Slides: “Bayesian Bias Correction: Critically evaluating sets of studies in the presence of publication bias”

I recently gave a lab presentation on the work we have been doing to attempt to mitigate the nefarious effects of publication bias, and I thought I’d share the slides here. The first iteration of the method (details given in Guan and Vandekerckhove, 2016), summarized in the first half of the slides, could be applied to single studies or to cases where a fixed effects meta-analysis would be appropriate. I have been working to extend the method to cases where one would perform a random-effects meta-analysis to account for heterogeneity in effects across studies, summarized in the second half of the slides. We’re working now to write this extension up and tidy up the code for dissemination.

Here are the slides (non-slideshare pdf available here):

 

New revision of How to become a Bayesian in eight easy steps

Quentin, Fabian, Peter, Beth and I recently resubmitted our manuscript titled “How to become a Bayesian in eight easy steps: An annotated reading list” that we initially submitted earlier this year. You can find an updated preprint here. The reviewer comments were pleasantly positive (and they only requested relatively minor changes), so I don’t expect we’ll have another revision. In the revised manuscript we include a little more discussion of the conceptual aspect of Bayes factors (in the summary of source 4), some new discussion on different Bayesian philosophies of how analysis should be done (in the introduction of the “Applied” section) and a few additions to the “Further reading” appendix, among other minor typographical corrections.

This was quite a minor revision. The largest change to the paper by far is our new short discussion on different Bayesian philosophies, which mainly revolve around the (ever-controversial!) issue of hypothesis testing. There is an understandable desire from users of statistics for a unitary set of rules and regulation–a simple list of procedures to follow–where if you do all the right steps you won’t piss off that scrupulous methods guy down the hall from you. Well, as it happens, statistics isn’t like that and you’ll never get that list. Statistics is not just a means to an end, as many substantive researchers tend to think, but an active scientific field itself. Statistics, like any field of study, is a human endeavor that has all sorts of debates and philosophical divides.

Rather than letting these divides turn you off from learning Bayes, I hope they prepare you for the vast analytic viewpoints you will likely encounter as Bayesian analyses become more mainstream. And who knows, maybe you’ll even feel inspired to approach your own substantive problems with a new frame of mind.  Here is an excerpt from our discussion:

Before moving on to our final four highlighted sources, it will be useful if readers consider some differences in perspective among practitioners of Bayesian statistics. The application of Bayesian methods is very much an active field of study, and as such, the literature contains a multitude of deep, important, and diverse viewpoints on how data analysis should be done, similar to the philosophical divides between Neyman–Pearson and Fisher concerning proper application of classical statistics (see Lehmann, 1993). The divide between subjective Bayesians, who elect to use priors informed by theory, and objective Bayesians, who instead prefer “uninformative” or default priors, has already been mentioned throughout the Theoretical sources section above.

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A second division of note exists between Bayesians who see a place for hypothesis testing in science, and those who see statistical inference primarily as a problem of estimation. ….

You’ll have to check out the paper to see how the rest of this discussion goes (see page 10).   🙂

Understanding Bayes: How to cheat to get the maximum Bayes factor for a given p value

OR less click-baity: What is the maximum Bayes factor you can get for a given p value? (Obvious disclaimer: Don’t cheat)

Starting to use and interpret Bayesian statistics can be hard at first. A recent recommendation that I like is from Zoltan Dienes and Neil Mclatchie, to “Report a B for every p.” Meaning, for every p value in the paper report a corresponding Bayes factor. This way the psychology community can start to build an intuition about how these two kinds of results can correspond. I think this is a great way to start using Bayes. And if as time goes on you want to flush those ps down the toilet, I won’t complain.

Researchers who start to report both Bayesian and frequentist results often go through a phase where they are surprised to find that their p<.05 results correspond to weak Bayes factors. In this Understanding Bayes post I hope to pump your intuitions a bit as to why this is the case. There is, in fact, an absolute maximum Bayes factor for a given p value. There are also other soft maximums it can achieve for different classes of prior distributions. And these maximum BFs may not be as high as you expect.

Absolute Maximum

The reason for the absolute maximum is actually straightforward. The Bayes factor compares how accurately two or more competing hypotheses predict the observed data. Usually one of those hypotheses is a point null hypothesis, which says there is no effect in the population (however defined). The alternative can be anything you like. It could be a point hypothesis motivated by theory or that you take from previous literature (uncommon), or it can be a (half-)normal (or other) distribution centered on the null (more common), or anything else. In any case, the fact is that to achieve the absolute maximum Bayes factor for a given p value you have to cheat. In real life you can never reach the absolute maximum in a normal course of analysis so its only use is as a benchmark illustration.

You have to make your alternative hypothesis the exact point hypothesis that maximizes the likelihood of the data. The likelihood function ranks all the parameter values by how well they predict the data, so if you make your point hypothesis equal to the mode of the likelihood function, it means that no other hypothesis or population parameter could make the data more likely. This illicit prior is known as the oracle prior, because it is the prior you would choose if you could see the result ahead of time. So in the figure below, the oracle prior would correspond to the high dot on the curve at the mode, and the null hypothesis is the lower dot on the curve. The Bayes factor is then just the ratio of these heights.

When you are doing a t-test, for example, the maximum of the likelihood function is simply the sample mean. So in this case, the oracle prior is a point hypothesis at exactly the sample mean. Let’s assume that we know the population SD=10, so we’re only interested in the population mean. We collect 100 participants and the sample mean we get is 1.96. Our z score in this case is

z = mean / standard error = 1.96 / (10/√100) = 1.96.

This means we obtain a p value of exactly .05. Publication and glory await us. But, in sticking with our B for every p mantra, we decide to calculate an oracle Bayes factor just to be complete. This can easily be done in R using the following 1 line of code:

dnorm(1.96, 1.96, 1)/dnorm(1.96, 0, 1)

And the answer you get is BF = 6.83. This is the absolute maximum Bayes factor you can possibly get for a p value that equals .05 in a t test (you get similar BFs for other types of tests). That is the amount of evidence that would bring a neutral reader who has prior probabilities of 50% for the null and 50% for the alternative to posterior probabilities of 12.8% for the null and 87.2% for the alternative. You might call that moderate evidence depending on the situation. For p of .01, this maximum increases to ~27.5, which is quite strong in most cases. But these values are for the best case ever, where you straight up cheat. When you can’t blatantly cheat the results are not so good.

Soft Maximum

Of course, nobody in their right mind would accept your analysis if you used an oracle prior. It is blatant cheating — but it gives a good benchmark. For p of .05 and the oracle prior, the best BF you can ever get is slightly less than 7. If you can’t blatantly cheat by using an oracle prior, the maximum Bayes factor you can get obviously won’t be as high. But it may surprise you how much smaller the maximum becomes if you decide to cheat more subtly.

The priors most people use for the alternative hypothesis in the Bayes factor are not point hypotheses, but distributed hypotheses. A common recommendation is a unimodal (i.e., one-hump) symmetric prior centered on the null hypothesis value. (There are times where you wouldn’t want to use a prior centered on the null value, but in those cases the maximum BF goes back to being the BF you get using an oracle prior.) I usually recommend using normal distribution priors, and JASP software uses a Cauchy distribution which is similar but with fatter tails. Most of the time the BFs you get are very similar.

So imagine that instead of using the blatantly cheating oracle prior, you use a subtle oracle prior. Instead of a point alternative at the observed mean, you use a normal distribution and pick the scale (i.e., the SD) of your prior to maximize the Bayes factor. There is a formula for this, but the derivation is very technical so I’ll let you read Berger and Sellke (1987, especially section 3) if you’re into that sort of torture.

It turns out, once you do the math, that when using a normal distribution prior the maximum Bayes factor you can get for a value of .05 is BF = 2.1. That is the amount of evidence that would bring a neutral reader who has prior probabilities of 50% for the null and 50% for the alternative to posterior probabilities of 32% for the null and 68% for the alternative. Barely different! That is very weak evidence. The maximum normal prior BF corresponding to of .01 is BF = 6.5. That is still hardly convincing evidence! You can find this bound for any t value you like (for any t greater than 1) using the R code below:

t = 1.96
maxBF = 1/(sqrt(exp(1))*t*exp(-t^2/2))

(You can get slightly different maximum values for different formulations of problem. Another form due to Sellke, Bayarri, & Berger [2001] is 1/[-e*p*ln(p)] for p<~.4, which for p=.05 returns BF = 2.45)

You might say, “Wait no I have a directional prediction, so I will use a half-normal prior that allows only positive values for the population mean. What is my maximum BF now?” Luckily the answer is simple: Just multiply the old maximum by:

2*(1 – p/2)

So for p of .05 and .01 the maximum 1-sided BFs are 4.1 and 13, respectively. (By the way, this trick works for converting most common BFs from 2- to 1-sided.)

Take home message

Do not be surprised if you start reporting Bayes factors and find that what you thought was strong evidence based on a p value of .05 or even .01 translates to a quite weak Bayes factor.

And I think this goes without saying, but don’t try to game your Bayes factors. We’ll know. It’s obvious. The best thing to do is use the prior distribution you find most reasonable for the problem at hand and then do a robustness check by seeing how much the conclusion you draw depends on the specific prior you choose. JASP software can do this for you automatically in many cases (e.g., for the Bayesian t-test; ps check out our official JASP tutorial videos!).

R code

The following is the R code to reproduce the figure, to find the max BF for oracle priors, and to find the max BF for subtle oracle priors. Tinker with it and see how your intuitions match the answers you get!

 

 

Video: “A Bayesian Perspective of the Reproducibility Project: Psychology”

I recently gave a talk at the University of Bristol’s Medical Research Council Integrative Epidemiology Unit, titled, “A Bayesian Perspective on the Reproducibility Project: Psychology,” in which I recount the results from our recently published Bayesian reanalysis of the RPP (you can read it in PLOS ONE). In that paper Joachim Vandekerckhove and I reassessed the evidence from the RPP and found that most of the original and replication studies only managed to obtain weak evidence.

I’m very grateful to Marcus Munafo for inviting me out to give this talk. And I’m also grateful to Jim Lumsden for help organizing. We recorded the talk’s audio and synced it to a screencast of my slides, so if you weren’t there you can still hear about it. 🙂

I’ve posted the slides on slideshare, and you can download a copy of the presentation by clicking here. (It says 83 slides, but the last ~30 slides are a technical appendix prepared for the Q&A)

If you think this is interesting and you’d like to learn more about Bayes, you can check out my Understanding Bayes tutorial series and also our paper, “How to become a Bayesian in eight easy steps.”

What does the ASA statement on p-values mean for psychology?

No single index should substitute for scientific reasoning.

— Official ASA statement

TLDR: The American Statistical Association’s officially stance is that p-values are bad measures of evidence. We as psychologists need to recalibrate our intuitions for what constitutes good evidence. See the full statement here. [Link fixed!]

The American Statistical Association just released its long-promised official statement regarding its stance on p-values. If you don’t remember (don’t worry, it was over a year ago), the ASA responded to Basic and Applied Social Psychology’s (BASP) widely publicized p-value ban by saying,

A group of more than two-dozen distinguished statistical professionals is developing an ASA statement on p-values and inference that highlights the issues and competing viewpoints. The ASA encourages the editors of this journal [BASP] and others who might share their concerns to consider what is offered in the ASA statement to appear later this year and not discard the proper and appropriate use of statistical inference.

This development is especially relevant for psychologists, since the p-value is ubiquitous in our literature. I think I have only ever seen a handful of papers without one. Are we using it correctly? What is proper? The ASA is here to set us straight.

The scope of the statement

The statement begins by saying “While the p-value can be a useful statistical measure, it is commonly misused and misinterpreted.” To help clarify how the p-value should be used, the ASA “believes that the scientific community could benefit from a formal statement clarifying several widely agreed upon principles underlying the proper use and interpretation of the p-value.” Their stated goal is to articulate “in non-technical terms a few select principles that could improve the conduct or interpretation of quantitative science, according to widespread consensus in the statistical community.”

So first things first: what is a p-value?

The ASA gives the following definition for a p-value:

a p-value is the probability under a specified statistical model that a statistical summary of the data (for example, the sample mean difference between two compared groups) would be equal to or more extreme than its observed value.

So the p-value is a probability statement about the observed data, and data more extreme than those observed, given an underlying statistical model (e.g., a null hypothesis) is true. How can we use this probability measure?

Six principles for using p-values

The basic gist of the statement is this: p-values can be used as a measure of the misfit between the data with a model (e.g., a null hypothesis), but that measure of misfit does not tell us the probability that the null hypothesis is true (as we all hopefully know by now). It does not tell us what action we should take — submit to a big name journal, abandon/continue a research line, implement an intervention, etc. It does not tell us how big or important the effect we’re studying is. And most importantly (in my opinion), it does not give us a meaningful measure of evidence regarding a model or hypothesis.

Here are the principles:

  1. P-values can indicate how incompatible the data are with a specified statistical model.
  2. P-values do not measure the probability that the studied hypothesis is true, or the probability that the data were produced by random chance alone.
  3. Scientific conclusions and business or policy decisions should not be based only on whether a p-value passes a specific threshold.
  4. Proper inference requires full reporting and transparency.
  5. A p-value, or statistical significance, does not measure the size of an effect or the importance of a result.
  6. By itself, a p-value does not provide a good measure of evidence regarding a model or hypothesis.

In the paper each principle is followed by a paragraph of detailed exposition. I recommend you take a look at the full statement.

So what does this mean for psychologists?

The ASA gives many explicit recommendations and it is worth reading their full (short!) report. I think the most important principle is principle 6. Psychologists mainly use p-values as a measure of the evidence we have obtained against the null hypothesis. You run your study, check the p-value, if p is below .05 then you have “significant” evidence against the null hypothesis, and then you feel justified in doubting it and consequently having confidence in your preferred substantive hypothesis.

The ASA tells us this is not good practice. Taking a p-value as strong evidence just because it is below .05 is actually misleading; the ASA specifically says “a p-value near 0.05 taken by itself offers only weak evidence against the null hypothesis.” I recently discussed a paper on this blog (Berger & Delampady, 1987 [pdf]) that showed exactly this: A p-value near .05 can only achieve a maximum Bayes factor of ~2 with most acceptable priors, which is a very weak level of evidence — and usually it is much weaker still.

The bottom line is this: We need to adjust our intuitions about what constitutes adequate evidence. Joachim Vandekerckhove and I recently concluded that one big reason effects “failed to replicate” in the Reproducibility Project: Psychology is that the evidence for their existence was unacceptably weak to begin with. When we properly evaluate the evidence from the original studies (even before taking publication bias into account) we see there was little reason to believe the effects ever existed in the first place. “Failed” replications are a natural consequence of our current low standards of evidence.

There are many (many, many) papers in the statistics literature showing that p-values overstate the evidence against the null hypothesis; now the ASA have officially taken this stance as well.

Choice quotes

Below I include some quotations think are most relevant to practicing psychologists.

Researchers should recognize that a p-value without context or other evidence provides limited information. For example, a p-value near 0.05 taken by itself offers only weak evidence against the null hypothesis. Likewise, a relatively large p-value does not imply evidence in favor of the null hypothesis; many other hypotheses may be equally or more consistent with the observed data. For these reasons, data analysis should not end with the calculation of a p-value when other approaches are appropriate and feasible.

 

In view of the prevalent misuses of and misconceptions concerning p-values, some statisticians prefer to supplement or even replace p-values with other approaches. These include methods that emphasize estimation over testing, such as confidence, credibility, or prediction intervals; Bayesian methods; alternative measures of evidence, such as likelihood ratios or Bayes Factors; and other approaches such as decision-theoretic modeling and false discovery rates

 

The widespread use of “statistical significance” (generally interpreted as “p ≤ 0.05”) as a license for making a claim of a scientific finding (or implied truth) leads to considerable distortion of the scientific process.

 

Whenever a researcher chooses what to present based on statistical results, valid interpretation of those results is severely compromised if the reader is not informed of the choice and its basis. Researchers should disclose the number of hypotheses explored during the study, all data collection decisions, all statistical analyses conducted and all p-values computed. Valid scientific conclusions based on p-values and related statistics cannot be drawn without at least knowing how many and which analyses were conducted, and how those analyses (including p-values) were selected for reporting.

 

Statistical significance is not equivalent to scientific, human, or economic significance. Smaller p-values do not necessarily imply the presence of larger or more important effects, and larger p-values do not imply a lack of importance or even lack of effect.