2015

December 15, 2015

If we want to shift from a closed science to an open science, there has to be change at several levels. In this process, it’s easy to push the responsibility (and the power) for reform onto “the system”: “If only journals changed their policy …”, “It’s the responsibility of the granting agencies to change XYZ”, or “Unless university boards change their hiring practices, it is futile to …”.

Beyond doubt, change has to occur at the institutional level. In particular, many journals have already done a lot (see, for example, the TOP guidelines or the new registered reports article format). But journal policies aren’t enough, particularly since they are often not enforced.

In this blog post, I want to advocate for a complementary position of agency and empowerment: Let’s focus on steps *each individual* can do!

Here I want to show 9 steps that each individual can do, starting today, to foster open science:

1) **Join the community**. Follow open science advocates on Twitter and blogs. While monitoring these tweets does not change anything per se, it can give you important updates about developments in open science, and useful hints about how to implement open science in practice. Here’s my personal, selective, and incomplete list of Twitter users that frequently tweet about open science: https://twitter.com/nicebread303/lists/openscience

2) **Engage open values in peer review.** I started to realize that my work as a reviewer is very valuable work. I review more than 6x the number of papers that I submit myself. I receive more requests than I can handle, so I have to decide anyway which request to accept and which not. Where should I allocate my reviewing resources to? I prefer not to allocate them to research that is closed and practically unverifiable. I’d rather allocate them to research that is transparent, verifiable, sustainable, and re-usable.

Exactly this is the goal of the PRO initiative (Peer Reviewer Openness initiative), which uses the reviewer’s role to foster open science practices. The vision of the initiative is to switch from an opt-in model to an opt-out model: Openness is the new default; if authors don’t want it, they have to explicitly opt out. Signatories of the initiative only provide a comprehensive review of a manuscript if (a) open data and open material is provided, or (b) a public justification is given in the manuscript why this is not possible. Since the two weeks of the initiative’s existence, more than 160 reviewers signed it. I think this group already can have some impact, and I hope that more will sign.

[Read the paper — Sign the Initiative — More resources for open science]

Previous posts on the PRO initiative by Richard Morey, Candice Morey, Rolf Zwaan, and Daniel Lakens

3) **Commit yourself to open science.** In our “Voluntary Commitment to Research Transparency and Open Science” we explain which principles of research transparency we will follow from the day of signature on (see also my blog post). If you like it, sign it, and show the world that your research can be trusted and verified. Or use it as an inspiration to craft your own transparency commitment, on the openness level that you feel comfortable with.

4) **Find local li****ke-minded people. **Find colleagues in your department that embrace the values of open science as you do. Found a local open science initiative where you can exchange about challenges, help each other with practical problems (How did that pre-registration work?), and talk about ways open science can be implemented in your specific field. Use this “coalition of the willing” as the starting point for the next step …

5) **Found a local Open-Science-Committee.** Explore whether your local open science initiative could be installed as an official open science committee (OSC) at your department/ institution. See our OSF project for information about our open science committee at the department psychology at LMU Munich. Maybe you can reuse and adapt some of our material. Not all of our faculty members have the same opinion about this committee, some are enthusiastic, some are more skeptical. But still, the department’s board unanimously decided to establish this committee in order to keep the discussion going. Our OSC has 32 members from all chairs and we meet two times each semester. Our OSC has 4 goals:

- Monitor the international developments in the area of open science and communicate them to the department.
- Organize workshops that teach skills for open science
- Develop concrete suggestions concerning tenure-track criteria, hiring criteria, PhD supervision and grading, teaching, curricula, etc.
- Channel the discussion concerning standards of research quality and transparency in the department. Explore in what way a department-wide consensus can be established concerning certain points of open science.

6) **Pre-register your next study**. Pre-registration is a new skill we have to learn, so the first try does not have to be perfect. For example, I had to revise two of my registrations because I forgot important parts in the first version. In my experience, writing a few pre-registration documents gives you a better feeling for how long they take, what they should contain, what level of detail is appropriate, etc.

You can even win 1000$ if you participate in the pre-reg challenge!

7) **Teach open science practices to students.** You could plan your next Research Methods course as a pre-registered replication study. See also this OSF collection of syllabi, the “Good Science, Bad Science” course from EJ Wagenmakers, and the OSF Collaborative Replications and Education Project (CREP).

8) **Submit a registered report.** Think about submitting a **registered report** if there’s a journal in your field that supports this format. In this new article format an introduction, methods section, and analysis plan is submitted *before* data is collected. This proposal is sent to review, and in the positive case you get an in-principle-acceptance and proceed to actual data collection. This means, the paper is published independent of the results (unless you screw up your data collection or analysis).

9) **Promote the values of open science in committees.** As a member of a job committee, you can argue for open science criteria and evaluate candidates (amongst other criteria, of course) whether they engage in open practices. For example, Betsy Levy Paluck wrote in her blog: “In a hiring capacity, I will appreciate applicants who, though they do not have a ton of publications, can link their projects to an online analysis registration, or have posted data and replication code. Why? I will infer that they were slowing down to do very careful work, that they are doing their best to build a cumulative science.”

These are 9 small and medium steps, which each researcher could implement to some extent. If enough researchers join us, we can change the face of research.

No comments | Trackback

November 3, 2015

If the *p*-value is < .05, then the probability of falsely rejecting the null hypothesis is <5%, right? That means, a maximum of 5% of all significant results is a false-positive (that’s what we control with the α rate).

Well, no. As you will see in a minute, the “false discovery rate” (aka. false-positive rate), which indicates the probability that a significant *p*-value actually is a false-positive, usually is much higher than 5%.

Oakes (1986) asked the following question to students and senior scientists:

You have a p-value of .01. Is the following statement true, or false?You know, if you decide to reject the null hypothesis, the probability that you are making the wrong decision.

The answer is “false” (you will learn why it’s false below). But 86% of all professors and lecturers in the sample who were teaching statistics (!) answered this question erroneously with “true”. Gigerenzer, Kraus, and Vitouch replicated this result in 2000 in a German sample (here, the “statistics lecturer” category had 73% wrong). Hence, it is a wide-spread error to confuse the *p*-value with the false discovery rate.

To answer the question “What’s the probability that a significant *p*-value indicates a true effect?”, we have to look at the **positive predictive value (PPV)** of a significant *p*-value. The PPV indicates the proportion of significant *p*-values which indicate a real effect amongst all significant *p*-values. Put in other words: *Given that a p-value is significant: What is the probability (in a frequentist sense) that it stems from a real effect?*

(The false discovery rate simply is 1-PPV: the probability that a significant *p*-value stems from a population with null effect).

That is, we are interested in a conditional probability Prob(effect is real | *p*-value is significant).

Inspired by Colquhoun (2014) one can visualize this conditional probability in the form of a tree-diagram (see below). Let’s assume, we carry out 1000 experiments for 1000 different research questions. We now have to make a couple of prior assumptions (which you can make differently in the app we provide below). For now, we assume that 30% of all studies have a real effect and the statistical test used has a power of 35% with an α level set to 5%. That is of the 1000 experiments, 300 investigate a real effect, and 700 a null effect. Of the 300 true effects, 0.35*300 = 105 are detected, the remaining 195 effects are non-significant false-negatives. On the other branch of 700 null effects, 0.05*700 = 35 *p*-values are significant by chance (false positives) and 665 are non-significant (true negatives).

This path is visualized here (completely inspired by Colquhoun, 2014):

Now we can compute the false discovery rate (FDR): 35 of (35+105) = 140 significant *p*-values actually come from a null effect. That means, 35/140 = 25% of all significant *p*-values do not indicate a real effect! That is much more than the alleged 5% level (see also Lakens & Evers, 2014, and Ioannidis, 2005)

Together with Michael Zehetleitner I developed an interactive app that computes and visualizes these numbers. For the computations, you have to choose 4 parameters.

Let’s go through the settings!

Some of our investigated hypotheses are actually true, and some are false. As a first parameter, we have to estimate what proportion of our investigated hypotheses is actually true.

Now, what is a good setting for the a priori proportion of true hypotheses? It’s certainly not near 100% – in this case only trivial and obvious research questions would be investigated, which is obviously not the case. On the other hand, the rate can definitely drop close to zero. For example, in pharmaceutical drug development “only one in every 5,000 compounds that makes it through lead development to the stage of pre-clinical development becomes an approved drug” (Wikipedia). Here, only 0.02% of all investigated hypotheses are true.

Furthermore, the number depends on the field – some fields are highly speculative and risky (i.e., they have a low prior probability), some fields are more cumulative and work mostly on variations of established effects (i.e., in these fields a higher prior probability can be expected).

But given that many journals in psychology exert a selection pressure towards novel, surprising, and counter-intuitive results (which a priori have a low probability of being true), I guess that the proportion is typically lower than 50%. My personal grand average gut estimate is around 25%.

(Also see this comment and this reply for a discussion about this estimate).

That’s easy. The default α level usually is 5%, but you can play with the impact of stricter levels on the FDR!

The average power in psychology has been estimated at 35% (Bakker, van Dijk, & Wicherts, 2012). An median estimate for neuroscience is at only 21% (Button et al., 2013). Even worse, both estimates can be expected to be inflated, as they are based on the average *published* effect size, which almost certainly is overestimated due to the significance filter (Ioannidis, 2008). Hence, the average true power is most likely smaller. Let’s assume an estimate of 25%.

Finally, let’s add some realism to the computations. We know that researchers employ “researchers degrees of freedom”, aka. questionable research practices, to optimize their *p*-value, and to push a “nearly significant result” across the magic boundary. How many reported significant *p*-values would not have been significant without *p*-hacking? That is hard to tell, and probably also field dependent. Let’s assume that 15% of all studies are *p*-hacked, intentionally or unintentionally.

When these values are defined, the app computes the FDR and PPV and shows a visualization:

With these settings, **only 39% of all significant studies are actually true**!

Wait – what was the success rate of the Reproducibility Project: Psychology?** 36% of replication projects found a significant effect** in a direct replication attempt. Just a coincidence? Maybe. Maybe not.

The formula to compute the FDR and PPV are based on Ioannidis (2005: “Why most published research findings are false“). A related, but different approach, was proposed by David Colquhoun in his paper “An investigation of the false discovery rate and the misinterpretation of p-values” [open access]. He asks: “How should one interpret the observation of, say, *p*=0.047 in a *single* experiment?”. The Ioannidis approach implemented in the app, in contrast, asks: “What is the FDR in a *set of studies* with p <= .05 and a certain power, etc.?”. Both approaches make sense, but answer different questions.

- See also Daniel Laken’s blog post about the same topic, and the interesting discussion below it.
- Will Gervais also wrote a blog post on the topic and also has a cool interactive app which displays the results in another style.
- Commenter SamGG pointed to another publication which has illuminating graphics:
Krzywinski, M., & Altman, N. (2013). Points of significance: Power and sample size.
*Nature Methods*,*10*, 1139–1140. doi:10.1038/nmeth.2738

September 29, 2015

Yesterday, we had the first meeting of our department’s Open Science Committee. I am happy that the committee has 20 members, representing every research unit of the department, and all groups from PhD students to full professors.

In the meeting, I first gave a quick overview about the replication crisis in psychology. I had the impression that we had a large consensus about the fact that we indeed have a problem, and that we should think about possible consequences. Then we started an open discussion where we collected questions, reservations, and ideas.

Here are some unordered topics of our discussions. Not all of them could be resolved at that meeting (which was not the goal), but eventually these stubs could result in a FAQ:

- It is important to acknowledge the
**diversity of our (sub)fields**. Even if we agree on the overarching values of open science, the specific implementations might differ. The current discussion often is focused on experimental laboratory (or online) research. What about existing large-scale data sets? What about sensitive video data from infant studies? What about I&O research in companies, where agreements with the work council forbid open data? Feasible protocols and solutions have to be developed in these fields. **Does the new focus on power lead to boring and low-risk “Mturk-research”**? This is certainly not the goal, but we should be aware that this could happen as an unintended side effect. For example, all ManyLab projects focused on easy-to-implement computer studies. Given the focus of the projects this is understandable; but we should not forget “the other” research.- We had a longer discussion which could be framed as “
**strategic choices vs. intrinsic motivation (and social mandate) to increase knowledge**”. From a moral point of view, the choice is clear. But we all are also individuals who have to feed our families (or, at least, ourselves), and the strategic perspective has an existential relevance to us.

Related to this question is also the next point: **What about the “middle” generation who soon will look for a job in academia?**Can we really recommend to go the open way? Without the possibility to*p*-hack, and with the goal to run high-powered studies (which typically have a larger*n*), individual productivity (aka: # of published papers) will decline. (Of course, “productivity” in terms of “increase in valid knowledge” will rise).

This would be my current answer:*I expect that the gain in reputation outweighs the potential loss in # of published papers.*Furthermore, we now have several techniques which allow us to assess the likelihood of*p*-hacking and the evidential value of a set of studies. If we present a paper with 4 studies and*p*s = .03, .04, .04, and .05, chances are high that we do not earn a lot of respect but rather sceptical frowns. Hence, with the increasing knowledge of healthy*p*-curves and other indicators, the old strategy of packing together too-good-to-be-true studies might soon backfire.

Finally, I’d advocate for an agentic position: It’s not some omnipotent external force that imposes an evil incentive structure on us.*We are the incentive structure!*At least at our department we can make sure that we do not incentivize massive*p*-hacking, but reward scientists that produce transparent, replicable, and honest research.- The new focus on replicability and transparency criteria does
*not*imply that other quality indicators (such as good theoretical foundations) are less important. - Some change can been achieved by positive, voluntary incentives. For example, the Open Science Badges led to 40% of papers having open data in the journal
*Psychological Science*. In other situations, we might need mandatory rules. Concerning this**voluntary/mandatory dimension**: When is which approach appropriate and more constructive? - An experience: Registered reports can take a long time in the review process – A problem for publication-based dissertations?
- We have to teach the field on what methods we base the conclusion that we have a replicability problem. In some discussions (not in our OSC ;-)) you can hear something like: “Some young greenhorns invent some fancy statistical index, and tell us that everything we have done is crap. First they should show that their method is valid!” It is our responsibility to explain the methods to researchers that do not follow the current replicability discussion so closely or are not so statistically savvy.
- Idea: Should we give an annual
**Open-Science-Award**at our department?

We have no ready-made answers for many of these questions. Most of them have to be tackled at multiple levels. Any comments and other perspectives on these open questions are appreciated!

One goal of the committee is to train our researchers in new tools and topics. I am happy to announce that we will host at least 4 talks/workshops in our department in the remainder of 2015:

- Sep 30, 2015: Jonathon Love (Amsterdam):
**JASP – A Fresh Way to Do Statistics (14-16, room 3322)** - Nov 5, 2015: Daniel Lakens (TU Eindhoven):
**Practical Recommendations to Increase the Informational Value of Studies** - End of November 2015 (TBA): Etienne LeBel:
**Introducing Curate Science (curatescience.org)** - Dec 2015 (TBA): Felix Schönbrodt:
**How to detect***p*-hacking and publication bias: A practical introduction to*p*-curve, R-index, etc.

The plan for the next meeting is to discuss our voluntary commitment to research transparency.