The Bayesian Reproducibility Project

[Edit: There is a now-published Bayesian reanalysis of the RPP. See here.]

The Reproducibility Project was finally published this week in Science, and an outpouring of media articles followed. Headlines included “More Than 50% Psychology Studies Are Questionable: Study”, “Scientists Replicated 100 Psychology Studies, and Fewer Than Half Got the Same Results”, and “More than half of psychology papers are not reproducible”.

Are these categorical conclusions warranted? If you look at the paper, it makes very clear that the results do not definitively establish effects as true or false:

After this intensive effort to reproduce a sample of published psychological findings, how many of the effects have we established are true? Zero. And how many of the effects have we established are false? Zero. Is this a limitation of the project design? No. It is the reality of doing science, even if it is not appreciated in daily practice. (p. 7)

Very well said. The point of this project was not to determine what proportion of effects are “true”. The point of this project was to see what results are replicable in an independent sample. The question arises of what exactly this means. Is an original study replicable if the replication simply matches it in statistical significance and direction? The authors entertain this possibility:

A straightforward method for evaluating replication is to test whether the replication shows a statistically significant effect (P < 0.05) with the same direction as the original study. This dichotomous vote-counting method is intuitively appealing and consistent with common heuristics used to decide whether original studies “worked.” (p. 4)

How did the replications fare? Not particularly well.

Ninety-seven of 100 (97%) effects from original studies were positive results … On the basis of only the average replication power of the 97 original, significant effects [M = 0.92, median (Mdn) = 0.95], we would expect approximately 89 positive results in the replications if all original effects were true and accurately estimated; however, there were just 35 [36.1%; 95% CI = (26.6%, 46.2%)], a significant reduction … (p. 4)

So the replications, being judged on this metric, did (frankly) horribly when compared to the original studies. Only 35 of the studies achieved significance, as opposed to the 89 expected and the 97 total. This gives a success rate of either 36% (35/97) out of all studies, or 39% (35/89) relative to the number of studies expected to achieve significance based on power calculations. Either way, pretty low. These were the numbers that most of the media latched on to.

Does this metric make sense? Arguably not, since the “difference between significant and not significant is not necessarily significant” (Gelman & Stern, 2006). Comparing significance levels across experiments is not valid inference. A non-significant replication result can be entirely consistent with the original effect, and yet count as a failure because it did not achieve significance. There must be a better metric.

The authors recognize this, so they also used a metric that utilized confidence intervals over simple significance tests. Namely, does the confidence interval from the replication study include the originally reported effect? They write,

This method addresses the weakness of the first test that a replication in the same direction and a P value of 0.06 may not be significantly different from the original result. However, the method will also indicate that a replication “fails” when the direction of the effect is the same but the replication effect size is significantly smaller than the original effect size … Also, the replication “succeeds” when the result is near zero but not estimated with sufficiently high precision to be distinguished from the original effect size. (p. 4)

So with this metric a replication is considered successful if the replication result’s confidence interval contains the original effect, and fails otherwise. The replication effect can be near zero, but if the CI is wide enough it counts as a non-failure (i.e., a “success”). A replication can also be quite near the original effect but have high precision, thus excluding the original effect and “failing”.

This metric is very indirect, and their use of scare-quotes around “succeeds” is telling. Roughly 47% of confidence intervals in the replications “succeeded” in capturing the original result. The problem with this metric is obvious: Replications with effects near zero but wide CIs get the same credit as replications that were bang on the original effect (or even larger) with narrow CIs. Results that don’t flat out contradict the original effects count as much as strong confirmations? Why should both of these types of results be considered equally successful?

Based on these two metrics, the headlines are accurate: Over half of the replications “failed”. But these two reproducibility metrics are either invalid (comparing significance levels across experiments) or very vague (confidence interval agreement). They also only offer binary answers: A replication either “succeeds” or “fails”, and this binary thinking leads to absurd conclusions in some cases like those mentioned above. Is replicability really so black and white? I will explain below how I think we should measure replicability in a Bayesian way, with a continuous measure that can find reasonable answers with replication effects near zero with wide CIs, effects near the original with tight CIs, effects near zero with tight CIs, replication effects that go in the opposite direction, and anything in between.

A Bayesian metric of reproducibility

I wanted to look at the results of the reproducibility project through a Bayesian lens. This post should really be titled, “A Bayesian …” or “One Possible Bayesian …” since there is no single Bayesian answer to any question (but those titles aren’t as catchy). It depends on how you specify the problem and what question you ask. When I look at the question of replicability, I want to know if is there evidence for replication success or for replication failure, and how strong that evidence is. That is, should I interpret the replication results as more consistent with the original reported result or more consistent with a null result, and by how much?

Verhagen and Wagenmakers (2014), and Wagenmakers, Verhagen, and Ly (2015) recently outlined how this could be done for many types of problems. The approach naturally leads to computing a Bayes factor. With Bayes factors, one must explicitly define the hypotheses (models) being compared. In this case one model corresponds to a probability distribution centered around the original finding (i.e. the posterior), and the second model corresponds to the null model (effect = 0). The Bayes factor tells you which model the replication result is more consistent with, and larger Bayes factors indicate a better relative fit. So it’s less about obtaining evidence for the effect in general and more about gauging the relative predictive success of the original effects. (footnote 1)

If the original results do a good job of predicting replication results, the original effect model will achieve a relatively large Bayes factor. If the replication results are much smaller or in the wrong direction, the null model will achieve a large Bayes factor. If the result is ambiguous, there will be a Bayes factor near 1. Again, the question is which model better predicts the replication result? You don’t want a null model to predict replication results better than your original reported effect.

A key advantage of the Bayes factor approach is that it allows natural grades of evidence for replication success. A replication result can strongly agree with the original effect model, it can strongly agree with a null model, or it can lie somewhere in between. To me, the biggest advantage of the Bayes factor is it disentangles the two types of results that traditional significance tests struggle with: a result that actually favors the null model vs a result that is simply insensitive. Since the Bayes factor is inherently a comparative metric, it is possible to obtain evidence for the null model over the tested alternative. This addresses my problem I had with the above metrics: Replication results bang on the original effects get big boosts in the Bayes factor, replication results strongly inconsistent with the original effects get big penalties in the Bayes factor, and ambiguous replication results end up with a vague Bayes factor.

Bayes factor methods are often criticized for being subjective, sensitive to the prior, and for being somewhat arbitrary. Specifying the models is typically hard, and sometimes more arbitrary models are chosen for convenience for a given study. Models can also be specified by theoretical considerations that often appear subjective (because they are). For a replication study, the models are hardly arbitrary at all. The null model corresponds to that of a skeptic of the original results, and the alternative model corresponds to a strong theoretical proponent. The models are theoretically motivated and answer exactly what I want to know: Does the replication result fit more with the original effect model or a null model? Or as Verhagen and Wagenmakers (2014) put it, “Is the effect similar to what was found before, or is it absent?” (p.1458 here).

Replication Bayes factors

In the following, I take the effects reported in figure 3 of the reproducibility project (the pretty red and green scatterplot) and calculate replication Bayes factors for each one. Since they have been converted to correlation measures, replication Bayes factors can easily be calculated using the code provided by Wagenmakers, Verhagen, and Ly (2015). The authors of the reproducibility project kindly provide the script for making their figure 3, so all I did was take the part of the script that compiled the converted 95 correlation effect sizes for original and replication studies. (footnote 2) The replication Bayes factor script takes the correlation coefficients from the original studies as input, calculates the corresponding original effect’s posterior distribution, and then compares the fit of this distribution and the null model to the result of the replication. Bayes factors larger than 1 indicate the original effect model is a better fit, Bayes factors smaller than 1 indicate the null model is a better fit. Large (or really small) Bayes factors indicate strong evidence, and Bayes factors near 1 indicate a largely insensitive result.

The replication Bayes factors are summarized in the figure below (click to enlarge). The y-axis is the count of Bayes factors per bin, and the different bins correspond to various strengths of replication success or failure. Results that fall in the bins left of center constitute support the null over the original result, and vice versa. The outer-most bins on the left or right contain the strongest replication failures and successes, respectively. The bins labelled “Moderate” contain the more muted replication successes or failures. The two central-most bins labelled “Insensitive” contain results that are essentially uninformative.

 

Rep_bfs

So how did we do?

You’ll notice from this crude binning system that there is quite a spread from super strong replication failure to super strong replication success. I’ve committed the sin of binning a continuous outcome, but I think it serves as a nice summary. It’s important to remember that Bayes factors of 2.5 vs 3.5, while in different bins, aren’t categorically different. Bayes factors of 9 vs 11, while in different bins, aren’t categorically different. Bayes factors of 15 and 90, while in the same bin, are quite different. There is no black and white here. These are the categories Bayesians often use to describe grades of Bayes factors, so I use them since they are familiar to many readers. If you have a better idea for displaying this please leave a comment. 🙂 Check out the “Results” section at the end of this post to see a table which shows the study number, the N in original and replications, the r values of each study, the replication Bayes factor and category I gave it, and the replication p-value for comparison with the Bayes factor. This table shows the really wide spread of the results. There is also code in the “Code” section to reproduce the analyses.

Strong replication failures and strong successes

Roughly 20% (17 out of 95) of replications resulted in relatively strong replication failures (2 left-most bins), with resultant Bayes factors at least 10:1 in favor of the null. The highest Bayes factor in this category was over 300,000 (study 110, “Perceptual mechanisms that characterize gender differences in decoding women’s sexual intent”). If you were skeptical of these original effects, you’d feel validated in your skepticism after the replications. If you were a proponent of the original effects’ replicability you’ll perhaps want to think twice before writing that next grant based around these studies.

Roughly 25% (23 out of 95) of replications resulted in relatively strong replication successes (2 right-most bins), with resultant Bayes factors at least 10:1 in favor of the original effect. The highest Bayes factor in this category was 1.3×10^32 (or log(bf)=74; study 113, “Prescribed optimism: Is it right to be wrong about the future?”) If you were a skeptic of the original effects you should update your opinion to reflect the fact that these findings convincingly replicated. If you were a proponent of these effects you feel validation in that they appear to be robust.

These two types of results are the most clear-cut: either the null is strongly favored or the original reported effect is strongly favored. Anyone who was indifferent to these effects has their opinion swayed to one side, and proponents/skeptics are left feeling either validated or starting to re-evaluate their position. There was only 1 very strong (BF>100) failure to replicate but there were quite a few very strong replication successes (16!). There were approximately twice as many strong (10<BF<100) failures to replicate (16) than strong replication successes (7).

Moderate replication failures and moderate successes

The middle-inner bins are labelled “Moderate”, and contain replication results that aren’t entirely convincing but are still relatively informative (3<BF<10). The Bayes factors in the upper end of this range are somewhat more convincing than the Bayes factors in the lower end of this range.

Roughly 20% (19 out of 95) of replications resulted in moderate failures to replicate (third bin from the left), with resultant Bayes factors between 10:1 and 3:1 in favor of the null. If you were a proponent of these effects you’d feel a little more hesitant, but you likely wouldn’t reconsider your research program over these results. If you were a skeptic of the original effects you’d feel justified in continued skepticism.

Roughly 10% (9 out of 95) of replications resulted in moderate replication successes (third bin from the right), with resultant Bayes factors between 10:1 and 3:1 in favor of the original effect. If you were a big skeptic of the original effects, these replication results likely wouldn’t completely change your mind (perhaps you’d be a tad more open minded). If you were a proponent, you’d feel a bit more confident.

Many uninformative “failed” replications

The two central bins contain replication results that are insensitive. In general, Bayes factors smaller than 3:1 should be interpreted only as very weak evidence. That is, these results are so weak that they wouldn’t even be convincing to an ideal impartial observer (neither proponent nor skeptic). These two bins contain 27 replication results. Approximately 30% of the replication results from the reproducibility project aren’t worth much inferentially!

A few examples:

  • Study 2, “Now you see it, now you don’t: repetition blindness for nonwords” BF = 2:1 in favor of null
  • Study 12, “When does between-sequence phonological similarity promote irrelevant sound disruption?” BF = 1.1:1 in favor of null
  • Study 80, “The effects of an implemental mind-set on attitude strength.” BF = 1.2:1 in favor of original effect
  • Study 143, “Creating social connection through inferential reproduction: Loneliness and perceived agency in gadgets, gods, and greyhounds” BF = 2:1 in favor of null

I just picked these out randomly. The types of replication studies in this inconclusive set range from attentional blink (study 2), to brain mapping studies (study 55), to space perception (study 167), to cross national comparisons of personality (study 154).

Should these replications count as “failures” to the same extent as the ones in the left 2 bins? Should studies with a Bayes factor of 2:1 in favor of the original effect count as “failures” as much as studies with 50:1 against? I would argue they should not, they should be called what they are: entirely inconclusive.

Interestingly, study 143 mentioned above was recently called out in this NYT article as a high-profile study that “didn’t hold up”. Actually, we don’t know if it held up! Identifying replications that were inconclusive using this continuous range helps avoid over-interpreting ambiguous results as “failures”.

Wrap up

To summarize the graphic and the results discussed above, this method identifies roughly as many replications with moderate success or better (BF>3) as the counting significance method (32 vs 35). (footnote 3) These successes can be graded based on their replication Bayes factor as moderate to very strong. The key insight from using this method is that many replications that “fail” based on the significance count are actually just inconclusive. It’s one thing to give equal credit to two replication successes that are quite different in strength, but it’s another to call all replications failures equally bad when they show a highly variable range. Calling a replication a failure when it is actually inconclusive has consequences for the original researcher and the perception of the field.

As opposed to the confidence interval metric, a replication effect centered near zero with a wide CI will not count as a replication success with this method; it would likely be either inconclusive or weak evidence in favor of the null. Some replications are indeed moderate to strong failures to replicate (36 or so), but nearly 30% of all replications in the reproducibility project (27 out of 95) were not very informative in choosing between the original effect model and the null model.

So to answer my question as I first posed it, are the categorical conclusions of wide-scale failures to replicate by the media stories warranted? As always, it depends.

  • If you count “success” as any Bayes factor that has any evidence in favor of the original effect (BF>1), then there is a 44% success rate (42 out of 95).
  • If you count “success” as any Bayes factor with at least moderate evidence in favor of the original effect (BF>3), then there is a 34% success rate (32 out of 95).
  • If you count  “failure” as any Bayes factor that has at least moderate evidence in favor of the null (BF<1/3), then there is a 38% failure rate (36 out of 95).
  • If you only consider the effects sensitive enough to discriminate the null model and the original effect model (BF>3 or BF<1/3) in your total, then there is a roughly 47% success rate (32 out of 68). This number jives (uncannily) well with the prediction John Ioannidis made 10 years ago (47%).

However you judge it, the results aren’t exactly great.

But if we move away from dichotomous judgements of replication success/failure, we see a slightly less grim picture. Many studies strongly replicated, many studies strongly failed, but many studies were in between. There is a wide range! Judgements of replicability needn’t be black and white. And with more data the inconclusive results could have gone either way.  I would argue that any study with 1/3<BF<3 shouldn’t count as a failure or a success, since the evidence simply is not convincing; I think we should hold off judging these inconclusive effects until there is stronger evidence. Saying “we didn’t learn much about this or that effect” is a totally reasonable thing to do. Boo dichotomization!

Try out this method!

All in all, I think the Bayesian approach to evaluating replication success is advantageous in 3 big ways: It avoids dichotomizing replication outcomes, it gives an indication of the range of the strength of replication successes or failures, and it identifies which studies we need to give more attention to (insensitive BFs). The Bayes factor approach used here can straighten out when a replication shows strong evidence in favor of the null model, strong evidence in favor of the original effect model, or evidence that isn’t convincingly in favor of either position. Inconclusive replications should be targeted for future replication, and perhaps we should look into why these studies that purport to have high power (>90%) end up with insensitive results (large variance, design flaw, overly optimistic power calcs, etc). It turns out that having high power in planning a study is no guarantee that one actually obtains convincingly sensitive data (Dienes, 2014; Wagenmakers et al., 2014).

I should note, the reproducibility project did try to move away from the dichotomous thinking about replicability by correlating the converted effect sizes (r) between original and replication studies. This was a clever idea, and it led to a very pretty graph (figure 3) and some interesting conclusions. That idea is similar in spirit to what I’ve laid out above, but its conclusions can only be drawn from batches of replication results. Replication Bayes factors allow one to compare the original and replication results on an effect by effect basis. This Bayesian method can grade a replication on its relative success or failure even if your reproducibility project only has 1 effect in it.

I should also note, this analysis is inherently context dependent. A different group of studies could very well show a different distribution of replication Bayes factors, where each individual study has a different prior distribution (based on the original effect). I don’t know how much these results would generalize to other journals or other fields, but I would be interested to see these replication Bayes factors employed if systematic replication efforts ever do catch on in other fields.

Acknowledgements and thanks

The authors of the reproducibility project have done us all a great service and I am grateful that they have shared all of their code, data, and scripts. This re-analysis wouldn’t have been possible without their commitment to open science. I am also grateful to EJ Wagenmakers, Josine Verhagen, and Alexander Ly for sharing the code to calculate the replication Bayes factors on the OSF. Many thanks to Chris Engelhardt and Daniel Lakens for some fruitful discussions when I was planning this post. Of course, the usual disclaimer applies and all errors you find should be attributed only to me.


 

Notes

footnote 1: Of course, a model that takes publication bias into account could fit better by tempering the original estimate, and thus show relative evidence for the bias-corrected effect vs either of the other models; but that’d be answering a different question than the one I want to ask.

footnote 2: I left out 2 results that I couldn’t get to work with the calculations. Studies 46 and 139, both appear to be fairly strong successes, but I’ve left them out of the reported numbers because I couldn’t calculate a BF.

footnote 3: The cutoff of BF>3 isn’t a hard and fast rule at all. Recall that this is a continuous measure. Bayes factors are typically a little more conservative than significance tests in supporting the alternative hypothesis. If the threshold for success is dropped to BF>2 the number of successes is 35 — an even match with the original estimate.

Results

This table is organized from smallest replication Bayes factor to largest (i.e., strongest evidence in favor of null to strongest evidence in favor of original effect). The Ns were taken from the final columns in the master data sheet,”T_N_O_for_tables” and “T_N_R_for_tables”. Some Ns are not integers because they presumably underwent df correction. There is also the replication p-value for comparison; notice that BFs>3 generally correspond to ps less than .05 — BUT there are some cases where they do not agree. If you’d like to see more about the studies you can check out the master data file in the reproducibility project OSF page (linked below).

R Code

If you want to check/modify/correct my code, here it is. If you find a glaring error please leave a comment below or tweet at me 🙂

References

Link to the reproducibility project OSF

Link to replication Bayes factors OSF

Dienes, Z. (2014). Using Bayes to get the most out of non-significant results. Frontiers in psychology, 5.

Gelman, A., & Stern, H. (2006). The difference between “significant” and “not significant” is not itself statistically significant. The American Statistician, 60(4), 328-331.

Open Science Collaboration (2015). Estimating the reproducibility of psychological science. Science 28 August 2015: 349 (6251), aac4716 [DOI:10.1126/science.aac4716]

Verhagen, J., & Wagenmakers, E. J. (2014). Bayesian tests to quantify the result of a replication attempt. Journal of Experimental Psychology: General,143(4), 1457.

Wagenmakers, E. J., Verhagen, A. J., & Ly, A. (in press). How to quantify the evidence for the absence of a correlation. Behavior Research Methods.

Wagenmakers, E. J., Verhagen, J., Ly, A., Bakker, M., Lee, M. D., Matzke, D., … & Morey, R. D. (2014). A power fallacy. Behavior research methods, 1-5.

Understanding Bayes: Visualization of the Bayes Factor

In the first post of the Understanding Bayes series I said:

The likelihood is the workhorse of Bayesian inference. In order to understand Bayesian parameter estimation you need to understand the likelihood. In order to understand Bayesian model comparison (Bayes factors) you need to understand the likelihood and likelihood ratios.

I’ve shown in another post how the likelihood works as the updating factor for turning priors into posteriors for parameter estimation. In this post I’ll explain how using Bayes factors for model comparison can be conceptualized as a simple extension of likelihood ratios.

There’s that coin again

Imagine we’re in a similar situation as before: I’ve flipped a coin 100 times and it came up 60 heads and 40 tails. The likelihood function for binomial data in general is:

\ P \big(X = x \big) \propto \ p^x \big(1-p \big)^{n-x}

and for this particular result:

\ P \big(X = 60 \big) \propto \ p^{60} \big(1-p \big)^{40}

The corresponding likelihood curve is shown below, which displays the relative likelihood for all possible simple (point) hypotheses given this data. Any likelihood ratio can be calculated by simply taking the ratio of the different hypotheses’s heights on the curve.

fig1

In that previous post I compared the fair coin hypothesis — H0: P(H)=.5 — vs one particular trick coin hypothesis — H1: P(H)=.75. For 60 heads out of 100 tosses, the likelihood ratio for these hypotheses is L(.5)/L(.75) = 29.9. This means the data are 29.9 times as probable under the fair coin hypothesis than this particular trick coin hypothesisBut often we don’t have theories precise enough to make point predictions about parameters, at least not in psychology. So it’s often helpful if we can assign a range of plausible values for parameters as dictated by our theories.

Enter the Bayes factor

Calculating a Bayes factor is a simple extension of this process. A Bayes factor is a weighted average likelihood ratio, where the weights are based on the prior distribution specified for the hypotheses. For this example I’ll keep the simple fair coin hypothesis as the null hypothesis — H0: P(H)=.5 — but now the alternative hypothesis will become a composite hypothesis — H1: P(θ). (footnote 1) The likelihood ratio is evaluated at each point of P(θ) and weighted by the relative plausibility we assign that value. Then once we’ve assigned weights to each ratio we just take the average to get the Bayes factor. Figuring out how the weights should be assigned (the prior) is the tricky part.

Imagine my composite hypothesis, P(θ), is a combination of 21 different point hypotheses, all evenly spaced out between 0 and 1 and all of these points are weighted equally (not a very realistic hypothesis!). So we end up with P(θ) = {0, .05, .10, .15, . . ., .9, .95, 1}. The likelihood ratio can be evaluated at every possible point hypothesis relative to H0, and we need to decide how to assign weights. This is easy for this P(θ); we assign zero weight for every likelihood ratio that is not associated with one of the point hypotheses contained in P(θ), and we assign weights of 1 to all likelihood ratios associated with the 21 points in P(θ).

This gif has the 21 point hypotheses of P(θ) represented as blue vertical lines (indicating where we put our weights of 1), and the turquoise tracking lines represent the likelihood ratio being calculated at every possible point relative to H0: P(H)=.5. (Remember, the likelihood ratio is the ratio of the heights on the curve.) This means we only care about the ratios given by the tracking lines when the dot attached to the moving arm aligns with the vertical P(θ) lines. [edit: this paragraph added as clarification]
gif11

The 21 likelihood ratios associated with P(θ) are:

{~0, ~0, ~0, ~0, ~0, ~0, ~0, ~0, .002, .08, 1, 4.5, 7.5, 4.4, .78, .03, ~0, ~0, ~0, ~0, ~0}

Since they are all weighted equally we simply average, and obtain BF = 18.3/21 = .87. In other words, the data (60 heads out of 100) are 1/.87 = 1.15 times more probable under the null hypothesis — H0: P(H)=.5 — than this particular composite hypothesis — H1: P(θ). Entirely uninformative! Despite tossing the coin 100 times we have extremely weak evidence that is hardly worth even acknowledging. This happened because much of P(θ) falls in areas of extremely low likelihood relative to H0, as evidenced by those 13 zeros above. P(θ) is flexible, since it covers the entire possible range of θ, but this flexibility comes at a price. You have to pay for all of those zeros with a lower weighted average and a smaller Bayes factor.

Now imagine I had seen a trick coin like this before, and I know it had a slight bias towards landing heads. I can use this information to make more pointed predictions. Let’s say I define P(θ) as 21 equally weighted point hypotheses again, but this time they are all equally spaced between .5 and .75, which happens to be the highest density region of the likelihood curve (how fortuitous!). Now P(θ) = {.50, .5125, .525, . . ., .7375, .75}.
gif22

The 21 likelihood ratios associated with the new P(θ) are:

{1.00, 1.5, 2.1, 2.8, 4.5, 5.4, 6.2, 6.9, 7.5, 7.3, 6.9, 6.2, 4.4, 3.4, 2.6, 1.8, .78, .47, .27, .14, .03}

They are all still weighted equally, so the simple average is BF = 72/21 = 3.4. Three times more informative than before, and in favor of P(θ) this time! And no zeros. We were able to add theoretically relevant information to H1 to make more accurate predictions, and we get rewarded with a Bayes boost. (But this result is only 3-to-1 evidence, which is still fairly weak.)

This new P(θ) is risky though, because if the data show a bias towards tails or a more extreme bias towards heads then it faces a very heavy penalty (many more zeros). High risk = high reward with the Bayes factor. Make pointed predictions that match the data and get a bump to your BF, but if you’re wrong then pay a steep price. For example, if the data were 60 tails instead of 60 heads the BF would be 10-to-1 against P(θ) rather than 3-to-1 for P(θ)!

Now, typically people don’t actually specify hypotheses like these. Typically they use continuous distributions, but the idea is the same. Take the likelihood ratio at each point relative to H0, weigh according to plausibilities given in P(θ), and then average.

A more realistic (?) example

Imagine you’re walking down the sidewalk and you see a shiny piece of foreign currency by your feet. You pick it up and want to know if it’s a fair coin or an unfair coin. As a Bayesian you have to be precise about what you mean by fair and unfair. Fair is typically pretty straightforward — H0: P(H)=.5 as before — but unfair could mean anything. Since this is a completely foreign coin to you, you may want to be fairly open-minded about it. After careful deliberation, you assign P(θ) a beta distribution, with shape parameters 10 and 10. That is, H1: P(θ) ~ Beta(10, 10). This means that if the coin isn’t fair, it’s probably close to fair but it could reasonably be moderately biased, and you have no reason to think it is particularly biased to one side or the other.

prior1010

Now you build a perfect coin-tosser machine and set it to toss 100 times (but not any more than that because you haven’t got all day). You carefully record the results and the coin comes up 33 heads out of 100 tosses. Under which hypothesis are these data more probable, H0 or H1? In other words, which hypothesis did the better job predicting these data?

This may be a continuous prior but the concept is exactly the same as before: weigh the various likelihood ratios based on the prior plausibility assignment and then average. The continuous distribution on P(θ) can be thought of as a set of many many point hypotheses spaced very very close together. So if the range of θ we are interested in is limited to 0 to 1, as with binomials and coin flips, then a distribution containing 101 point hypotheses spaced .01 apart, can effectively be treated as if it were continuous. The numbers will be a little off but all in all it’s usually pretty close. So imagine that instead of 21 hypotheses you have 101, and their relative plausibilities follow the shape of a Beta(10, 10). (footnote 2)

gif33

Since this is not a uniform distribution, we need to assign varying weights to each likelihood ratio. Each likelihood ratio associated with a point in P(θ) is simply multiplied by the respective density assigned to it under P(θ). For example, the density of P(θ) at .4 is 2.44. So we multiply the likelihood ratio at that point, L(.4)/L(.5) = 128, by 2.44, and add it to the accumulating total likelihood ratio. Do this for every point and then divide by the total number of points, in this case 101, to obtain the approximate Bayes factor. The total weighted likelihood ratio is 5564.9, divide it by 101 to get 55.1, and there’s the Bayes factor. In other words, the data are roughly 55 times more probable under this composite H1 than under H0. The alternative hypothesis H1 did a much better job predicting these data than did the null hypothesis H0.

The actual Bayes factor is obtained by integrating the likelihood with respect to H1’s density distribution and then dividing by the (marginal) likelihood of H0. Essentially what it does is cut P(θ) into slices infinitely thin before it calculates the likelihood ratios, re-weighs, and averages. That Bayes factor comes out to 55.7, which is basically the same thing we got through this ghetto visualization demonstration!

Take home

The take-home message is hopefully pretty clear at this point: When you are comparing a point null hypothesis with a composite hypothesis, the Bayes factor can be thought of as a weighted average of every point hypothesis’s likelihood ratio against H0, and the weights are determined by the prior density distribution of H1. Since the Bayes factor is a weighted average based on the prior distribution, it’s really important to think hard about the prior distribution you choose for H1. In a previous post, I showed how different priors can converge to the same posterior with enough data. The priors are often said to “wash out” in estimation problems like that. This is not necessarily the case for Bayes factors. The priors you choose matter, so think hard!

Notes

Footnote 1: A lot of ink has been spilled arguing about how one should define P(θ). I talked about it a little a previous post.

Footnote 2: I’ve rescaled the likelihood curve to match the scale of the prior density under H1. This doesn’t affect the values of the Bayes factor or likelihood ratios because the scaling constant cancels itself out.

R code

The general public has no idea what “statistically significant” means

The title of this piece shouldn’t shock anyone who has taken an introductory statistics course. Statistics is full of terms that have a specific statistical meaning apart from their everyday meaning. A few examples:

Significant, confidence, power, random, mean, normal, credible, moment, bias, interaction, likelihood, error, loadings, weights, hazard, risk, bootstrap, information, jack-knife, kernel, reliable, validity; and that’s just the tip of the iceberg. (Of course, one’s list gets bigger the more statistics courses one takes.)

It should come as no surprise that the general public mistakes a term’s statistical meaning for its general english meaning when nearly every word has some sort of dual-meaning.

Philip Tromovitch (2015) has recently put out a neat paper in which he surveyed a little over 1,000 members of the general public on their understanding of the meaning of “significant,” a term which has a very precise statistical definition: assuming the null hypothesis is true (usually defined as no effect), discrepancies as large or larger than this result would be so rare that we should act as if the null hypothesis isn’t true and we won’t often be wrong.

However, in everyday english, something that is significant means that it is noteworthy or worth our attention. Rather than give a cliched dictionary definition, I asked my mother what she thought. She says she would interpret a phrase such as, “there was a significant drop in sales from 2013 to 2014” to indicate that the drop in sales was “pretty big, like quite important.” (thanks mom 🙂 ) But that’s only one person. What did Tromovitch’s survey respondents think?

Tromovitch surveyed a total of 1103 people. He asked 611 of his respondents to answer this multiple choice question, and the rest answered a variant as an open ended question. Here is the multiple choice question to his survey respondents:

When scientists declare that the finding in their study is “significant,” which of the following do you suspect is closest to what they are saying:

  • the finding is large
  • the finding is important
  • the finding is different than would be expected by chance
  • the finding was unexpected
  • the finding is highly accurate
  • the finding is based on a large sample of data

Respondents choosing the first two responses were considered to be incorrectly using general english, choosing the third answer was considered correct, and choosing any of the final three were considered other incorrect answer. He separated general public responses from those with doctorate degrees (n=15), but he didn’t get any information on what topic their degree was in, so I’ll just refer to the rest of the sample’s results from here on since the doctorate sample should really be taken with a grain of salt.

Roughly 50% of respondents gave a general english interpretation of the “significant” results (options 1 or 2), roughly 40% chose one of the other three wrong responses (options 4, 5, or 6), and less than 10% actually chose the correct answer (option 3). Even if they were totally guessing you’d expect them to get close to 17% correct (1/6), give or take.

But perhaps multiple choice format isn’t the best way to get at this, since the prompt itself provides many answers that sound perfectly reasonable. Tromovitch also asked this as an open-ended question to see what kind of responses people would generate themselves. One variant of the prompt explicitly mentions that he wants to know about statistical significance, while the other simply mentions significance. The exact wording was this:

Scientists sometimes conclude that the finding in their study is “[statistically] significant.” If you were updating a dictionary of modern American English, how would you define the term “[statistically] significant”?

Did respondents do any better when they can answer freely? Not at all. Neither prompt had a very high success rate; they had correct response rates at roughly 4% and 1%. This translates to literally 12 correct answers out of the total 492 respondents of both prompts combined (including phd responses). Tromovitch includes all of these responses in the appendix so you can read the kinds of answers that were given and considered to be correct.

If you take a look at the responses you’ll see that most of them imply some statement about the probability of one hypothesis or the other being true, which isn’t allowed by the correct definition of statistical significance! For example, one answer coded as correct said, “The likelihood that the result/findings are not due to chance and probably true” is blatantly incorrect. The probability that the results are not due to chance is not what statistical significance tells you at all. Most of the responses coded as “correct” by Tromovitch are quite vague, so it’s not clear that even those correct responders have a good handle on the concept. No wonder the general public looks at statistics as if they’re some hand-wavy magic. They don’t get it at all.

snape 2

My takeaway from this study is the title of this piece: the general public has no idea what statistical significance means. That’s not surprising when you consider that researchers themselves often don’t know what it means! Even professors who teach research methods and statistics get this wrong. Results from Haller & Krauss (2002), building off of Oakes (1986), suggest that it is normal for students, academic researchers, and even methodology instructors to endorse incorrect interpretations of p-values and significance tests. That’s pretty bad. It’s one thing for first-year students or the lay public to be confused, but educated academics and methodology instructors too? If you don’t buy the survey results, open up any journal issue in any psychology journal and you’ll find tons of examples of misinterpretation and confusion.

Recently Hoekstra, Morey, Rouder, & Wagenmakers (2014) demonstrated that confidence intervals are similarly misinterpreted by researchers, despite recent calls (Cumming, 2014) to totally abandon significance tests in lieu of confidence intervals. Perhaps we could toss out the whole lot and start over with something that actually makes sense? Maybe we could try teaching something that people can actually understand?

I’ve heard of this cool thing called Bayesian statistics we could try.

 

References

Cumming, G. (2014). The new statistics: Why and how. Psychological Science25(1), 7-29.

Haller, H., & Krauss, S. (2002). Misinterpretations of significance: A problem students share with their teachers. Methods of Psychological Research, 7(1), 1-20.

Hoekstra, R., Morey, R. D., Rouder, J. N., & Wagenmakers, E. J. (2014). Robust misinterpretation of confidence intervals. Psychonomic Bulletin & Review, 21(5), 1157-1164.

Oakes, M. W. (1986). Statistical inference: A commentary for the social and behavioural sciences. Wiley.

Tromovitch, P. (2015). The lay public’s misinterpretation of the meaning of ‘significant’: A call for simple yet significant changes in scientific reporting. Journal of Research Practice, 1(1), 1.