Monthly Archives: September 2015

Oy Faye! What are the odds of not conflating simple conditional probability and likelihood with Bayesian success stories?

Posted on September 30, 2015 by Mayo
Unknown

Faye Flam

ONE YEAR AGO, the NYT “Science Times” (9/29/14) published Fay Flam’s article, first blogged here.

Congratulations to Faye Flam for finally getting her article published at the Science Times at the New York Times, “The odds, continually updated” after months of reworking and editing, interviewing and reinterviewing. I’m grateful that one remark from me remained. Seriously I am. A few comments: The Monty Hall example is simple probability not statistics, and finding that fisherman who floated on his boots at best used likelihoods. I might note, too, that critiquing that ultra-silly example about ovulation and voting–a study so bad they actually had to pull it at CNN due to reader complaints[i]–scarcely required more than noticing the researchers didn’t even know the women were ovulating[ii]. Experimental design is an old area of statistics developed by frequentists; on the other hand, these ovulation researchers really believe their theory (and can point to a huge literature)….. Anyway, I should stop kvetching and thank Faye and the NYT for doing the article at all[iii]. Here are some excerpts:

30BAYES-master675

silly pic that accompanied the NYT article

…….When people think of statistics, they may imagine lists of numbers — batting averages or life-insurance tables. But the current debate is about how scientists turn data into knowledge, evidence and predictions. Concern has been growing in recent years that some fields are not doing a very good job at this sort of inference. In 2012, for example, a team at the biotech company Amgen announced that they’d analyzed 53 cancer studies and found it could not replicate 47 of them.

Similar follow-up analyses have cast doubt on so many findings in fields such as neuroscience and social science that researchers talk about a “replication crisis”

Continue reading →

Categories: Bayesian/frequentist, Statistics | Leave a comment

3 YEARS AGO (SEPTEMBER 2012): MEMORY LANE

Posted on September 28, 2015 by Mayo
3 years ago...
3 years ago…

MONTHLY MEMORY LANE: 3 years ago: September 2012. I mark in red three posts that seem most apt for general background on key issues in this blog.[1] (Once again it was tough to pick just 3; many of the ones I selected are continued in the following posts, so please check out subsequent dates of posts that interest you…)

September 2012

[1] excluding those reblogged fairly recently. Posts that are part of a “unit” or a group of “U-Phils” count as one. Monthly memory lanes began at the blog’s 3-year anniversary in Sept, 2014.

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

G.A. Barnard: The “catch-all” factor: probability vs likelihood

Posted on September 26, 2015 by Mayo
Barnard

G.A.Barnard 23 sept. 1915- 30 July 2002

 From the “The Savage Forum” (pp 79-84 Savage, 1962)[i] 

 BARNARD:…Professor Savage, as I understand him, said earlier that a difference between likelihoods and probabilities was that probabilities would normalize because they integrate to one, whereas likelihoods will not. Now probabilities integrate to one only if all possibilities are taken into account. This requires in its application to the probability of hypotheses that we should be in a position to enumerate all possible hypotheses which might explain a given set of data. Now I think it is just not true that we ever can enumerate all possible hypotheses. … If this is so we ought to allow that in addition to the hypotheses that we really consider we should allow something that we had not thought of yet, and of course as soon as we do this we lose the normalizing factor of the probability, and from that point of view probability has no advantage over likelihood. This is my general point, that I think while I agree with a lot of the technical points, I would prefer that this is talked about in terms of likelihood rather than probability. I should like to ask what Professor Savage thinks about that, whether he thinks that the necessity to enumerate hypotheses exhaustively, is important.

SAVAGE: Surely, as you say, we cannot always enumerate hypotheses so completely as we like to think. The list can, however, always be completed by tacking on a catch-all ‘something else’. In principle, a person will have probabilities given ‘something else’ just as he has probabilities given other hypotheses. In practice, the probability of a specified datum given ‘something else’ is likely to be particularly vague­–an unpleasant reality. The probability of ‘something else’ is also meaningful of course, and usually, though perhaps poorly defined, it is definitely very small. Looking at things this way, I do not find probabilities unnormalizable, certainly not altogether unnormalizable. Continue reading →

Categories: Barnard, highly probable vs highly probed, phil/history of stat, Statistics | 20 Comments

George Barnard: 100th birthday: “We need more complexity” (and coherence) in statistical education

Posted on September 23, 2015 by Mayo
barnard-1979-picture

G.A. Barnard: 23 September, 1915 – 30 July, 2002

The answer to the question of my last post is George Barnard, and today is his 100th birthday*. The paragraphs stem from a 1981 conference in honor of his 65th birthday, published in his 1985 monograph: “A Coherent View of Statistical Inference” (Statistics, Technical Report Series, University of Waterloo). Happy Birthday George!

[I]t seems to be useful for statisticians generally to engage in retrospection at this time, because there seems now to exist an opportunity for a convergence of view on the central core of our subject. Unless such an opportunity is taken there is a danger that the powerful central stream of development of our subject may break up into smaller and smaller rivulets which may run away and disappear into the sand.

I shall be concerned with the foundations of the subject. But in case it should be thought that this means I am not here strongly concerned with practical applications, let me say right away that confusion about the foundations of the subject is responsible, in my opinion, for much of the misuse of the statistics that one meets in fields of application such as medicine, psychology, sociology, economics, and so forth. It is also responsible for the lack of use of sound statistics in the more developed areas of science and engineering. While the foundations have an interest of their own, and can, in a limited way, serve as a basis for extending statistical methods to new problems, their study is primarily justified by the need to present a coherent view of the subject when teaching it to others. One of the points I shall try to make is, that we have created difficulties for ourselves by trying to oversimplify the subject for presentation to others. It would surely have been astonishing if all the complexities of such a subtle concept as probability in its application to scientific inference could be represented in terms of only three concepts––estimates, confidence intervals, and tests of hypotheses. Yet one would get the impression that this was possible from many textbooks purporting to expound the subject. We need more complexity; and this should win us greater recognition from scientists in developed areas, who already appreciate that inference is a complex business while at the same time it should deter those working in less developed areas from thinking that all they need is a suite of computer programs.

Continue reading →

Categories: Barnard, phil/history of stat, Statistics | 9 Comments

Statistical rivulets: Who wrote this?

Posted on September 22, 2015 by Mayo
questionmark pink

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[I]t seems to be useful for statisticians generally to engage in retrospection at this time, because there seems now to exist an opportunity for a convergence of view on the central core of our subject. Unless such an opportunity is taken there is a danger that the powerful central stream of development of our subject may break up into smaller and smaller rivulets which may run away and disappear into the sand.

I shall be concerned with the foundations of the subject. But in case it should be thought that this means I am not here strongly concerned with practical applications, let me say right away that confusion about the foundations of the subject is responsible, in my opinion, for much of the misuse of the statistics that one meets in fields of application such as medicine, psychology, sociology, economics, and so forth. It is also responsible for the lack of use of sound statistics in the more developed areas of science and engineering. While the foundations have an interest of their own, and can, in a limited way, serve as a basis for extending statistical methods to new problems, their study is primarily justified by the need to present a coherent view of the subject when teaching it to others. One of the points I shall try to make is, that we have created difficulties for ourselves by trying to oversimplify the subject for presentation to others. It would surely have been astonishing if all the complexities of such a subtle concept as probability in its application to scientific inference could be represented in terms of only three concepts––estimates, confidence intervals, and tests of hypotheses. Yet one would get the impression that this was possible from many textbooks purporting to expound the subject. We need more complexity; and this should win us greater recognition from scientists in developed areas, who already appreciate that inference is a complex business while at the same time it should deter those working in less developed areas from thinking that all they need is a suite of computer programs.

Who wrote this and when?

Categories: Error Statistics, Statistics | Leave a comment

Popper on pseudoscience: a comment on Pigliucci (i), (ii) 9/18, (iii) 9/20

Posted on September 16, 2015 by Mayo
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Jump to Part (ii) 9/18/15 and (iii) 9/20/15 updates

I heard a podcast the other day in which the philosopher of science, Massimo Pigliucci, claimed that Popper’s demarcation of science fails because it permits pseudosciences like astrology to count as scientific! Now Popper requires supplementing in many ways, but we can get far more mileage out of Popper’s demarcation than Pigliucci supposes.

Pigliucci has it that, according to Popper, mere logical falsifiability suffices for a theory to be scientific, and this prevents Popper from properly ousting astrology from the scientific pantheon. Not so. In fact, Popper’s central goal is to call our attention to theories that, despite being logically falsifiable, are rendered immune from falsification by means of ad hoc maneuvering, sneaky face-saving devices, “monster-barring” or “conventionalist stratagems”. Lacking space on Twitter (where the “Philosophy Bites” podcast was linked), I’m placing some quick comments here. (For other posts on Popper, please search this blog.) Excerpts from the classic two pages in Conjectures and Refutations (1962, pp. 36-7) will serve our purpose:

It is easy to obtain confirmations, or verifications, for nearly every theory–if we look for confirmations.

Popper

Popper

Confirmations should count only if they are the result of risky predictions; that is [if the theory or claim H is false] we should have expected an event which was incompatible with the theory [or claim]….

Every genuine test of a theory is an attempt to falsify it, or to refute it. Testability is falsifiability, but there are degrees of testability, some theories are more testable..

Confirming evidence should not count except when it is the result of a genuine test of the theory, and this means that it can be presented as a serious but unsuccessful attempt to falsify the theory. (I now speak of such cases as ‘corroborating evidence’).

Continue reading →

Categories: Error Statistics, Popper, pseudoscience, Statistics | Tags: , | 7 Comments

(Part 3) Peircean Induction and the Error-Correcting Thesis

Posted on September 14, 2015 by Mayo
C. S. Peirce: 10 Sept, 1839-19 April, 1914

C. S. Peirce: 10 Sept, 1839-19 April, 1914

Last third of “Peircean Induction and the Error-Correcting Thesis”

Deborah G. Mayo
Transactions of the Charles S. Peirce Society 41(2) 2005: 299-319

Part 2 is here.

8. Random sampling and the uniformity of nature

We are now at the point to address the final move in warranting Peirce’s SCT. The severity or trustworthiness assessment, on which the error correcting capacity depends, requires an appropriate link (qualitative or quantitative) between the data and the data generating phenomenon, e.g., a reliable calibration of a scale in a qualitative case, or a probabilistic connection between the data and the population in a quantitative case. Establishing such a link, however, is regarded as assuming observed regularities will persist, or making some “uniformity of nature” assumption—the bugbear of attempts to justify induction.

But Peirce contrasts his position with those favored by followers of Mill, and “almost all logicians” of his day, who “commonly teach that the inductive conclusion approximates to the truth because of the uniformity of nature” (2.775). Inductive inference, as Peirce conceives it (i.e., severe testing) does not use the uniformity of nature as a premise. Rather, the justification is sought in the manner of obtaining data. Justifying induction is a matter of showing that there exist methods with good error probabilities. For this it suffices that randomness be met only approximately, that inductive methods check their own assumptions, and that they can often detect and correct departures from randomness.

… It has been objected that the sampling cannot be random in this sense. But this is an idea which flies far away from the plain facts. Thirty throws of a die constitute an approximately random sample of all the throws of that die; and that the randomness should be approximate is all that is required. (1.94)

Continue reading →

Categories: C.S. Peirce, Error Statistics, phil/history of stat | Leave a comment

(Part 2) Peircean Induction and the Error-Correcting Thesis

Posted on September 12, 2015 by Mayo
C. S. Peirce 9/10/1839 – 4/19/1914

C. S. Peirce
9/10/1839 – 4/19/1914

Continuation of “Peircean Induction and the Error-Correcting Thesis”

Deborah G. Mayo
Transactions of the Charles S. Peirce Society: A Quarterly Journal in American Philosophy, Volume 41, Number 2, 2005, pp. 299-319

Part 1 is here.

There are two other points of confusion in critical discussions of the SCT, that we may note here:

I. The SCT and the Requirements of Randomization and Predesignation

The concern with “the trustworthiness of the proceeding” for Peirce like the concern with error probabilities (e.g., significance levels) for error statisticians generally, is directly tied to their view that inductive method should closely link inferences to the methods of data collection as well as to how the hypothesis came to be formulated or chosen for testing.

This account of the rationale of induction is distinguished from others in that it has as its consequences two rules of inductive inference which are very frequently violated (1.95) namely, that the sample be (approximately) random and that the property being tested not be determined by the particular sample x— i.e., predesignation.

The picture of Peircean induction that one finds in critics of the SCT disregards these crucial requirements for induction: Neither enumerative induction nor H-D testing, as ordinarily conceived, requires such rules. Statistical significance testing, however, clearly does. Continue reading →

Categories: Bayesian/frequentist, C.S. Peirce, Error Statistics, Statistics | Leave a comment

Peircean Induction and the Error-Correcting Thesis (Part I)

Posted on September 11, 2015 by Mayo
C. S. Peirce: 10 Sept, 1839-19 April, 1914

C. S. Peirce: 10 Sept, 1839-19 April, 1914

Yesterday was C.S. Peirce’s birthday. He’s one of my all time heroes. You should read him: he’s a treasure chest on essentially any topic. I only recently discovered a passage where Popper calls Peirce one of the greatest philosophical thinkers ever (I don’t have it handy). If Popper had taken a few more pages from Peirce, he would have seen how to solve many of the problems in his work on scientific inference, probability, and severe testing. I’ll blog the main sections of a (2005) paper of mine over the next few days. It’s written for a very general philosophical audience; the statistical parts are pretty informal. I first posted it in 2013. Happy (slightly belated) Birthday Peirce.

Peircean Induction and the Error-Correcting Thesis
Deborah G. Mayo
Transactions of the Charles S. Peirce Society: A Quarterly Journal in American Philosophy, Volume 41, Number 2, 2005, pp. 299-319

Peirce’s philosophy of inductive inference in science is based on the idea that what permits us to make progress in science, what allows our knowledge to grow, is the fact that science uses methods that are self-correcting or error-correcting:

Induction is the experimental testing of a theory. The justification of it is that, although the conclusion at any stage of the investigation may be more or less erroneous, yet the further application of the same method must correct the error. (5.145)

Inductive methods—understood as methods of experimental testing—are justified to the extent that they are error-correcting methods. We may call this Peirce’s error-correcting or self-correcting thesis (SCT):

Self-Correcting Thesis SCT: methods for inductive inference in science are error correcting; the justification for inductive methods of experimental testing in science is that they are self-correcting. Continue reading →

Categories: Bayesian/frequentist, C.S. Peirce, Error Statistics, Statistics | Leave a comment

All She Wrote (so far): Error Statistics Philosophy: 4 years on

Posted on September 5, 2015 by Mayo
metablog old fashion typewriter

D.G. Mayo with her  blogging typewriter

Error Statistics Philosophy: Blog Contents (4 years)
By: D. G. Mayo [i]

Dear Reader: It’s hard to believe I’ve been blogging for 4 whole years (as of Sept. 3, 2015)! A big celebration is taking place at the Elbar Room as I type this. (Remember the 1 year anniversary here? Remember that hideous blogspot? Oy!) Please peruse the offerings below, and take advantage of some of the super contributions and discussions by readers! I don’t know how much longer I’ll continue blogging; in the past 6 months I’ve mostly been focusing on completing my book, “How to Tell What’s True About Statistical Inference.” I plan to experiment with some new ideas and novel pursuits in the coming months. Stay tuned, and thanks for reading! Best Wishes, D. Mayo

September 2011

October 2011

November 2011

December 2011

Continue reading →

Categories: blog contents, Metablog, Statistics | Leave a comment

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