Dora Matzke

Bio: Dora Matzke is an academic researcher from University of Amsterdam. The author has contributed to research in topics: Bayesian probability & Bayes factor. The author has an hindex of 30, co-authored 70 publications receiving 5321 citations.

Bayesian inference for psychology. Part II: Example applications with JASP

Abstract: Bayesian hypothesis testing presents an attractive alternative to p value hypothesis testing. Part I of this series outlined several advantages of Bayesian hypothesis testing, including the ability to quantify evidence and the ability to monitor and update this evidence as data come in, without the need to know the intention with which the data were collected. Despite these and other practical advantages, Bayesian hypothesis tests are still reported relatively rarely. An important impediment to the widespread adoption of Bayesian tests is arguably the lack of user-friendly software for the run-of-the-mill statistical problems that confront psychologists for the analysis of almost every experiment: the t-test, ANOVA, correlation, regression, and contingency tables. In Part II of this series we introduce JASP (http://www.jasp-stats.org), an open-source, cross-platform, user-friendly graphical software package that allows users to carry out Bayesian hypothesis tests for standard statistical problems. JASP is based in part on the Bayesian analyses implemented in Morey and Rouder’s BayesFactor package for R. Armed with JASP, the practical advantages of Bayesian hypothesis testing are only a mouse click away.

Bayesian inference for psychology. Part I: Theoretical advantages and practical ramifications.

Abstract: Bayesian parameter estimation and Bayesian hypothesis testing present attractive alternatives to classical inference using confidence intervals and p values. In part I of this series we outline ten prominent advantages of the Bayesian approach. Many of these advantages translate to concrete opportunities for pragmatic researchers. For instance, Bayesian hypothesis testing allows researchers to quantify evidence and monitor its progression as data come in, without needing to know the intention with which the data were collected. We end by countering several objections to Bayesian hypothesis testing. Part II of this series discusses JASP, a free and open source software program that makes it easy to conduct Bayesian estimation and testing for a range of popular statistical scenarios (Wagenmakers et al. this issue).

Statistical Evidence in Experimental Psychology An Empirical Comparison Using 855 t Tests

Abstract: Statistical inference in psychology has traditionally relied heavily on p-value significance testing. This approach to drawing conclusions from data, however, has been widely criticized, and two types of remedies have been advocated. The first proposal is to supplement p values with complementary measures of evidence, such as effect sizes. The second is to replace inference with Bayesian measures of evidence, such as the Bayes factor. The authors provide a practical comparison of p values, effect sizes, and default Bayes factors as measures of statistical evidence, using 855 recently published t tests in psychology. The comparison yields two main results. First, although p values and default Bayes factors almost always agree about what hypothesis is better supported by the data, the measures often disagree about the strength of this support; for 70% of the data sets for which the p value falls between .01 and .05, the default Bayes factor indicates that the evidence is only anecdotal. Second, effect sizes can provide additional evidence to p values and default Bayes factors. The authors conclude that the Bayesian approach is comparatively prudent, preventing researchers from overestimating the evidence in favor of an effect.

A consensus guide to capturing the ability to inhibit actions and impulsive behaviors in the stop-signal task

Abstract: Response inhibition is essential for navigating everyday life. Its derailment is considered integral to numerous neurological and psychiatric disorders, and more generally, to a wide range of behavioral and health problems. Response-inhibition efficiency furthermore correlates with treatment outcome in some of these conditions. The stop-signal task is an essential tool to determine how quickly response inhibition is implemented. Despite its apparent simplicity, there are many features (ranging from task design to data analysis) that vary across studies in ways that can easily compromise the validity of the obtained results. Our goal is to facilitate a more accurate use of the stop-signal task. To this end, we provide 12 easy-to-implement consensus recommendations and point out the problems that can arise when they are not followed. Furthermore, we provide user-friendly open-source resources intended to inform statistical-power considerations, facilitate the correct implementation of the task, and assist in proper data analysis.

Psychological interpretation of the ex-Gaussian and shifted Wald parameters: A diffusion model analysis

Abstract: A growing number of researchers use descriptive distributions such as the ex-Gaussian and the shifted Wald to summarize response time data for speeded two-choice tasks. Some of these researchers also assume that the parameters of these distributions uniquely correspond to specific cognitive processes. We studied the validity of this cognitive interpretation by relating the parameters of the ex-Gaussian and shifted Wald distributions to those of the Ratcliff diffusion model, a successful model whose parameters have well-established cognitive interpretations. In a simulation study, we fitted the ex-Gaussian and shifted Wald distributions to data generated from the diffusion model by systematically varying its parameters across a wide range of plausible values. In an empirical study, the two descriptive distributions were fitted to published data that featured manipulations of task difficulty, response caution, and a priori bias. The results clearly demonstrate that the ex-Gaussian and shifted Wald parameters do not correspond uniquely to parameters of the diffusion model. We conclude that researchers should resist the temptation to interpret changes in the ex-Gaussian and shifted Wald parameters in terms of cognitive processes. Supporting materials may be downloaded from http://pbr.psychonomic-journals .org/content/supplemental.

An Introduction To The Event Related Potential Technique

Abstract: Thank you for downloading an introduction to the event related potential technique. Maybe you have knowledge that, people have look hundreds times for their favorite readings like this an introduction to the event related potential technique, but end up in malicious downloads. Rather than reading a good book with a cup of tea in the afternoon, instead they are facing with some malicious bugs inside their laptop.

The Diffusion Decision Model: Theory and Data for Two-Choice Decision Tasks

Abstract: The diffusion decision model allows detailed explanations of behavior in two-choice discrimination tasks. In this article, the model is reviewed to show how it translates behavioral data—accuracy, mean response times, and response time distributions—into components of cognitive processing. Three experiments are used to illustrate experimental manipulations of three components: stimulus difficulty affects the quality of information on which a decision is based; instructions emphasizing either speed or accuracy affect the criterial amounts of information that a subject requires before initiating a response; and the relative proportions of the two stimuli affect biases in drift rate and starting point. The experiments also illustrate the strong constraints that ensure the model is empirically testable and potentially falsifiable. The broad range of applications of the model is also reviewed, including research in the domains of aging and neurophysiology.

Test Driven Development: By Example

Abstract: From the Book: “Clean code that works” is Ron Jeffries’ pithy phrase. The goal is clean code that works, and for a whole bunch of reasons: Clean code that works is a predictable way to develop. You know when you are finished, without having to worry about a long bug trail.Clean code that works gives you a chance to learn all the lessons that the code has to teach you. If you only ever slap together the first thing you think of, you never have time to think of a second, better, thing. Clean code that works improves the lives of users of our software.Clean code that works lets your teammates count on you, and you on them.Writing clean code that works feels good.But how do you get to clean code that works? Many forces drive you away from clean code, and even code that works. Without taking too much counsel of our fears, here’s what we do—drive development with automated tests, a style of development called “Test-Driven Development” (TDD for short). In Test-Driven Development, you: Write new code only if you first have a failing automated test.Eliminate duplication. Two simple rules, but they generate complex individual and group behavior. Some of the technical implications are:You must design organically, with running code providing feedback between decisionsYou must write your own tests, since you can’t wait twenty times a day for someone else to write a testYour development environment must provide rapid response to small changesYour designs must consist of many highly cohesive, loosely coupled components, just to make testing easy The two rules imply an order to the tasks ofprogramming: 1. Red—write a little test that doesn’t work, perhaps doesn’t even compile at first 2. Green—make the test work quickly, committing whatever sins necessary in the process 3. Refactor—eliminate all the duplication created in just getting the test to work Red/green/refactor. The TDD’s mantra. Assuming for the moment that such a style is possible, it might be possible to dramatically reduce the defect density of code and make the subject of work crystal clear to all involved. If so, writing only code demanded by failing tests also has social implications: If the defect density can be reduced enough, QA can shift from reactive to pro-active workIf the number of nasty surprises can be reduced enough, project managers can estimate accurately enough to involve real customers in daily developmentIf the topics of technical conversations can be made clear enough, programmers can work in minute-by-minute collaboration instead of daily or weekly collaborationAgain, if the defect density can be reduced enough, we can have shippable software with new functionality every day, leading to new business relationships with customers So, the concept is simple, but what’s my motivation? Why would a programmer take on the additional work of writing automated tests? Why would a programmer work in tiny little steps when their mind is capable of great soaring swoops of design? Courage. Courage Test-driven development is a way of managing fear during programming. I don’t mean fear in a bad way, pow widdle prwogwammew needs a pacifiew, but fear in the legitimate, this-is-a-hard-problem-and-I-can’t-see-the-end-from-the-beginning sense. If pain is nature’s way of saying “Stop!”, fear is nature’s way of saying “Be careful.” Being careful is good, but fear has a host of other effects: Makes you tentativeMakes you want to communicate lessMakes you shy from feedbackMakes you grumpy None of these effects are helpful when programming, especially when programming something hard. So, how can you face a difficult situation and: Instead of being tentative, begin learning concretely as quickly as possible.Instead of clamming up, communicate more clearly.Instead of avoiding feedback, search out helpful, concrete feedback.(You’ll have to work on grumpiness on your own.) Imagine programming as turning a crank to pull a bucket of water from a well. When the bucket is small, a free-spinning crank is fine. When the bucket is big and full of water, you’re going to get tired before the bucket is all the way up. You need a ratchet mechanism to enable you to rest between bouts of cranking. The heavier the bucket, the closer the teeth need to be on the ratchet. The tests in test-driven development are the teeth of the ratchet. Once you get one test working, you know it is working, now and forever. You are one step closer to having everything working than you were when the test was broken. Now get the next one working, and the next, and the next. By analogy, the tougher the programming problem, the less ground should be covered by each test. Readers of Extreme Programming Explained will notice a difference in tone between XP and TDD. TDD isn’t an absolute like Extreme Programming. XP says, “Here are things you must be able to do to be prepared to evolve further.” TDD is a little fuzzier. TDD is an awareness of the gap between decision and feedback during programming, and techniques to control that gap. “What if I do a paper design for a week, then test-drive the code? Is that TDD?” Sure, it’s TDD. You were aware of the gap between decision and feedback and you controlled the gap deliberately. That said, most people who learn TDD find their programming practice changed for good. “Test Infected” is the phrase Erich Gamma coined to describe this shift. You might find yourself writing more tests earlier, and working in smaller steps than you ever dreamed would be sensible. On the other hand, some programmers learn TDD and go back to their earlier practices, reserving TDD for special occasions when ordinary programming isn’t making progress. There are certainly programming tasks that can’t be driven solely by tests (or at least, not yet). Security software and concurrency, for example, are two topics where TDD is not sufficient to mechanically demonstrate that the goals of the software have been met. Security relies on essentially defect-free code, true, but also on human judgement about the methods used to secure the software. Subtle concurrency problems can’t be reliably duplicated by running the code. Once you are finished reading this book, you should be ready to: Start simplyWrite automated testsRefactor to add design decisions one at a time This book is organized into three sections. An example of writing typical model code using TDD. The example is one I got from Ward Cunningham years ago, and have used many times since, multi-currency arithmetic. In it you will learn to write tests before code and grow a design organically.An example of testing more complicated logic, including reflection and exceptions, by developing a framework for automated testing. This example also serves to introduce you to the xUnit architecture that is at the heart of many programmer-oriented testing tools. In the second example you will learn to work in even smaller steps than in the first example, including the kind of self-referential hooha beloved of computer scientists.Patterns for TDD. Included are patterns for the deciding what tests to write, how to write tests using xUnit, and a greatest hits selection of the design patterns and refactorings used in the examples. I wrote the examples imagining a pair programming session. If you like looking at the map before wandering around, you may want to go straight to the patterns in Section 3 and use the examples as illustrations. If you prefer just wandering around and then looking at the map to see where you’ve been, try reading the examples through and refering to the patterns when you want more detail about a technique, then using the patterns as a reference. Several reviewers have commented they got the most out of the examples when they started up a programming environment and entered the code and ran the tests as they read. A note about the examples. Both examples, multi-currency calculation and a testing framework, appear simple. There are (and I have seen) complicated, ugly, messy ways of solving the same problems. I could have chosen one of those complicated, ugly, messy solutions to give the book an air of “reality.” However, my goal, and I hope your goal, is to write clean code that works. Before teeing off on the examples as being too simple, spend 15 seconds imagining a programming world in which all code was this clear and direct, where there were no complicated solutions, only apparently complicated problems begging for careful thought. TDD is a practice that can help you lead yourself to exactly that careful thought.

Using Bayes to get the most out of non-significant results

Abstract: No scientific conclusion follows automatically from a statistically non-significant result, yet people routinely use non-significant results to guide conclusions about the status of theories (or the effectiveness of practices). To know whether a non-significant result counts against a theory, or if it just indicates data insensitivity, researchers must use one of: power, intervals (such as confidence or credibility intervals), or else an indicator of the relative evidence for one theory over another, such as a Bayes factor. I argue Bayes factors allow theory to be linked to data in a way that overcomes the weaknesses of the other approaches. Specifically, Bayes factors use the data themselves to determine their sensitivity in distinguishing theories (unlike power), and they make use of those aspects of a theory’s predictions that are often easiest to specify (unlike power and intervals, which require specifying the minimal interesting value in order to address theory). Bayes factors provide a coherent approach to determining whether non-significant results support a null hypothesis over a theory, or whether the data are just insensitive. They allow accepting and rejecting the null hypothesis to be put on an equal footing. Concrete examples are provided to indicate the range of application of a simple online Bayes calculator, which reveal both the strengths and weaknesses of Bayes factors.