Category Archives: P-Curve

Z-Curve: An even better p-curve

P-Curve, P-Hacking., Z-Curve

So far Simmons, Nelson, and Simonsohn have not commented on this blog post. I now submitted it as a commentary to JEP-General. Let’s see whether it will be send out for review and whether they will comment as (anonymous) reviewers.

Abstract

P-Curve was a first attempt to take the problem of selection for significance seriously and to evaluate whether a set of studies provides credible evidence against the null-hypothesis after taking selection bias into account. Here I showed that p-curve has serious limitations and provides misleading evidence about the strength of evidence against the null-hypothesis. I showed that all of the information that is provided by a p-curve analysis (Simonsohn, Nelson, & Simmons, 2014) is also provided by a z-curve analysis (Bartos & Schimmack, 2021). Moreover, z-curve provides additional information about the presence and the amount of selection bias. As z-curve is superior than p-curve, the rational choice is to use z-curve to examine the credibility of significant results.

Keywords: Publication Bias, Selection Bias, Z-Curve, P-Curve, Expected Replication Rate, Expected Discovery Rate, File-Drawer, Power

Introduction

In 2011, it dawned on psychologists that something was wrong with their science. Daryl Bem had just published an article with nine studies that showed an incredible finding (Bem, 2011). Participants’ responses were influenced by random events that had not yet occurred. Since then, the flaws in research practices have become clear and it has been shown that they are not limited to mental time travel (Schimmack, 2020). For decades, psychologists assumed that statistically significant results reveal true effects and reported only statistically significant results (Motyl et al., 2017; Sterling, 1959; Sterling et al., 1995). However, selective reporting of significant results undermines the purpose of significance testing to distinguish true and false hypotheses. If only significant results are reported, most published results could be false positive results (Simmons, Nelson, & Simonsohn, 2011).

Selective reporting of significant results also undermines the credibility of meta-analyses (Rosenthal, 1979), which explains why meta-analyses also suggest humans posses psychic abilities (Bem & Honorton, 1994). Thus, selection bias not only invalidates the results of original studies, it also threatens the validity of conclusions based on meta-analyses that do not take selection bias into account.

Concerns about a replication crisis in psychology led to an increased focus on replication studies. An ambitious project found that only 37% of studies in (cognitive & social) experimental psychology could be replicated (Open Science Collaboration, 2015). This dismal result created a crisis of confidence in published results. To alleviate these concerns, psychologists developed new methods to detect publication bias. These new methods showed that Bem’s paranormal results were obtained with the help of questionable research practices (Francis, 2012; Schimmack, 2012), which explained why replication attempts were unsuccessful (Galak et al., 2012). Furthermore, Francis showed that many published articles in the prestigious journal Psychological Science show signs of publication bias (Francis, 2014). However, the presence of publication bias does not imply that the published results are false (positives). Publication bias may merely inflate effect sizes without invalidating the main theoretical claims. To address the latter question it is necessary to conduct meta-analyses that take publication bias into account. In this article, I compare two methods that were developed for this purpose; p-curve (Simonsohn et al., 2014), and z-curve (Bartos & Schimmack, 2021; Brunner & Schimmack, 2020). P-curve was introduced in 2014 and has already been used in many articles. Z-curve was developed in 2015, but was only published recently in a peer-reviewed journal. Experimental psychologists who are familiar with speed-accuracy tradeoffs may not be surprised to learn that z-curve is a superior method. As Brunner and Schimmack (2020) demonstrated with simulation studies, p-curve often produces inflated estimates of the evidential value of original studies. This bias was not detected by the developers of p-curve because they did not evaluate their method with simulation studies. Moreover, their latest version of p-curve was never peer-reviewed. In this article, I first provide a critical review of p-curve and then show how z-curve addresses all of them.

P-Curve

P-curve is a name for a family of statistical tests that have been combined into the p-curve app that researchers can use to conduct p-curve analyses, henceforth called p-curve . The latest version of p-curve is version 4.06 that was last updated on November 30, 2017 (p-curve.com).

The first part of a p-curve analysis is a p-curve plot. A p-curve plot is a histogram of all significant p-values where p-values are placed into five bins, namely p-values ranging from 0 to .01, .01 to .02, .02 to .03, .03 to .04, and .04 to .05. If the set of studies contains mostly studies with true effects that have been tested with moderate to high power, there are more p-values between 0 and .01 than between .04 and .05. This pattern has been called a right-skewed distribution by the p-curve authors. If the distribution is flat or reversed (more p-values between .04 and .05 than between 0 and .01), the data lack evidential value; that is, the results are more consistent with the null-hypothesis than with the presence of a real effect.

The main limitation of p-curve plots is that it is difficult to evaluate ambiguous cases. To aid in the interpretation of p-curve plots, p-curve also provides statistical tests of evidential value. One test is a significance tests against the null-hypothesis that all significant p-values are false positive results. If this null-hypothesis can be rejected with the traditional alpha criterion of .05, it is possible to conclude that at least some of the significant results are not false positives. The main problem with this significance test is that it does not provide information about effect sizes. A right-skewed p-curve with a significant p-values may be due to weak evidence with many false positive results or strong evidence with few false positives.

To address this concern, the p-curve app also provides an estimate of statistical power. When studies are heterogeneous (i.e., different sample sizes or effect sizes or both) this estimate is an estimate of mean unconditional power (Bartos & Schimmack, 2021; Brunner & Schimmack, 2020). Unconditional power refers to the fact that a significant result may be a false positive result. Unconditional power does not condition on the presence of an effect (i.e., the null-hypothesis is false). When the null-hypothesis is true, a result has a probability of alpha (typically 5%) to be significant. Thus, a p-curve analysis that includes some false positive results, includes some studies with a probability equal to alpha and others with probabilities greater than alpha.

To illustrate the p-curve app, I conducted a meta-analysis of all published articles by Leif D. Nelson, one of the co-authors of p-curve  I found 119 studies with codable data and coded the most focal hypothesis for each of these studies. I then submitted the data to the online p-curve app. Figure 1 shows the output.

Visual inspection of the p-curve plot shows a right-skewed distribution with 57% of the p-values between 0 and .01 and only 6% of p-values between .04 and .05. The statistical tests against the null-hypothesis that all of the significant p-values are false positives is highly significant. Thus, at least some of the p-values are likely to be true positives. Finally, the power estimate is very high, 97%, with a tight confidence interval ranging from 96% to 98%. Somewhat redundant with this information, the p-curve app also provides a significance test for the hypothesis that power is less than 33%. This test is not significant, which is not surprising given the estimated power of 97%.

The p-curve results are surprising. After all, Nelson openly stated that he used questionable research practices before he became aware of the high false positive risk associated with these practices. “We knew many researchers—including ourselves—who readily admitted to dropping dependent variables, conditions, or participants to achieve significance.” (Simmons, Nelson, & Simonsohn, 2018, p. 255). The impressive estimate of 97% power is in stark contrast to the claim that questionable research practices were used to produce Nelson’s results. A z-curve analysis of the data shows that the p-curve results provide false information about the robustness of Nelson’s published results.

Z-Curve

Like p-curve, z-curve analyses are supplemented by a plot of the data. The main difference is that p-values are converted into z-scores using the formula for the inverse normal distribution; z = qnorm(1-p/2). The second difference is that significant and non-significant p-values are plotted. The third difference is that z-curve plots have a much finer resolution than p-curve plots. Whereas p-curve bins all z-scores from 2.58 to infinity into one bin (p < .01), z-curve uses the information about the distribution of z-scores all the way up to z = 6 (p = .000000002; 1/500,000,000). Z-statistics greater than 6 are assigned a power of 1.

Visual inspection of the z-curve plot reveals something that the p-curve plot does not show, namely there is clear evidence for the presence of selection bias. Whereas p-curve suggests that “highly” significant results (0 to .01) are much more common than “just” significant results (.04 to .05), z-curve shows that just significant results (.05 to .005) are much more frequent than highly significant (p < .005) results. The difference is due to the implicit definition of high and low in the two plots. The high frequency of highly significant (p < .01) results in the p-curve plots is due to the wide range of values that are lumped together into this bin. Once it is clear that many p-values are clustered just below .05 (z > 1.96, the vertical red line), it is immediately notable that there are too few just non-significant (z < 1.96) values. This steep drop in frequencies for just significant to just not significant values is inconsistent with random sampling error. Thus, publication bias is readily visible by visual inspection of a z-curve plot. In contrast, p-curve plots provide no information about publication bias because non-significant results are not shown. Even worse, right skewed distributions are often falsely interpreted as evidence that there is no publication bias or use of questionable research practices (e.g., Rusz, Le Pelley, Kompier, Mait, & Bijleveld, 2020). This misinterpretation of p-curve plots can be easily avoided by inspection of z-curve plots.

The second part of a z-curve analysis uses a finite mixture model to estimate two statistical parameters of the data. These parameters are called the expected discovery rate and the expected replication rate (Bartos & Schimmack, 2021). Another term for these parameters is mean power before selection and mean power after selection for significance (Brunner & Schimmack, 2020). The meaning of these terms is best understood with a simple example where a researcher tests 100 false hypotheses and 100 true hypotheses with 100% power. The outcome of this study produces significant and non-significant p-values. The expected value for the frequency of significant p-values is 100 for the 100 true hypotheses tested with 100% power and 5% for the 100 false hypotheses that produce 5 significant results when alpha is set to 5%. Thus, we are expecting 105 significant results and 95 non-significant results. In this example, the discovery rate is 105/200 = 52.5%. With real data, the discovery rate is often not known because not all statistical tests are published. When selection for significance is present, the observed discovery rate is an inflated estimate of the actual discovery rate. For example, if 50 of the 95 non-significant results are missing, the observed discovery rate is 105/150 = 70%. Z-curve.2.0 uses the distribution of the significant z-scores to estimate the discovery rate by taking selection bias into account. That is, it uses the truncated distribution for z-scores greater than 1.96 to estimate the shape of the full distribution (i.e., the grey curve in Figure 2). This produces an estimate of the mean power before selection for significance. As significance is determined by power and sampling error, the estimate of mean power provides an estimate of the expected discovery rate. Figure 2 shows an observed discovery rate of 87%. This is in line with estimates of discovery rates around 90% in psychology journals (Motyl et al., 2017; Sterling, 1959; Sterling et al., 1995). However, the z-curve estimate of the expected discovery rate is only 27%. The bootstrapped, robust confidence interval around this estimate ranges from 5% to 51%. As this interval does not include the value for the observed discovery rate, the results provide statistically significant evidence that questionable research practices were used to produce 89% significant results. Moreover, the difference between the observed and expected discovery rate is large. This finding is consistent with Nelson’s admission that many questionable research practices were used to achieve significant results (Simmons et al., 2018). In contrast, p-curve provides no information about the presence or amount of selection bias.

The power estimate provided by the p-curve app is the mean power of studies with a significant result. Mean power for these studies is equal or greater to the mean power of all studies because studies with higher power are more likely to produce a significant result (Brunner & Schimmack, 2020). Bartos and Schimmack (2021) refer to mean power after selection for significance as the expected replication rate. To explain this term, it is instructive to see how selection for significance influences mean power in the example with 100 test of true null-hypotheses and 100 tests of true alternative hypotheses with 100% power. We expect only 5 false positive results and 100 true positive results. The average power of these 105 studies is (5  * .05 + 100 * 1)/105 = 95.5%.  This is much higher than the mean power before selection for significance which was based on 100 rather than just 5 tests of a true null-hypothesis. For Nelson’s data, p-curve produced an estimate of 97% power. Thus, p-curve predicts that 96% of replication attempts of Nelson’s published results would produce a significant result again. The z-curve estimate in Figure 2 shows that this is a dramatically inflated estimate of the expected replication rate. The z-curve estimate is only 52% with a robust 95% confidence interval ranging from 40% to 68%. Simulation studies show that z-curve estimates are close to the simulated values, whereas p-curve estimates are inflated when the studies are heterogeneous (Brunner & Schimmack, 2020). The p-curve authors have been aware of this bias in p-curve estimates since January 2018 (Simmons, Nelson, & Simonsohn, 2018), but they have not changed their app or warned users about this problem. The present example clearly shows that p-curve estimates can be highly misleading and that it is unscientific to use or interpret p-curve estimates of the expected replication rate.

Published Example

Since p-curve was introduced, it has been cited in over 500 articles and it has been used in many meta-analyses. While some meta-analyses correctly interpreted p-curve results to demonstrate merely that a set of studies have some evidential value (i.e., the nil-hypothesis that all significant results are false positives), others went further and drew false conclusions from a p-curve analysis. Moreover, meta-analyses that used p-curve missed the opportunity to quantify the amount of selection bias in a literature. To illustrate how meta-analysts can benefit from a z-curve analysis, I reexamined a meta-analysis of the effects of reward stimuli on attention (Rusz, et al., 2020).

Using their open data (https://osf.io/rgeb6/), I first reproduced their p-curve analysis using the p-curve app (http://www.p-curve.com/app4/). Figure 3 show that 42% of the p-values are between .01 and 0, whereas only 7% of the p-values are between .04 and .05. The figure also shows that the observed p-curve is similar to the p-curve that is predicted by a homogeneous set of studies with 33% power. Nevertheless, power is estimated to be 52%. Rusz et al. (2020) interpret these results as evidence that “this set of studies contains evidential value for reward-driven distraction” and that “It provides no evidence for p-hacking” (p. 886).

Figure 4 shows the z-curve for the same data. Visual inspection of the z-curve plot shows that there are many more just-significant than just-not-significant results. This impression is confirmed by a comparison of the observed discovery rate (74%) versus the expected discovery rate (27%). The bootstrapped, robust 95% confidence interval, 8% to 58%, does not include the observed discovery rate. Thus, there is statistically significant evidence that questionable research practices inflated the percentage of significant results. The expected replication rate is also lower (37%) than the p-curve estimate (52%). With an average power of 37%, it is clear that published studies are underpowered. Based on these results, it is clear that effect-size meta-analysis that do not take selection bias into account produce inflated effect size estimates. Moreover, when the ERR is higher than the EDR, studies are heterogenous, which means that some studies have even less power than the average power of 37%, and some of these may be false positive results. It is therefore unclear which reward stimuli and which attention paradigms show a theoretically significant effect and which do not. However, meta-analysts often falsely generalize an average effect to individual studies. For example, Rusz et al. (2020) concluded from their significant average effect size (d ~ .3) that high-reward stimuli impair cognitive performance “across different paradigms and across different reward cues” (p. 887). This conclusion is incorrect because they mean effect size is inflated and could be based on subsets of reward stimuli and paradigms. To demonstrate that a specific reward stimulus influences performance on a specific task would require high powered replication studies for the various combinations of rewards and paradigms. At present, the meta-analysis merely shows that some rewards can interfere with some tasks.

Conclusion

Simonsohn et al. (2014) introduced p-curve as a statistical tool to correct for publication bias and questionable research practices in meta-analyses. In this article, I critically reviewed p-curve and showed several limitations and biases in p-curve results. The first p-curve methods focussed on statistical significance and did not quantify the strength of evidence against the null-hypothesis that all significant results are false positives. This problem was solved by introducing a method that quantified strength of evidence as the mean unconditional power of studies with significant results. However, the estimation method was never validated with simulation studies. Independent simulation studies showed that p-curve systematically overestimates power when effect sizes or sample sizes are heterogeneous. In the present article, this bias inflated mean power for Nelson’s published results from 52% to 97%. This is not a small or negligible deviation. Rather, it shows that p-curve results can be extremely misleading. In an application to a published meta-analysis, the bias was less extreme, but still substantial, 37% vs. 52%, a 15 percentage points difference. As the amount of bias is unknown unless p-curve results are compared to z-curve results, researchers can simply use z-curve to obtain an estimate of mean power after selection for significance or the expected replication rate.

Z-curve not only provides a better estimate of the expected replication rate. It also provides an estimate of the expected discovery rate; that is the percentage of results that are significant if all studies were available (i.e., after researchers empty their file drawer). This estimate can be compared to the observed discovery rate to examine whether selection bias is present and how large it is. In contrast, p-curve provides no information about the presence of selection bias and the use of questionable research practices.

In sum, z-curve does everything that p-curve does better and it provides additional information. As z-curve is better than p-curve on all features, the rational choice is to use z-curve in future meta-analyses and to reexamine published p-curve analyses with z-curve. To do so, researchers can use the free R-package zcurve (Bartos & Schimmack, 2020).

References

Bartoš, F., & Schimmack, U. (2020). “zcurve: An R Package for Fitting Z-curves.” R package version 1.0.0

Bartoš, F., & Schimmack, U. (2021). Z-curve.2.0: Estimating the replication and discovery rates. Meta-Psychology, in press.

Bem, D. J. (2011). Feeling the future: Experimental evidence for anomalous retroactive influences on cognition and affect. Journal of Personality and Social Psychology, 100, 407–425. http://dx.doi.org/10.1037/a0021524

Bem, D. J., & Honorton, C. (1994). Does psi exist? Replicable evidence for an anomalous process of information transfer. Psychological Bulletin, 115(1), 4–18. https://doi.org/10.1037/0033-2909.115.1.4

Brunner, J. & Schimmack, U. (2020). Estimating population mean power under conditions of heterogeneity and selection for significance. Meta-Psychology, 4, https://doi.org/10.15626/MP.2018.874

Francis, G. (2012). Too good to be true: Publication bias in two prominent studies from experimental psychology. Psychonomic Bulletin & Review, 19, 151–156. http://dx.doi.org/10.3758/s13423-012-0227-9

Francis G., (2014). The frequency of excess success for articles in Psychological Science. Psychonomic Bulletin and Review, 21, 1180–1187. https://doi.org/10.3758/s13423-014-0601-x

Galak, J., LeBoeuf, R. A., Nelson, L. D., & Simmons, J. P. (2012). Correcting the past: Failures to replicate. Journal of Personality and Social Psychology, 103, 933–948. http://dx.doi.org/10.1037/a0029709

Motyl, M., Demos, A. P., Carsel, T. S., Hanson, B. E., Melton, Z. J., Mueller, A. B., Prims, J. P., Sun, J., Washburn, A. N., Wong, K. M., Yantis, C., & Skitka, L. J. (2017). The state of social and personality science: Rotten to the core, not so bad, getting better, or getting worse? Journal of Personality and Social Psychology, 113(1), 34–58. https://doi.org/10.1037/pspa0000084

Open Science Collaboration. (2015). Estimating the reproducibility of psychological science. Science, 349(6251), aac4716–aac4716. https://doi.org/10.1126/science.aac4716

Rosenthal, R. (1979). The file drawer problem and tolerance for null results. Psychological Bulletin, 86(3), 638–641. https://doi.org/10.1037/0033-2909.86.3.638

Rusz, D., Le Pelley, M. E., Kompier, M. A. J., Mait, L., & Bijleveld, E. (2020). Reward-driven distraction: A meta-analysis. Psychological Bulletin, 146(10), 872–899. https://doi.org/10.1037/bul0000296

Schimmack, U. (2012). The ironic effect of significant results on the credibility of multiple-study articles. Psychological Methods, 17, 551–566. https://doi.org/10.1037/a0029487

Schimmack, U. (2020). A meta-psychological perspective on the decade of replication failures in social psychology. Canadian Psychology/Psychologie canadienne. 61 (4), 364-376. https://doi.org/10.1037/cap0000246

Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2011). False-positive psychology: Undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychological Science, 22, 1359–1366. http://dx.doi.org/10.1177/0956797611417632

Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2018). False-positive citations. Perspectives on Psychological Science, 13(2), 255–259. https://doi.org/10.1177/1745691617698146

Simonsohn, U., Nelson, L. D., & Simmons, J. P. (2014). P-curve: A key to the file-drawer. Journal of Experimental Psychology: General, 143(2), 534–547. https://doi.org/10.1037/a0033242

Sterling, T. D. (1959). Publication decision and the possible effects on inferences drawn from tests of significance – or vice versa. Journal of the American Statistical Association, 54, 30–34. https://doi.org/10.2307/2282137

Sterling, T. D., Rosenbaum, W. L., & Weinkam, J. J. (1995). Publication decisions revisited: The effect of the outcome of statistical tests on the decision to publish and vice versa. The American Statistician, 49, 108–112. https://doi.org/10.2307/2684823

Smart P-Hackers Have File-Drawers and Are Not Detected by Left-Skewed P-Curves

P-Curve, Z-Curve

Abstract

In the early 2010s, two articles suggested that (a) p-hacking is common, (b) false positives are prevalent, and (c) left-skewed p-curves reveal p-hacking to produce false positive results (Simmons et al., 2011; Simonsohn, 2014a). However, empirical application of p-curve have produced few left-skewed p-curves. This raises question about the absence of left-skewed z-curves. One explanation is that some p-hacking strategies do not produce notable left skew and that these strategies may be used more often because they require fewer resources. Another explanation could be that file-drawering is much more common than p-packing. Finally, it could be that most of the time p-hacking is used to inflate true effect sizes rather than to chase false positive results. P-curve plots do not allow researchers to distinguish these alternative hypotheses. Thus, p-curve should be replaced by more powerful tools that detect publication bias or p-hacking and estimate the amount of evidence against the null-hypothesis. Fortunately, there is an app for this (zcurve package).

Introduction

Simonsohn, Nelson, and Simmons (2014) coined the term p-hacking for a set of questionable research practices that increase the chances of obtaining a statistically significant result. In the worst case scenario, p-hacking can produce significant results without a real effect. In this case, the statistically significant result is entirely explained by p-hacking.

Simonsohn et al. (2014) make a clear distinction between p-hacking and publication bias. Publication bias is unlikely to produce a large number of false positive results because it requires 20 attempts to produce a single significant result in either direction or 40 attempts to get a significant result with a predicted direction. In contrast, “p-hacking can allow researchers to get most studies to reveal significant relationships between truly unrelated variables (Simmons et al., 2011)” (p. 535).

There have been surprisingly few investigations of the best way to p-hack studies. Some p-hacking strategies may work in simulation studies that do not impose limits on resources, but they may not be practical in real applications of p-hacking. I postulate that the main goal of p-hacking is to get significant results with minimal resources rather than with a minimum number of studies and that p-hacking is more efficient with a file drawer of studies that are abandoned.

Simmons et al. (2011) and Simonsohn et al. (2014) suggest one especially dumb p-hacking strategy, namely simply collecting more data until a significant result emerges.

“For example, consider a researcher who p-hacks by analyzing data after every five per-condition participants and ceases upon obtaining significance.” (Simonsohn et al., 2014).

This strategy is known to produce more p-values close to .04 than .01.

The main problem with this strategy is that sample sizes can get very large before the significant result emerges. I limited the maximum sample size before a researcher would give up to N = 200. A limit of 20 makes sense because N = 200 would allow a researcher to run 20 studies with the starting sample size of N = 10 to get a significant result. The p-curve plot shows a similar distribution as the simulation in the p-curve article.

The success rate was 25%. This means, 75% of studies with N = 200 produced a non-significant result that had to be put in the file-drawer. Figure 2 shows the distribution of sample sizes for the significant results.

The key finding is that the chances of a significant results drop drastically after the first attempt. The reason is that the most favorable results in the first trial produce a significant result in the first trial. As a result, the non-significant ones are less favorable. It would be better to start a new study because the chances to get a significant result are higher than adding participants after an unsuccessful attempt. In short, just adding participants to get significant is a dumb p-hacking method.

Simonsohn et al. (2014) do not disclose the stopping rule, but they do show that they got only 5.6% significant results compared to the 25% with N = 200. This means they stopped much earlier. Simulation suggest that they stopped when N = 30 (n = 15 per cell) did not produce a significant result (1 million simulations, success rate = 5.547%). The success rates for N = 10, 20, and 30 were 2.5%, 1.8%, and 1.3%, respectively. These probabilities can be compared to a probability of 2.5 for each test with N = 10. It is clear that trying three studies is a more efficient strategy than to add participants until N reaches 30. Moreover, neither strategy avoids producing a file drawer. To avoid a file-drawer, researchers would need to combine several questionable research practices (Simmons et al., 2011).

Simmons et al. (2011) proposed that researchers can add covariates to increase the number of statistical tests and to increase the chances of producing a significant result. Another option is to include several dependent variables. To simplify the simulation, I am assuming that dependent variables and covariates are independent of each other. Sample size has no influence on these results. To make the simulation consistent with typical results in actual studies, I used n = 20 per cell. Adding covariates or additional dependent variables requires the same amount of resources. For example, participants make additional ratings for one more item and this item is either used as a covariate or as a dependent variable. Following Simmons et al. (2011), I first simulated a scenario with 10 covariates.

The p-curve plot is similar to the repeated peaking plot and is called left-skewed. The success rate, however, is disappointing. Only 4.48% of results were statistically significant. This suggests that collecting data to be used as covariates is another dumb p-hacking strategy.

Adding dependent variables is much more efficient. In the simple scenario, with independent DVs, the probability of obtaining a significant result equals 1-(1-.025)^11 = 24.31%. A simulation with 100,000 trials produced a percentage of 24.55%. More important, the p-curve is flat.

Correlation among the dependent variables produces a slight left-skewed distribution, but not as much as the other p-hacking methods. With a population correlation of r = .3, the percentages are 17% for p < .01 and 22% for p between .04 and .05.

These results provide three insights into p-hacking that have been overlooked. First, some p-hacking methods are more effective than others. Second, the amount of left-skewness varies across p-hacking methods. Third, efficient p-hacking produces a fairly large file-drawer of studies with non-significant results because it is inefficient to add participants to data that failed to produce a significant result.

Implications

False P-curve Citations

The p-curve authors made it fairly clear what p-curve does and what it does not do. The main point of a p-curve analysis is to examine whether a set of significant results was obtained at least partially with some true effects. That is, at least in a subset of the studies the null-hypothesis was false. The authors call this evidential value. A right-skewed p-curve suggests that a set of significant results have evidential value. This is the only valid inference that can be drawn from p-curve plots.

“We say that a set of significant findings contains evidential value when we can rule out selective reporting as the sole [italics added] explanation of those findings” (p. 535).

The emphasize on selective reporting as the sole explanation is important. A p-curve that shows evidential value can still be biased by p-hacking and publication bias, which can lead to inflated effect size estimates.

To make sure that I interpret the article correctly, I asked one of the authors on twitter and the reply confirmed that p-curve is not a bias test, but strictly a test that some real effects contributed to a right-skewed p-curve. The answer also explains why the p-curve authors did not care about testing for bias. They assume that bias is almost always present; which makes it unnecessary to test for it.

Although the authors stated the purpose of p-curve plots clearly, many meta-analysists have misunderstood the meaning of a p-curve analysis and have drawn false conclusions about right-skewed p-curves. For example, Rivers (2017) writes that a right-skewed p-curve suggests “that the WIT effect is a) likely to exist, and b) unlikely biased by extensive p-hacking.” The first inference is correct. The second one is incorrect because p-curve is not a bias detection method. A right-skewed p-curve could be a mixture of real effects and bias due to selective reporting.

Rivers also makes a misleading claim that a flat p-curve shows the lack of evidential value, whereas “a significantly left-skewed distribution indicates that the effect under consideration may be biased by p-hacking.” These statements are wrong because a flat p-curve can also be produced by p-hacking, especially when a real effect is also present.

Rivers is by no means the only one who misinterpreted p-curve results. Using the 10 most highly cited articles that applied p-curve analysis, we can see the same mistake in several articles. A tutorial for biologists claims “p-curve can, however, be used to identify p-hacking, by only considering significant findings” (Head, 2015, p. 3). Another tutorial for biologists repeats this false interpretation of p-curves. “One proposed method for identifying P-hacking is ‘P-curve’ analysis” (Parker et al., 2016, p. 714). A similar false claim is made by Polanin et al. (2016). “The p-curve is another method that attempts to uncover selective reporting, or “p-hacking,” in primary reports (Simonsohn, Nelson, Leif, & Simmons, 2014)” (p. 211). The authors of a meta-analysis of personality traits claim that they conduct p-curve analyses “to check whether this field suffers from publication bias” (Muris et al., 2017, 186). Another meta-analysis on coping also claims “p-curve analysis (Simonsohn, Nelson, & Simmons, 2014) allows the detection of selective reporting by researchers who “file-drawer” certain parts of their studies to reach statistical significance” (Cheng et al., 2014; p. 1594).

Shariff et al.’s (2016) article on religious priming effects provides a better explanation of p-curve, but their final conclusion is still misleading. “These results suggest that the body of studies reflects a true effect of religious priming, and not an artifact of publication bias and p-hacking.” (p. 38). The first part is correct, but the second part is misleading. The correct claim would be “not solely the result of publication bias and p-hacking”, but it is possible that publication bias and p-hacking inflate effect size estimates in this literature. The skew of p-curves simply does not tell us about this. The same mistake is made by Weingarten et al. (2016). “When we included all studies (published or unpublished) with clear hypotheses for behavioral measures (as outlined in our p-curve disclosure table), we found no evidence of p-hacking (no left-skew), but dual evidence of a right-skew and flatter than 33% power.” (p. 482). While a left-skewed p-curve does reveal p-hacking, the absence of left-skew does not ensure that p-hacking was absent. The same mistake is made by Steffens et al. (2017), who interpret a right-skewed p-curve as evidence “that the set of studies contains evidential value and that there is no evidence of p-hacking or ambitious p-hacking” (p. 303).

Although some articles correctly limit the interpretation of the p-curve to the claim that the data contain evidential value (Combs et al., 2015; Rand, 2016; Siks et al., 2018), the majority of applied p-curve articles falsely assume that p-curve can reveal the presence or absence of p-hacking or publication bias. This is incorrect. A left-skewed p-curve does provide evidence of p-hacking, but the absence of left-skew does not imply that p-hacking is absent.

How prevalent are left-skewed p-curves?

After 2011, psychologists were worried that many published results might be false positive results that were obtained with p-hacking (Simmons et al., 2011). As the combination of p-hacking in the absence of a real effect does produce left-skewed p-curves, one might expect that a large percentage of p-curve analyses revealed left-skewed distributions. However, empirical examples of left-skewed p-curves are extremely rare. Take, power-posing as an example. It is widely assumed these days that original evidence for power-posing was obtained with p-hacking and that the real effect size of power-posing is negligible. Thus, power-posing would be expected to show a left-skewed p-curve.

Simmons and Simonsohn (2017) conducted a p-curve analysis of the power-posing literature. They did not observe a left-skewed p-curve. Instead, the p-curve was flat, which justifies the conclusion that the studies contain no evidential value (i.e., we cannot reject the null-hypothesis that all studies tested a true null-hypothesis). The interpretation of this finding is misleading.

“In this Commentary, we rely on p-curve analysis to answer the following question: Does the literature reviewed by Carney et al. (2015) suggest the existence of an effect once one accounts for selective reporting? We conclude that it does not. The distribution of p values from those 33 studies is indistinguishable from what would be expected if (a) the average effect size were zero and (b) selective reporting (of studies or analyses) were solely responsible for the significant effects that were published”

The interpretation only focus on selective reporting (or testing of independent DVs) as a possible explanation for lack of evidential value. However, usually the authors emphasize p-hacking as the most likely explanation for significant results without evidential value. Ignoring p-hacking is deceptive because a flat p-curve can occur as a combination of p-hacking and real effect, as the authors showed themselves (Simonsohn et al., 2014).

Another problem is that significance testing is also one-sided. A right-skewed p-curve can be used to reject the null-hypotheses that all studies are false positives, but the absence of significant right skew cannot be used to infer the lack of evidential value. Thus, p-curve cannot be used to establish that there is no evidential value in a set of studies.

There are two explanations for the surprising lack of left-skewed p-curves in actual studies. First, p-hacking may be much less prevalent than is commonly assumed and the bigger problem is publication bias which does not produce a left-skewed distribution. Alternatively, false positive results are much rarer than has been assumed in the wake of the replication crisis. The main reason for replication failures could be that published studies report inflated effect sizes and that replication studies with unbiased effect size estimates are underpowered and produce false negative results.

How useful are Right-skewed p-curves?

In theory, left-skew is diagnostic of p-hacking, but in practice left-skew is rarely observed. This leaves right-skew as the only diagnostic information of p-curve plots. Right skew can be used to reject the null-hypothesis that all of the significant results tested a true null-hypothesis. The problem with this information is shared by all significance tests. It does not provide evidence about the effect size. In this case, it does not provide evidence about the percentage of significant results that are true positives (the false positive risk), nor does it quantify the strength of evidence.

This problem has been addressed by other methods that quantify how strong the evidence against the null-hypothesis is. Confusingly, the p-curve authors used the term p-curve for a method that estimates the strength of evidence in terms of the unconditional power of the set of studies (Simonsohn et al., 2014b). The problem with these power estimates is that they are biased when studies are heterogeneous (Bartos & Schimmack, 2021; Brunner & Schimmack, 2020). Simulation studies show that z-curve is a superior method to quantify the strength of evidence against the null-hypothesis. In addition, z-curve.2.0 provides additional information about the false positive risk; that is the maximum number of significant results that may be false positives.

In conclusion, p-curve plots no longer produce meaningful information. Left-skew can be detected in z-curves plots as well as in p-curve plots and is extremely rare. Right skew is diagnostic of evidential value, but does not quantify the strength of evidence. Finally, p-curve plots are not diagnostic when data contain evidential value and bias due to p-hacking or publication bias.

An Even Better P-curve

P-Curve

It is my pleasure to post the first guest post on the R-Index blog.  The blog post is written by my colleague and partner in “crime”-detection, Jerry Brunner.  I hope we will see many more guest posts by Jerry in the future.

GUEST POST:

Jerry Brunner
Department of Statistical Sciences
University of Toronto

First, my thanks to the mysterious Dr. R for the opportunity to do this guest post. At issue are the estimates of population mean power produced by the online p-curve app. The current version is 4.06, available at http://www.p-curve.com/app4/pcurve4.php. As the p-curve team (Simmons, Nelson, and Simonsohn) observe in their blog post entitled “P-curve handles heterogeneity just fine” at http://datacolada.org/67, the app does well on average as long as there is not too much heterogeneity in power. They show in one of their examples that it can over-estimate mean power when there is substantial heterogeneity.

Heterogeneity in power is produced by heterogeneity in effect size and heterogeneity in sample size. In the simulations reported at http://datacolada.org/67, sample size varies over a fairly narrow range — as one might expect from a meta-analysis of small-sample studies. What if we wanted to estimate mean power for sets of studies with large heterogeneity in sample sizes or an entire discipline, or sub-areas, or journals, or psychology departments? Sample size would be much more variable.

This post gives an example in which the p-curve app consistently over-estimates population mean power under realistic heterogeneity in sample size. To demonstrate that heterogeneity in sample size alone is a problem for the online pcurve app, population effect size was held constant.

In 2016, Brunner and Schimmack developed an alternative p-curve method (p-curve 2.1), which performs much better than the online app p-curve 4.06. P-curve 2.1 is fully documented and evaluated in Brunner and Schimmack (2018). This is the most recent version of the notorious and often-rejected paper mentioned in https://replicationindex.com/201/03/25/open-discussion-forum. It has been re-written once again, and submitted to Meta-psychology. It will shortly be posted during the open review process, but in the meantime I have put a copy on my website at http://www.utstat.toronto.edu/~brunner/papers/Zcurve6.7.pdf.

P-curve 2.1 is based on Simonsohn, Nelson and Simmons’ (2014) p-curve estimate of effect size. It is designed specifically for the situation where there is heterogeneity in sample size, but just a single fixed effect size. P-curve 2.1 is a simple, almost trivial application of p-curve 2.0. It first uses the p-curve 2.0 method to estimate a common effect size. It then combines that estimated effect size and the observed sample sizes to calculate an estimated power for each significance test in the sample. The sample mean of the estimated power values is the p-curve 2.1 estimate.

One of the virtues of p-curve is that it allows for publication bias, using only significant test statistics as input. The population mean power being estimated is the mean power of the sub-population of tests that happened to be significant. To compare the performance of p-curve 4.06 to p-curve 2.1, I simulated samples of significant test statistics with a single effect size, and realistic heterogeneity in sample size.

Here’s how I arrived at the “realistic” sample sizes. In another project, Uli Schimmack had harvested a large number of t and F statistics from the journal Psychological Science, from the years 2001-2015. I used N = df + 2 to calculate implied total sample sizes. I then eliminated all sample sizes less than 20 and greater than 500, and randomly sampled 5,000 of the remaining numbers. These 5,000 numbers will be called the “Psychological Science urn.” They are available at http://www.utstat.toronto.edu/~brunner/data/power/PsychScience.urn3.txt, and can be read directly into R with the scan function.

The numbers in the Psychological Science urn are not exactly sample sizes and they are not a true random sample. In particular, truncating the distribution at 500 makes them less heterogeneous than real sample sizes, since web surveys with enormous sample sizes are eliminated. Still, I believe the numbers in the Psychological Science urn may be fairly reflective of the sample sizes in psychology journals. Certainly, they are better than anything I would be able to make up. Figure 1 shows a histogram, which is right skewed as one might expect.

Figure1

By sampling with replacement from the Psychological Science urn, one could obtain a random sample of sample sizes, similar to sampling without replacement from a very large population of studies. However, that’s not what I did. Selection for significance tends to select larger sample sizes, because tests based on smaller sample sizes have lower power and so are less likely to be significant. The numbers in the Psychological Science urn come from studies that passed the filter of publication bias. It is the distribution of sample size after selection for significance that should match Figure 1.

To take care of this issue, I constructed a distribution of sample size before selection and chose an effect size that yielded (a) population mean power after selection equal to 0.50, and (b) a population distribution of sample size after selection that exactly matched the relative frequencies in the Psychological Science urn. The fixed effect size, in a metric of Cohen (1988, p. 216) was w = 0.108812. This is roughly Cohen’s “small” value of w = 0.10. If you have done any simulations involving literal selection for significance, you will realize that getting the numbers to come out just right by trial and error would be nearly impossible. I got the job done by using a theoretical result from Brunner and Schimmack (2018). Details are given at the end of this post, after the results.

I based the simulations on k=1,000 significant chi-squared tests with 5 degrees of freedom. This large value of k (the number of studies, or significance tests on which the estimates are based) means that estimates should be very accurate. To calculate the estimates for p-curve 4.06, it was easy enough to get R to write input suitable for pasting into the online app. For p-curve 2.1, I used the function heteroNpcurveCHI, part of a collection developed for the Brunner and Schimmack paper. The code for all the functions is available at http://www.utstat.toronto.edu/~brunner/Rfunctions/estimatR.txt. Within R, the functions can be defined with source("http://www.utstat.toronto.edu/~brunner/Rfunctions/estimatR.txt"). Then to see a list of functions, type functions() at the R prompt.

Recall that population mean power after selection is 0.50. The first time I ran the simulation, the p-curve 4.06 estimate was 0.64, with a 95% confidence interval from from 0.61 to 0.66.. The p-curve 2.1 estimate was 0.501. Was this a fluke? The results of five more independent runs are given in the table below. Again, the true value of mean power after selection for significance is 0.50.

Estimate
P-curve 2.1 P-curve 4.06 P-curve 4.06 Confidence Interval
0.510 0.64 0.61 0.67
0.497 0.62 0.59 0.65
0.502 0.62 0.59 0.65
0.509 0.64 0.61 0.67
0.487 0.61 0.57 0.64

It is clear that the p-curve 4.06 estimates are consistently too high, while p-curve 2.1 is on the money. One could argue that an error of around twelve percentage points is not too bad (really?), but certainly an error of one percentage point is better. Also, eliminating sample sizes greater than 500 substantially reduced the heterogeneity in sample size. If I had left the huge sample sizes in, the p-curve 4.06 estimates would have been ridiculously high.

Why did p-curve 4.06 fail? The answer is that even with complete homogeneity in effect size, the Psychological Science urn was heterogeneous enough to produce substantial heterogeneity in power. Figure 2 is a histogram of the true (not estimated) power values.

Figure2

Figure 2 shows that that even under homogeneity in effect size, a sample size distribution matching the Psychological Science urn can produce substantial heterogeneity in power, with a mode near one even though the mean is 0.50. In this situation, p-curve 4.06 fails. P-curve 2.1 is clearly preferable, because it specifically allows for heterogeneity in sample size.

Of course p-curve 2.1 does assume homogeneity in effect size. What happens when effect size is heterogeneous too? The paper by Brunner and Schimmack (2018) contains a set of large-scale simulation studies comparing estimates of population mean power from p-curve, p-uniform, maximum likelihood and z-curve, a new method dreamed up by Schimmack. The p-uniform method is based on van Assen, van Aertand and Wicherts (2014), extended to power estimation as in p-curve 2.1. The p-curve method we consider in the paper is p-curve 2.1. It does okay as long as heterogeneity in effect size is modest. Other methods may be better, though. To summarize, maximum likelihood is most accurate when its assumptions about the distribution of effect size are satisfied or approximately satisfied. When effect size is heterogeneous and the assumptions of maximum likelihood are not satisfied, z-curve does best.

I would not presume to tell the p-curve team what to do, but I think they should replace p-curve 4.06 with something like p-curve 2.1. They are free to use my heteroNpcurveCHI and heteroNpcurveF functions if they wish. A reference to Brunner and Schimmack (2018) would be appreciated.

Details about the simulations

Before selection for significance, there is a bivariate distribution of sample size and effect size. This distribution is affected by the selection process, because tests with higher effect size or sample size (or especially, both) are more likely to be significant. The question is, exactly how does selection affect the joint distribution? The answer is in Brunner and Schimmack (2018). This paper is not just a set of simulation studies. It also has a set of “Principles” relating the population distribution of power before selection to its distribution after selection. The principles are actually theorems, but I did not want it to sound too mathematical. Anyway, Principle 6 says that to get the probability of a (sample size, effect size) pair after selection, take the probability before selection, multiply by the power calculated from that pair, and divide by the population mean power before selection.

In the setting we are considering here, there is just a single effect size, so it’s even simpler. The probability of a (sample size, effect size) pair is just the probability of the sample size. Also, we know the probability distribution of sample size after selection. It’s the relative frequencies of the Psychological Science urn. Solving for the probability of sample size before selection yields this rule: the probability of sample size before selection equals the probability of sample size after selection, divided by the power for that sample size, and multiplied by population mean power before selection.

This formula will work for any fixed effect size. That is, for any fixed effect size, there is a probability distribution of sample size before selection that makes the distribution of sample size after selection exactly match the Psychological Science frequencies in Figure 1. Effect size can be anything. So, choose the effect size that makes expected (that is, population mean) power after selection equal to some nice value like 0.50.

Here’s the R code. First, we read the Psychological Science urn and make a table of probabilities.

rm(list=ls())

options(scipen=999) # To avoid scientific notation

source("http://www.utstat.toronto.edu/~brunner/Rfunctions/estimatR.txt"); functions()

PsychScience = scan("http://www.utstat.toronto.edu/~brunner/data/power/PsychScience.urn3.txt")

hist(PsychScience, xlab='Sample size',breaks=100, main = 'Figure 1: The Psychological Science Urn')

# A handier urn, for some purposes

nvals = sort(unique(PsychScience)) # There are 397 rather than 8000 values

nprobs = table(PsychScience)/sum(table(PsychScience))

# sum(nvals*nprobs) = 81.8606 = mean(PsychScience)

For any given effect size, the frequencies from the Psychological Science urn can be used to calculate expected power after selection. Minimizing the (squared) difference between this value and the desired mean power yields the required effect size.

# Minimize this function to find effect size giving desired power 

# after selection for significance.

fun = function(es,wantpow,dfreedom) 

    {

    alpha = 0.05; cv=qchisq(1-alpha,dfreedom)

    epow = sum( (1-pchisq(cv,df=dfreedom,ncp=nvals*es))*nprobs ) 

    # cat("es = ",es," Expected power = ",epow,"\n")

    (epow-wantpow)^2    

    } # End of all the fun

# Find needed effect size for chi-square with df=5 and desired 

# population mean power AFTER selection.



popmeanpower = 0.5 # Change this value if you wish

EffectSize = nlminb(start=0.01, objective=fun,lower=0,df=5,wantpow=popmeanpower)$par

EffectSize # 0.108812

Calculate the probability distribution of sample size before selection.

# The distribution of sample size before selection is proportional to the

# distribution after selection divided by power, term by term.

crit = qchisq(0.95,5)

powvals = 1-pchisq(crit,5,ncp=nvals*EffectSize)

Pn = nprobs/powvals 

EG = 1/sum(Pn)

cat("Expected power before selection = ",EG,"\n")

Pn = Pn*EG # Probability distribution of n before selection

Generate test statistics before selection.

nsim = 50000 # Initial number of simulated statistics. This is over-kill. Change the value if you wish.

set.seed(4444)



# For repeated simulations, execute the rest of the code repeatedly.

nbefore = sample(nvals,size=nsim,replace=TRUE,prob=Pn)

ncpbefore = nbefore*EffectSize

powbefore = 1-pchisq(crit,5,ncp=ncpbefore)

Ybefore = rchisq(nsim,5,ncp=ncpbefore)

Select for significance.

sigY = Ybefore[Ybefore>crit]

sigN = nbefore[Ybefore>crit]

sigPOW = 1-pchisq(crit,5,ncp=sigN*EffectSize)

hist(sigPOW, xlab='Power',breaks=100,freq=F ,main = 'Figure 2: Power After Selection for Significance')

Estimate mean power both ways.

# Two estimates of expected power before selection

c( length(sigY)/nsim , mean(powbefore) ) 

c(popmeanpower, mean(sigPOW)) # Golden

length(sigY)



k = 1000 # Select 1,000 significant results.

Y = sigY[1:k]; n = sigN[1:k]; TruePower = sigPOW[1:k]



# Estimate with p-curve 2.1

heteroNpcurveCHI(Y=Y,dfree=5,nn=n) # 0.5058606 the first time.



# Write out chi-squared statistics for pasting into the online app

for(j in 1:k) cat("chi2(5) =",Y[j],"\n")

References

Brunner, J. and Schimmack, U. (2018). Estimating population mean power under conditions of heterogeneity and selection for significance. Under review. Available at http://www.utstat.toronto.edu/~brunner/papers/Zcurve6.7.pdf.

Cohen, J. (1988). Statistical power analysis for the behavioral sciences (2nd Edition), Hillsdale, New Jersey: Erlbaum.

Simonsohn, U., Nelson, L. D., & Simmons, J. P. (2014). P-curve and effect size: correcting for publication bias using only significant results. Perspectives on Psychological Science, 9, 666-681.

van Assen, M. A. L. M., van Aert, R. C. M., & Wicherts, J. M. (2014). Meta-analysis using effect size distributions of only statistically significant studies. Psychological methods, 20, 293-309.

Visual Inspection of Strength of Evidence: P-Curve vs. Z-Curve

P-Curve, Pcurve, Power, Powergraph, Strength of Evidence, Z-Curve, Zcurve

Statistics courses often introduce students to a bewildering range of statistical test.  They rarely point out how test statistics are related.  For example, although t-tests may be easier to understand than F-tests, every t-test could be performed as an F-test and the F-value in the F-test is simply the square of the t-value (t^2 or t*t).

At an even more conceptual level, all test statistics are ratios of the effect size (ES) and the amount of sampling error (ES).   The ratio is sometimes called the signal (ES) to noise (ES) ratio.  The higher the signal to noise ratio (ES/SE), the stronger the observed results deviate from the hypothesis that the effect size is zero.  This hypothesis is often called the null-hypothesis, but this terminology has created some confusing.  It is also sometimes called the nil-hypothesis the zero-effect hypothesis or the no-effect hypothesis.  Most important, the test-statistic is expected to average zero if the same experiment could be replicated a gazillion times.

The test statistics of statistical tests cannot be directly compared.  A t-value of 2 in a study with N = 10 participants provides weaker evidence against the null-hypothesis than a z-score of 1.96.  and an F-value of 4 with df(1,40) provides weaker evidence than an F(10,200) = 4 result.  It is only possible to compare test values directly that have the same sampling distribution (z with z, F(1,40) with F(1,40), etc.).

There are three solutions to this problem. One solution is to use effect sizes as the unit of analysis. This is useful if the aim is effect size estimation.  Effect size estimation has become the dominant approach in meta-analysis.  This blog post is not about effect size estimation.  I just mention it because many readers may be familiar with effect size meta-analysis, but not familiar with meta-analysis of test statistics that reflect the ratio of effect size and sampling error (Effect size meta-analysis: unit = ES; Test Statistic Meta-Analysis: unit ES/SE).

P-Curve

There are two approaches to standardize test statistics so that they have a common unit of measurement.  The first approach goes back to Ronald Fisher, who is considered the founder of modern statistics for researchers.  Following Fisher it is common practice to convert test-statistics into p-values (for this blog post assumes that you are familiar with p-values).   P-values have the same meaning independent of the test statistic that was used to compute them.   That is, p = .05 based on a z-test, t-test, or an F-test provide equally strong evidence against the null-hypothesis (Bayesians disagree, but that is a different story).   The use of p-values as a common metric to examine strength of evidence (evidential value) was largely forgotten, until Simonsohn, Simmons, and Nelson (SSN) used p-values to develop a statistical tool that takes publication bias and questionable research practices into account.  This statistical approach is called p-curve.  P-curve is a family of statistical methods.  This post is about the p-curve plot.

A p-curve plot is essentially a histogram of p-values with two characteristics. First, it only shows significant p-values (p < .05, two-tailed).  Second, it plots the p-values between 0 and .05 with 5 bars.  The Figure shows a p-curve for Motyl et al.’s (2017) focal hypothesis tests in social psychology.  I only selected t-test and F-tests from studies with between-subject manipulations.

p.curve.motyl

The main purpose of a p-curve plot is to examine whether the distribution of p-values is uniform (all bars have the same height).  It is evident that the distribution for Motyl et al.’s data is not uniform.  Most of the p-values fall into the lowest range between 0 and .01. This pattern is called “rigth-skewed.”  A right-skewed plot shows that the set of studies has evidential value. That is, some test statistics are based on non-zero effect sizes.  The taller the bar on the left is, the greater the proportion of studies with an effect.  Importantly, meta-analyses of p-values do not provide information about effect sizes because p-values take effect size and sampling error into account.

The main inference that can be drawn from a visual inspection of a p-curve plot is how unlikely it is that all significant results are false positives; that is, the p-value is below .05 (statistically significant), but this strong deviation from 0 was entirely due to sampling error, while the true effect size is 0.

The next Figure also shows a plot of p-values.  The difference is that it shows the full range of p-values and that it differentiates more between p-values because p = .09 provides weaker evidence than p = .0009.

all.p.curve.motyl.png

The histogram shows that most p-values are below p < .001.  It also shows very few non-significant results.  However, this plot is not more informative than the actual p-curve plot. The only conclusion that is readily visible is that the distribution is not uniform.

The main problem with p-value plots is that p-values do not have interval scale properties.  This means, the difference between p = .4 and p = .3 is not the same as the difference between p = .10 and p = .00 (e.g., .001).

Z-Curve  

Stouffer developed an alternative method to Fisher’s p-value meta-analysis.  Every p-value can be transformed into a z-scores that corresponds to a particular p-value.  It is important to distinguish between one-sided and two-sided p-values.  The transformation requires the use of one-sided p-values, which can be obtained by simply dividing a two-sided p-value by 2.  A z-score of -1.96 corresponds to a one-sided p-value of 0.025 and a z-score of 1.96 corresponds to a one-sided p-values of 0.025.  In a two sided test, the sign no longer matters and the two p-values are added to yield 0.025 + 0.025 = 0.05.

In a standard meta-analysis, we would want to use one-sided p-values to maintain information about the sign.  However, if the set of studies examines different hypothesis (as in Motyl et al.’s analysis of social psychology in general) the sign is no longer important.   So, the transformed two-sided p-values produce absolute (only positive) z-scores.

The formula in R is Z = -qnorm(p/2)   [p = two.sided p-value]

For very strong evidence this formula creates problems. that can be solved by using the log.P=TRUE option in R.

Z = -qnorm(log(p/2), log.p=TRUE)

p.to.z.transformation.png

The plot shows the relationship between z-scores and p-values.  While z-scores are relatively insensitive to variation in p-values from .05 to 1, p-values are relatively insensitive to variation in z-scores from 2 to 15.

only.sig.p.to.z.transformation

The next figure shows the relationship only for significant p-values.  Limiting the distribution of p-values does not change the fact that p-values and z-values have very different distributions and a non-linear relationship.

The advantage of using (absolute) z-scores is that z-scores have ratio scale properties.  A z-score of zero has real meaning and corresponds to the absence of evidence for an effect; the observed effect size is 0.  A z-score of 2 is twice as strong as a z-score of 1. For example, given the same sampling error the effect size for a z-score of 2 is twice as large as the effect size for a z-score of 1 (e.g., d = .2, se = .2, z = d/se = 1,  d = 4, se = .2, d/se = 2).

It is possible to create the typical p-curve plot with z-scores by selecting only z-scores above z = 1.96. However, this graph is not informative because the null-hypothesis does not predict a uniform distribution of z-scores.   For z-values the central tendency of z-values is more important.  When the null-hypothesis is true, p-values have a uniform distribution and we would expect an equal number of p-values between 0 and 0.025 and between 0.025 and 0.050.   A two-sided p-value of .025 corresponds to a one-sided p-value of 0.0125 and the corresponding z-value is 2.24

p = .025
-qnorm(log(p/2),log.p=TRUE)
[1] 2.241403

Thus, the analog to a p-value plot is to examine how many significant z-scores fall into the region from 1.96 to 2.24 versus the region with z-values greater than 2.24.

z.curve.plot1.png

The histogram of z-values is called z-curve.  The plot shows that most z-values are in the range between 1 and 6, but the histogram stretches out to 20 because a few studies had very high z-values.  The red line shows z = 1.96. All values on the left are not significant with alpha = .05 and all values on the right are significant (p < .05).  The dotted blue line corresponds to p = .025 (two tailed).  Clearly there are more z-scores above 2.24 than between 1.96 and 2.24.  Thus, a z-curve plot provides the same information as a p-curve plot.  The distribution of z-scores suggests that some significant results reflect true effects.

However, a z-curve plot provides a lot of additional information.  The next plot removes the long tail of rare results with extreme evidence and limits the plot to z-scores in the range between 0 and 6.  A z-score of six implies a signal to noise ratio of 6:1 and corresponds to a p-value of p = 0.000000002 or 1 out of 2,027,189,384 (~ 2 billion) events. Even particle physics settle for z = 5 to decide that an effect was observed if it is so unlikely for a test result to occur by chance.

> pnorm(-6)*2
[1] 1.973175e-09

Another addition to the plot is to include a line that identifies z-scores between 1.65 and 1.96.  These z-scores correspond to two-sided p-values between .05 and .10. These values are often published as weak but sufficient evidence to support the inference that a (predicted) effect was detected. These z-scores also correspond to p-values below .05 in one-sided tests.

z.curve.plot2

A major advantage of z-scores over p-values is that p-values are conditional probabilities based on the assumption that the null-hypothesis is true, but this hypothesis can be safely rejected with these data.  So, the actual p-values are not important because they are conditional on a hypothesis that we know to be false.   It is like saying, I would be a giant if everybody else were 1 foot tall (like Gulliver in Lilliput), but everybody else is not 1 foot tall and I am not a giant.

Z-scores are not conditioned on any hypothesis. They simply show the ratio of the observed effect size and sampling error.  Moreover, the distribution of z-scores tell us something about the ratio of the true effect sizes and sampling error.  The reason is that sampling error is random and like any random variable has a mean of zero.  Therefore, the mode, median, or mean of a z-curve plot tells us something about ratio of the true effect sizes and sampling error.  The more the center of a distribution is shifted to the right, the stronger is the evidence against the null-hypothesis.  In a p-curve plot, this is reflected in the height of the bar with p-values below .01 (z > 2.58), but a z-curve plot shows the actual distribution of the strength of evidence and makes it possible to see where the center of a distribution is (without more rigorous statistical analyses of the data).

For example, in the plot above it is not difficult to see the mode (peak) of the distribution.  The most common z-values are between 2 and 2.2, which corresponds to p-values of .046 (pnorm(-2.2)*2) and .028 (pnorm(-2.2)*2).   This suggests that the modal study has a ratio of 2:1 for effect size over sampling error.

The distribution of z-values does not look like a normal distribution. One explanation for this is that studies vary in sampling errors and population effect sizes.  Another explanation is that the set of studies is not a representative sample of all studies that were conducted.   It is possible to test this prediction by trying to fit a simple model to the data that assumes representative sampling of studies (no selection bias or p-hacking) and that assumes that all studies have the same ratio of population effect size over sampling error.   The median z-score provides an estimate of the center of the sampling distribution.  The median for these data is z = 2.56.   The next picture shows the predicted sampling distribution of this model, which is an approximately normal distribution with a folded tail.

 

z.curve.plot3

A comparison of the observed and predicted distribution of z-values shows some discrepancies. Most important is that there are too few non-significant results.  This observation provides evidence that the results are not a representative sample of studies.  Either non-significant results were not reported or questionable research practices were used to produce significant results by increasing the type-I error rate without reporting this (e.g., multiple testing of several DVs, or repeated checking for significance during the course of a study).

It is important to see the difference between the philosophies of p-curve and z-curve. p-curve assumes that non-significant results provide no credible evidence and discards these results if they are reported.  Z-curve first checks whether non-significant results are missing.  In this way, p-curve is not a suitable tool for assessing publication bias or other problems, whereas even a simple visual inspection of z-curve plots provides information about publication bias and questionable research practices.

z.curve.plot4.png

The next graph shows a model that selects for significance.  It no longer attempts to match the distribution of non-significant results.  The objective is only to match the distribution of significant z-values.  You can do this by hand and simply try out different values for the center of the normal distribution.  The lower the center, the more z-scores are missing because they are not significant.  As a result, the density of the predicted curve needs to be adjusted to reflect the fact that some of the area is missing.

center.z = 1.8  #pick a value
z = seq(0,6,.001)  #create the range of z-values
y = dnorm(z,center.z,1) + dnorm(z,-center.z,1)  # get the density for a folded normal
y2 = y #duplicate densities
y2[x < 1.96] = 0   # simulate selection bias, density for non-significant results is zero
scale = sum(y2)/sum(y)  # get the scaling factor so that area under the curve of only significant results is 1.
y = y / scale   # adjust the densities accordingly

# draw a histogram of z-values
# input is  z.val.input
# example; z.val.input = rnorm(1000,2)
hist(z.val.input,freq=FALSE,xlim=c(0,6),ylim=c(0,1),breaks=seq(0,20,.2), xlab=””,ylab=”Density”,main=”Z-Curve”)

abline(v=1.96,col=”red”)   # draw the line for alpha = .05 (two-tailed)
abline(v=1.65,col=”red”,lty=2)  # draw marginal significance (alpha = .10 (two-tailed)

par(new=TRUE) #command to superimpose next plot on histogram

# draw the predicted sampling distribution
plot(x,y,type=”l”,lwd=4,ylim=c(0,1),xlim=c(0,6),xlab=”(absolute) z-values”,ylab=””)

Although this model fits the data better than the previous model without selection bias, it still has problems fitting the data.  The reason is that there is substantial heterogeneity in the true strength of evidence.  In other words, the variability in z-scores is not just sampling error but also variability in sampling errors (some studies have larger samples than others) and population effect sizes (some studies examine weak effects and others examine strong effects).

Jerry Brunner and I developed a mixture model to fit a predicted model to the observed distribution of z-values.  In a nutshell the mixture model has multiple (folded) normal distributions.  Jerry’s z-curve lets the center of the normal distribution move around and give different weights to them.  Uli’s z-curve uses fixed centers one standard deviation apart (0,1,2,3,4,5 & 6) and uses different weights to fit the model to the data.  Simulation studies show that both methods work well.  Jerry’s method works a bit better if there is little variability and Uli’s method works a bit better with large variability.

The next figure shows the result for Uli’s method because the data have large variability.

z.curve.plot5

The dark blue line in the figure shows the density distribution for the observed data.  A density distribution assigns densities to an observed distribution that does not fit a mathematical sampling distribution like the standard normal distribution.   We use the Kernel Density Estimation method implemented in the R base package.

The grey line shows the predicted density distribution based on Uli’s z-curve method.  The z-curve plot makes it easy to see the fit of the model to the data, which is typically very good.  The model result of the model is the weighted average of the true power that corresponds to the center of the simulated normal distributions.  For this distribution,  the weighted average is 48%.

The 48% estimate can be interpreted in two ways.  First, it means that if researchers randomly sampled from the set of studies in social psychology and were able to exactly reproduce the original study (including sample size),  they have a probability of 48% to replicate a significant result with alpha = .05.  The complementary interpretation is that if researchers were successful in replicating all studies exactly,  the reproducibility project is expected to produce 48% significant results and 52% non-significant results.  Because average power of studies predicts the success of exact replication studies, Jerry and I refer to the average power of studies that were selected for significance replicability.  Simulation studies show that our z-curve methods have good large sample accuracy (+/- 2%) and we adjust for the small estimation bias in large samples by computing a conservative confidence interval that adds 2% to the upper limit and 2% to the lower limit.

Below is the R-Code to obtain estimates of replicability from a set of z-values using Uli’s method.

<<<Download Zcurve R.Code>>>

Install R.Code on your computer, then run from anywhere with the following code

location =  <user folder>  #provide location information where z-curve code is stored
source(paste0(location,”fun.uli.zcurve.sharing.18.1.R”))  #read the code
run.zcurve(z.val.input)  #get z-curve estimates with z-values as input