining to the whole population. Continue reading →

Categories: Neyman, phil/history of stat, Spanos, Statistics | Tags: , | Leave a comment

Philosophy of Statistics Comes to the Big Apple! APS 2015 Annual Convention — NYC

Posted on April 13, 2015 by Mayo

Start Spreading the News…..

aps_2015_logo_cropped-1

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 The Philosophy of Statistics: Bayesianism, Frequentism and the Nature of Inference,
2015 APS Annual Convention
Saturday, May 23  2:00 PM- 3:50 PM in Wilder
(Marriott Marquis 1535 B’way)

 

 

gelman5

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Andrew Gelman

Professor of Statistics & Political Science
Columbia University

SENN FEB

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Stephen Senn

Head of Competence Center
for Methodology and Statistics (CCMS)

Luxembourg Institute of Health

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Slide1

D. Mayo headshot

D.G. Mayo, Philosopher


morey

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Richard Morey, Session Chair & Discussant

Senior Lecturer
School of Psychology
Cardiff University
Categories: Announcement, Bayesian/frequentist, Statistics | 8 Comments

Heads I win, tails you lose? Meehl and many Popperians get this wrong (about severe tests)!

Posted on April 8, 2015 by Mayo
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bending of starlight.

[T]he impressive thing about the 1919 tests of Einstein ‘s theory of gravity] is the risk involved in a prediction of this kind. If observation shows that the predicted effect is definitely absent, then the theory is simply refuted. The theory is incompatible with certain possible results of observation—in fact with results which everybody before Einstein would have expected. This is quite different from the situation I have previously described, [where]..it was practically impossible to describe any human behavior that might not be claimed to be a verification of these [psychological] theories.” (Popper, CR, [p. 36))

 

Popper lauds Einstein’s General Theory of Relativity (GTR) as sticking its neck out, bravely being ready to admit its falsity were the deflection effect not found. The truth is that even if no deflection effect had been found in the 1919 experiments it would have been blamed on the sheer difficulty in discerning so small an effect (the results that were found were quite imprecise.) This would have been entirely correct! Yet many Popperians, perhaps Popper himself, get this wrong.[i] Listen to Popperian Paul Meehl (with whom I generally agree).

The stipulation beforehand that one will be pleased about substantive theory T when the numerical results come out as forecast, but will not necessarily abandon it when they do not, seems on the face of it to be about as blatant a violation of the Popperian commandment as you could commit. For the investigator, in a way, is doing…what astrologers and Marxists and psychoanalysts allegedly do, playing heads I win, tails you lose.” (Meehl 1978, 821)

No, there is a confusion of logic. A successful result may rightly be taken as evidence for a real effect H, even though failing to find the effect need not be taken to refute the effect, or even as evidence as against H. This makes perfect sense if one keeps in mind that a test might have had little chance to detect the effect, even if it existed. The point really reflects the asymmetry of falsification and corroboration. Popperian Alan Chalmers wrote an appendix to a chapter of his book, What is this Thing Called Science? (1999)(which at first had criticized severity for this) once I made my case. [i] Continue reading →

Categories: fallacy of non-significance, philosophy of science, Popper, Severity, Statistics | Tags: | 2 Comments

Joan Clarke, Turing, I.J. Good, and “that after-dinner comedy hour…”

Posted on April 4, 2015 by Mayo

I finally saw The Imitation Game about Alan Turing and code-breaking at Bletchley Park during WWII. This short clip of Joan Clarke, who was engaged to Turing, includes my late colleague I.J. Good at the end (he’s not second as the clip lists him). Good used to talk a great deal about Bletchley Park and his code-breaking feats while asleep there (see note[a]), but I never imagined Turing’s code-breaking machine (which, by the way, was called the Bombe and not Christopher as in the movie) was so clunky. The movie itself has two tiny scenes including Good. Below I reblog: “Who is Allowed to Cheat?”—one of the topics he and I debated over the years. Links to the full “Savage Forum” (1962) may be found at the end (creaky, but better than nothing.)

[a]”Some sensitive or important Enigma messages were enciphered twice, once in a special variation cipher and again in the normal cipher. …Good dreamed one night that the process had been reversed: normal cipher first, special cipher second. When he woke up he tried his theory on an unbroken message – and promptly broke it.” This, and further examples may be found in this obituary

[b] Pictures comparing the movie cast and the real people may be found here. Continue reading →

Categories: Bayesian/frequentist, optional stopping, Statistics, strong likelihood principle | 7 Comments

Are scientists really ready for ‘retraction offsets’ to advance ‘aggregate reproducibility’? (let alone ‘precautionary withdrawals’)

Posted on April 1, 2015 by Mayo
images

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Given recent evidence of the irreproducibility of a surprising number of published scientific findings, the White House’s Office of Science and Technology Policy (OSTP) sought ideas for “leveraging its role as a significant funder of scientific research to most effectively address the problem”, and announced funding for projects to “reset the self-corrective process of scientific inquiry”. (first noted in this post.)ostp

I was sent some information this morning with a rather long description of the project that received the top government award thus far (and it’s in the millions). I haven’t had time to read the proposal*, which I’ll link to shortly, but for a clear and quick description, you can read the excerpt of an interview of the OSTP representative by the editor of the Newsletter for Innovation in Science Journals (Working Group), Jim Stein, who took the lead in writing the author check list for Nature.

Stein’s queries are in burgundy, OSTP’s are in blue. Occasional comments from me are in black, which I’ll update once I study the fine print of the proposal itself. Continue reading →

Categories: junk science, reproducibility, science communication, Statistics | 9 Comments

Your (very own) personalized genomic prediction varies depending on who else was around?

Posted on March 28, 2015 by Mayo
images

personalized medicine roulette

As if I wasn’t skeptical enough about personalized predictions based on genomic signatures, Jeff Leek recently had a surprising post about a “A surprisingly tricky issue when using genomic signatures for personalized medicine“.  Leek (on his blog Simply Statistics) writes:

My student Prasad Patil has a really nice paper that just came out in Bioinformatics (preprint in case paywalled). The paper is about a surprisingly tricky normalization issue with genomic signatures. Genomic signatures are basically statistical/machine learning functions applied to the measurements for a set of genes to predict how long patients will survive, or how they will respond to therapy. The issue is that usually when building and applying these signatures, people normalize across samples in the training and testing set.

….it turns out that this one simple normalization problem can dramatically change the results of the predictions. In particular, we show that the predictions for the same patient, with the exact same data, can change dramatically if you just change the subpopulations of patients within the testing set.

Here’s an extract from the paper,”Test set bias affects reproducibility of gene signatures“:

Test set bias is a failure of reproducibility of a genomic signature. In other words, the same patient, with the same data and classification algorithm, may be assigned to different clinical groups. A similar failing resulted in the cancellation of clinical trials that used an irreproducible genomic signature to make chemotherapy decisions (Letter (2011)).

This is a reference to the Anil Potti case:

Letter, T. C. (2011). Duke Accepts Potti Resignation; Retraction Process Initiated with Nature Medicine.

But far from the Potti case being some particularly problematic example (see here and here), at least with respect to test set bias, this article makes it appear that test set bias is a threat to be expected much more generally. Going back to the abstract of the paper: Continue reading →

Categories: Anil Potti, personalized medicine, Statistics | 10 Comments

Objectivity in Statistics: “Arguments From Discretion and 3 Reactions”

Posted on March 21, 2015 by Mayo

dirty hands

We constantly hear that procedures of inference are inescapably subjective because of the latitude of human judgment as it bears on the collection, modeling, and interpretation of data. But this is seriously equivocal: Being the product of a human subject is hardly the same as being subjective, at least not in the sense we are speaking of—that is, as a threat to objective knowledge. Are all these arguments about the allegedly inevitable subjectivity of statistical methodology rooted in equivocations? I argue that they are! [This post combines this one and this one, as part of our monthly “3 years ago” memory lane.]

“Argument from Discretion” (dirty hands)

Insofar as humans conduct science and draw inferences, it is obvious that human judgments and human measurements are involved. True enough, but too trivial an observation to help us distinguish among the different ways judgments should enter, and how, nevertheless, to avoid introducing bias and unwarranted inferences. The issue is not that a human is doing the measuring, but whether we can reliably use the thing being measured to find out about the world.

Remember the dirty-hands argument? In the early days of this blog (e.g., October 13, 16), I deliberately took up this argument as it arises in evidence-based policy because it offered a certain clarity that I knew we would need to come back to in considering general “arguments from discretion”. To abbreviate:

  1. Numerous  human judgments go into specifying experiments, tests, and models.
  2. Because there is latitude and discretion in these specifications, they are “subjective.”
  3. Whether data are taken as evidence for a statistical hypothesis or model depends on these subjective methodological choices.
  4. Therefore, statistical inference and modeling is invariably subjective, if only in part.

We can spot the fallacy in the argument much as we did in the dirty hands argument about evidence-based policy. It is true, for example, that by employing a very insensitive test for detecting a positive discrepancy d’ from a 0 null, that the test has low probability of finding statistical significance even if a discrepancy as large as d’ exists. But that doesn’t prevent us from determining, objectively, that an insignificant difference from that test fails to warrant inferring evidence of a discrepancy less than d’.

Test specifications may well be a matter of  personal interest and bias, but, given the choices made, whether or not an inference is warranted is not a matter of personal interest and bias. Setting up a test with low power against d’ might be a product of your desire not to find an effect for economic reasons, of insufficient funds to collect a larger sample, or of the inadvertent choice of a bureaucrat. Or ethical concerns may have entered. But none of this precludes our critical evaluation of what the resulting data do and do not indicate (about the question of interest). The critical task need not itself be a matter of economics, ethics, or what have you. Critical scrutiny of evidence reflects an interest all right—an interest in not being misled, an interest in finding out what the case is, and others of an epistemic nature. Continue reading →

Categories: Objectivity, Statistics | Tags: , | 6 Comments

Stephen Senn: The pathetic P-value (Guest Post)

Posted on March 16, 2015 by Mayo
S. Senn

S. Senn

Stephen Senn
Head of Competence Center for Methodology and Statistics (CCMS)
Luxembourg Institute of Health

The pathetic P-value

This is the way the story is now often told. RA Fisher is the villain. Scientists were virtuously treading the Bayesian path, when along came Fisher and gave them P-values, which they gladly accepted, because they could get ‘significance’ so much more easily. Nearly a century of corrupt science followed but now there are signs that there is a willingness to return to the path of virtue and having abandoned this horrible Fisherian complication:

We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started …

A condition of complete simplicity..

And all shall be well and
All manner of thing shall be well

TS Eliot, Little Gidding

Consider, for example, distinguished scientist David Colquhoun citing the excellent scientific journalist Robert Matthews as follows

“There is an element of truth in the conclusion of a perspicacious journalist:

‘The plain fact is that 70 years ago Ronald Fisher gave scientists a mathematical machine for turning baloney into breakthroughs, and flukes into funding. It is time to pull the plug. ‘

Robert Matthews Sunday Telegraph, 13 September 1998.” [1]

However, this is not a plain fact but just plain wrong. Even if P-values were the guilty ‘mathematical machine’ they are portrayed to be, it is not RA Fisher’s fault. Putting the historical record right helps one to understand the issues better. As I shall argue, at the heart of this is not a disagreement between Bayesian and frequentist approaches but between two Bayesian approaches: it is a conflict to do with the choice of prior distributions[2].

Fisher did not persuade scientists to calculate P-values rather than Bayesian posterior probabilities; he persuaded them that the probabilities that they were already calculating and interpreting as posterior probabilities relied for this interpretation on a doubtful assumption. He proposed to replace this interpretation with one that did not rely on the assumption. Continue reading →

Categories: P-values, S. Senn, statistical tests, Statistics | 148 Comments

All She Wrote (so far): Error Statistics Philosophy: 3.5 years on

Posted on March 12, 2015 by Mayo

 

metablog old fashion typewriter

D.G. Mayo with typewriter

Error Statistics Philosophy: Blog Contents (3.5 years)
By: D. G. Mayo [i]

September 2011

October 2011

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Categories: blog contents, Metablog, Statistics | 1 Comment

A puzzle about the latest test ban (or ‘don’t ask, don’t tell’)

Posted on March 5, 2015 by Mayo
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A large number of people have sent me articles on the “test ban” of statistical hypotheses tests and confidence intervals at a journal called Basic and Applied Social Psychology (BASP)[i]. Enough. One person suggested that since it came so close to my recent satirical Task force post, that I either had advance knowledge or some kind of ESP. Oh please, no ESP required.None of this is the slightest bit surprising, and I’ve seen it before; I simply didn’t find it worth blogging about. Statistical tests are being banned, say the editors, because they purport to give probabilities of null hypotheses (really?) and do not, hence they are “invalid”.[ii] (Confidence intervals are thrown in the waste bin as well—also claimed “invalid”).“The state of the art remains uncertain” regarding inferential statistical procedures, say the editors.  I don’t know, maybe some good will come of all this.

Yet there’s a part of their proposal that brings up some interesting logical puzzles, and logical puzzles are my thing. In fact, I think there is a mistake the editors should remedy, lest authors be led into disingenuous stances, and strange tangles ensue. I refer to their rule that authors be allowed to submit papers whose conclusions are based on allegedly invalid methods so long as, once accepted, they remove any vestiges of them!

“Question 1. Will manuscripts with p-values be desk rejected automatically?

Answer to Question 1. No. If manuscripts pass the preliminary inspection, they will be sent out for review. But prior to publication, authors will have to remove all vestiges of the NHSTP (p-values, t-values, F-values, statements about “significant” differences or lack thereof, and so on).”

Now if these measures are alleged to be irrelevant and invalid instruments for statistical inference, then why should they be included in the peer review process at all? Will reviewers be told to ignore them? That would only seem fair: papers should not be judged by criteria alleged to be invalid, but how will reviewers blind themselves to them? It would seem the measures should be excluded from the get-go. If they are included in the review, why shouldn’t the readers see what the reviewers saw when they recommended acceptance?

But here’s where the puzzle really sets in. If the authors must free their final papers from such encumbrances as sampling distributions and error probabilities, what will be the basis presented for their conclusions in the published paper? Presumably, from the notice, they are allowed only mere descriptive statistics or non-objective Bayesian reports (added: actually can’t tell which kind of Bayesianism they allow, given the Fisher reference which doesn’t fit*). Won’t this be tantamount to requiring authors support their research in a way that is either (actually) invalid, or has little to do with the error statistical properties that were actually reported and on which the acceptance was based?[ii] Continue reading →

Categories: P-values, reforming the reformers, Statistics | 73 Comments

“Probabilism as an Obstacle to Statistical Fraud-Busting”

Posted on March 1, 2015 by Mayo
Boston Colloquium 2013-2014

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“Is the Philosophy of Probabilism an Obstacle to Statistical Fraud Busting?” was my presentation at the 2014 Boston Colloquium for the Philosophy of Science):“Revisiting the Foundations of Statistics in the Era of Big Data: Scaling Up to Meet the Challenge.”  

 As often happens, I never put these slides into a stand alone paper. But I have incorporated them into my book (in progress*), “How to Tell What’s True About Statistical Inference”. Background and slides were posted last year.

Slides (draft from Feb 21, 2014) 

Download the 54th Annual Program

Cosponsored by the Department of Mathematics & Statistics at Boston University.

Friday, February 21, 2014
10 a.m. – 5:30 p.m.
Photonics Center, 9th Floor Colloquium Room (Rm 906)
8 St. Mary’s Street

*Seeing a light at the end of tunnel, finally.
Categories: P-values, significance tests, Statistical fraudbusting, Statistics | 7 Comments

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