New paper in Journal of Memory and Language: Share the code, not just the data

Here is an important paper for the field of psycholionguistics that just came out in JML. It is led by Dr. Anna Laurinavichyute and was commissioned by the editor of JML (Prof. Kathy Rastle).

Share the code, not just the data: A case study of the reproducibility of articles published in the Journal of Memory and Language under the open data policy

Download here: https://doi.org/10.1016/j.jml.2022.104332

Ever wondered how the probability of the null hypothesis being true changes given a significant result?

TRIGGER WARNING: These simulations might fundamentally shake your belief system. USE WITH CARE.

In a recently accepted paper in the open access journal Quantitative Methods for Psychology that Daniel Schad led, we discuss how, using Bayes' rule, one can explore the change in the probability of a null hypothesis being true (call it theta) when you get a significant effect. The paper, which was inspired by a short comment in McElreath's book (first edition), shows that theta does not necessarily change much even if you get a significant result. The probability theta can change dramatically under certain conditions, but those conditions are either so stringent or so trivial that it renders many of the significance-based conclusions in psychology and psycholinguistics questionable at the very least.

You can do your own simulations, under assumptions that you consider more appropriate for your own research problem, using this shiny app (below), or play with the source code: here.

  

New(ish) paper: Share the code, not just the data: A case study of the reproducibility of JML articles published under the open data policy

Here's an important new paper led by Dr. Anna Laurinavichyute on the reproducibility of published analyses. This paper by commissioned by the editor in chief of the Journal of Memory and Language, Kathy Rastle.

Title: Share the code, not just the data: A case study of the reproducibility of JML articles published under the open data policy

Abstract:

In 2019 the Journal of Memory and Language instituted an open data and code policy; this policy requires that, as a rule, code and data be released at the latest upon publication. How effective is this policy? We compared 59 papers published before, and 59 papers published after, the policy took effect. After the policy was in place, the rate of data sharing increased by more than 50%. We further looked at whether papers published under the open data policy were reproducible, in the sense that the published results should be possible to regenerate given the data, and given the code, when code was provided. For 8 out of the 59 papers, data sets were inaccessible. The reproducibility rate ranged from 34% to 56%, depending on the reproducibility criteria. The strongest predictor of whether an attempt to reproduce would be successful is the presence of the analysis code: it increases the probability of reproducing reported results by almost 40%. We propose two simple steps that can increase the reproducibility of published papers: share the analysis code, and attempt to reproduce one’s own analysis using only the shared materials.

PDF: here.

Summer School on Statistical Methods for Linguistics and Psychology, Sept. 12-16, 2022 (applications close April 1)

The Sixth Summer School on Statistical Methods for Linguistics and Psychology will be held in Potsdam, Germany, September 12-16, 2022.  Like the previous editions of the summer school, this edition will have two frequentist and two Bayesian streams. Currently, this summer school is being planned as an in-person event.

The application form closes April 1, 2022. We will announce the decisions on or around April 15, 2022.

Course fee: There is no fee because the summer school is funded by the Collaborative Research Center (Sonderforschungsbereich 1287). However, we will charge 40 Euros to cover costs for coffee and snacks during the breaks and social hours. And participants will have to pay for their own accommodation. 

For details, see: https://vasishth.github.io/smlp2022/

 Curriculum:

1. Introduction to Bayesian data analysis (maximum 30 participants). Taught by Shravan Vasishth, assisted by Anna Laurinavichyute, and Paula Lissón

This course is an introduction to Bayesian modeling, oriented towards linguists and psychologists. Topics to be covered: Introduction to Bayesian data analysis, Linear Modeling, Hierarchical Models. We will cover these topics within the context of an applied Bayesian workflow that includes exploratory data analysis, model fitting, and model checking using simulation. Participants are expected to be familiar with R, and must have some experience in data analysis, particularly with the R library lme4.
Course Materials Previous year's course web page: all materials (videos etc.) from the previous year are available here.
Textbook: here. We will work through the first six chapters.

2. Advanced Bayesian data analysis (maximum 30 participants). Taught by Bruno Nicenboim, assisted by Himanshu Yadav

This course assumes that participants have some experience in Bayesian modeling already using brms and want to transition to Stan to learn more advanced methods and start building simple computational cognitive models. Participants should have worked through or be familiar with the material in the first five chapters of our book draft: Introduction to Bayesian Data Analysis for Cognitive Science. In this course, we will cover Parts III to V of our book draft: model comparison using Bayes factors and k-fold cross validation, introduction and relatively advanced models with Stan, and simple computational cognitive models.

 Course Materials Textbook here. We will start from Part III of the book (Advanced models with Stan). Participants are expected to be familiar with the first five chapters.

3. Foundational methods in frequentist statistics (maximum 30 participants). Taught by Audrey Buerki, Daniel Schad, and João Veríssimo.

Participants will be expected to have used linear mixed models before, to the level of the textbook by Winter (2019, Statistics for Linguists), and want to acquire a deeper knowledge of frequentist foundations, and understand the linear mixed modeling framework more deeply. Participants are also expected to have fit multiple regressions. We will cover model selection, contrast coding, with a heavy emphasis on simulations to compute power and to understand what the model implies. We will work on (at least some of) the participants' own datasets. This course is not appropriate for researchers new to R or to frequentist statistics.

Course Materials Textbook draft here. 

4.  Advanced methods in frequentist statistics with Julia (maximum 30 participants). Taught by Reinhold Kliegl, Phillip Alday, Julius Krumbiegel, and Doug Bates.
Applicants must have experience with linear mixed models and be interested in learning how to carry out such analyses with the Julia-based MixedModels.jl package) (i.e., the analogue of the R-based lme4 package). MixedModels.jl has some significant advantages. Some of them are: (a) new and more efficient computational implementation, (b) speed — needed for, e.g., complex designs and power simulations, (c) more flexibility for selection of parsimonious mixed models, and (d) more flexibility in taking into account autocorrelations or other dependencies — typical EEG-, fMRI-based time series (under development). We do not expect profound knowledge of Julia from participants; the necessary subset of knowledge will be taught on the first day of the course. We do expect a readiness to install Julia and the confidence that with some basic instruction participants will be able to adapt prepared Julia scripts for their own data or to adapt some of their own lme4-commands to the equivalent MixedModels.jl-commands. The course will be taught in a hybrid IDE. There is already the option to execute R chunks from within Julia, meaning one needs Julia primarily for execution of MixedModels.jl commands as replacement of lme4. There is also an option to call MixedModels.jl from within R and process the resulting object like an lme4-object. Thus, much of pre- and postprocessing (e.g., data simulation for complex experimental designs; visualization of partial-effect interactions or shrinkage effects) can be carried out in R.
Course Materials Github repo: here.

New paper in Computational Brain and Behavior: Sample size determination in Bayesian Linear Mixed Models

We've just had a paper accepted in Computational Brain and Behavior, an open access journal of the Society for Mathematical Psychology. 

Even though I am not a psychologist, I feel an increasing affinity to this field compared to psycholinguistics proper. I will be submitting more of my papers to this journal and other open access journals (Glossa Psycholx, Open Mind in particular) in the future. 

Some things I liked about this journal:

- A fast and well-informed, intelligent, useful set of reviews. The reviewers actually understand what they are talking about! It's refreshing to find people out there who speak my language (and I don't mean English or Hindi). Also, the reviewers signed their reviews. This doesn't usually happen.

- Free availability of the paper after publication; I didn't have to do anything to make this happen. By contrast, I don't even have copies of my own articles published in APA journals. The same goes for Elsevier journals like the Journal of Memory and Language. Either I shell out $$$ to make the paper open access, or I learn to live with the arXiv version of my paper. 

-  The proofing was *excellent*. By contrast, the Journal of Memory and Language adds approximately 500 mistakes into my papers every time they publish it (then we have to correct them, if we catch them at all). E.g., in this paper we had to issue a correction about a German example; this error was added by the proofer! Another surprising example of JML actually destroying our paper's formatting is this one; here, the arXiv version has better formatting than the published paper, which cost several thousand Euros! 

- LaTeX is encouraged. By contrast, APA journals demand that papers be submitted in W**d. 

Here is the paper itself: here, we present an approach, adapted from the work of two statisticians (Wang and Gelfand), for determining approximate sample size needed for drawing meaningful inferences using Bayes factors in hierarchical models (aka linear mixed models). The example comes from a psycholinguistic study but the method is general. Code and data are of course available online.

The pdf: https://link.springer.com/article/10.1007/s42113-021-00125-y

 

Book: Sentence comprehension as a cognitive process: A computational approach (Vasishth and Engelmann)

 

My book with Felix Engelmann has just been published. It puts together in one place 20 years of research on retrieval models, carried out by my students, colleagues, and myself.

New paper on the reproducibility of JML articles (2019-21) after the open data policy was introduced

 New paper by Anna Laurinavichyute and me:

The (ir)reproducibility of published analyses: A case study of 57 JML articles published between 2019 and 2021

Download from: https://psyarxiv.com/hf297/