Noah Smith thinks p-values work. Read my lips — they don’t!

12 Aug, 2015 at 16:24 | Posted in Statistics & Econometrics | 5 Comments

Noah Smith has a post up trying to defend p-values and traditional statistical significance testing against the increasing attacks launched against it:

Suddenly, everyone is getting really upset about p-values and statistical significance testing. The backlash has reached such a frenzy that some psych journals are starting to ban significance testing. Though there are some well-known problems with p-values and significance testing, this backlash doesn’t pass the smell test. When a technique has been in wide use for decades, it’s certain that LOTS of smart scientists have had a chance to think carefully about it. The fact that we’re only now getting the backlash means that the cause is something other than the inherent uselessness of the methodology.

Hmm …

That doesn’t sound very convincing.

Maybe we should apply yet another smell test …

A non-trivial part of teaching statistics is made up of learning students to perform significance testing. A problem I have noticed repeatedly over the years, however, is that no matter how careful you try to be in explicating what the probabilities generated by these statistical tests – p values – really are, still most students misinterpret them.

This is not to blame on students’ ignorance, but rather on significance testing not being particularly transparent (conditional probability inference is difficult even to those of us who teach and practice it). A lot of researchers fall pray to the same mistakes. So — given that it anyway is very unlikely than any population parameter is exactly zero, and that contrary to assumption most samples in social science and economics are not random or having the right distributional shape — why continue to press students and researchers to do null hypothesis significance testing, testing that relies on weird backward logic that students and researchers usually don’t understand?

Statistical significance doesn’t say that something is important or true. And since there already are far better and more relevant testing that can be done, it is high time to give up on this statistical fetish.

Jager and Leek may well be correct in their larger point, that the medical literature is broadly correct. But I don’t think the statistical framework they are using is appropriate for the questions they are asking. My biggest problem is the identification of scientific hypotheses and statistical “hypotheses” of the “theta = 0″ variety.

Based on the word “empirical” title, I thought the authors were going to look at a large number of papers with p-values and then follow up and see if the claims were replicated. But no, they don’t follow up on the studies at all! What they seem to be doing is collecting a set of published p-values and then fitting a mixture model to this distribution, a mixture of a uniform distribution (for null effects) and a beta distribution (for non-null effects). Since only statistically significant p-values are typically reported, they fit their model restricted to p-values less than 0.05. But this all assumes that the p-values have this stated distribution. You don’t have to be Uri Simonsohn to know that there’s a lot of p-hacking going on. Also, as noted above, the problem isn’t really effects that are exactly zero, the problem is that a lot of effects are lots in the noise and are essentially undetectable given the way they are studied.

Jager and Leek write that their model is commonly used to study hypotheses in genetics and imaging. I could see how this model could make sense in those fields … but I don’t see this model applying to published medical research, for two reasons. First … I don’t think there would be a sharp division between null and non-null effects; and, second, there’s just too much selection going on for me to believe that the conditional distributions of the p-values would be anything like the theoretical distributions suggested by Neyman-Pearson theory.

So, no, I don’t at all believe Jager and Leek when they write, “we are able to empirically estimate the rate of false positives in the medical literature and trends in false positive rates over time.” They’re doing this by basically assuming the model that is being questioned, the textbook model in which effects are pure and in which there is no p-hacking.

Andrew Gelman

Indeed. If anything, this underlines how important it is — and on this Noah Smith and yours truly agree — not to equate science with statistical calculation. All science entail human judgement, and using statistical models doesn’t relieve us of that necessity. Working with misspecified models, the scientific value of significance testing is actually zero –  even though you’re making valid statistical inferences! Statistical models and concomitant significance tests are no substitutes for doing real science. Or as a noted German philosopher once famously wrote:

There is no royal road to science, and only those who do not dread the fatiguing climb of its steep paths have a chance of gaining its luminous summits.

In its standard form, a significance test is not the kind of “severe test” that we are looking for in our search for being able to confirm or disconfirm empirical scientific hypothesis. This is problematic for many reasons, one being that there is a strong tendency to accept the null hypothesis since they can’t be rejected at the standard 5% significance level. In their standard form, significance tests bias against new hypotheses by making it hard to disconfirm the null hypothesis.

And as shown over and over again when it is applied, people have a tendency to read “not disconfirmed” as “probably confirmed.” Standard scientific methodology tells us that when there is only say a 10 % probability that pure sampling error could account for the observed difference between the data and the null hypothesis, it would be more “reasonable” to conclude that we have a case of disconfirmation. Especially if we perform many independent tests of our hypothesis and they all give about the same 10 % result as our reported one, I guess most researchers would count the hypothesis as even more disconfirmed.

Most importantly — we should never forget that the underlying parameters we use when performing significance tests are model constructions. Our p-values mean next to nothing if the model is wrong. As eminent mathematical statistician David Freedman writes:

I believe model validation to be a central issue. Of course, many of my colleagues will be found to disagree. For them, fitting models to data, computing standard errors, and performing significance tests is “informative,” even though the basic statistical assumptions (linearity, independence of errors, etc.) cannot be validated. This position seems indefensible, nor are the consequences trivial. Perhaps it is time to reconsider.

Statistical significance tests DO NOT validate models!

In journal articles a typical regression equation will have an intercept and several explanatory variables. The regression output will usually include an F-test, with p – 1 degrees of freedom in the numerator and n – p in the denominator. The null hypothesis will not be stated. The missing null hypothesis is that all the coefficients vanish, except the intercept.

If F is significant, that is often thought to validate the model. Mistake. The F-test takes the model as given. Significance only means this: if the model is right and the coefficients are 0, it is very unlikely to get such a big F-statistic. Logically, there are three possibilities on the table:
i) An unlikely event occurred.
ii) Or the model is right and some of the coefficients differ from 0.
iii) Or the model is wrong.
So?