Bayesian inference for psychology,part III: Parameter estimation in nonstandard models

We demonstrate the use of three popular Bayesian software packages that enable researchers to estimate parameters in a broad class of models that are commonly used in psychological research. We focus on WinBUGS, JAGS, and Stan, and show how they can be interfaced from R and MATLAB. We illustrate the use of the packages through two fully worked examples; the examples involve a simple univariate linear regression and fitting a multinomial processing tree model to data from a classic false-memory experiment. We conclude with a comparison of the strengths and weaknesses of the packages. Our example code, data, and this text are available via https://osf.io/ucmaz/.     

Dutch taboo norms

This article provides norms for general taboo, personal taboo, insult, valence, and arousal for 672 Dutch words, including 202 taboo words. Norms were collected using a 7-point Likert scale and based on ratings by psychology students from the Erasmus University Rotterdam in The Netherlands. The sample consisted of 87 psychology students (58 females, 29 males). We obtained high reliability based on split-half analyses. Our norms show high correlations with arousal and valence ratings collected by another Dutch word-norms study (Moors et al.,, Behavior Research Methods, 45, 169–177, 2013). Our results show that the previously found quadratic relation (i.e., U-shaped pattern) between valence and arousal also holds when only taboo words are considered. Additionally, words rated high on taboo tended to be rated low on valence, but some words related to sex rated high on both taboo and valence. Words that rated high on taboo rated high on insult, again with the exception of words related to sex many of which rated low on insult. Finally, words rated high on taboo and insult rated high on arousal. The Dutch Taboo Norms (DTN) database is a useful tool for researchers interested in the effects of taboo words on cognitive processing. The data associated with this paper can be accessed via the Open Science Framework (https://osf.io/vk782/).     

A novel blink detection method based on pupillometry noise

Pupillometry (or the measurement of pupil size) is commonly used as an index of cognitive load and arousal. Pupil size data are recorded using eyetracking devices that provide an output containing pupil size at various points in time. During blinks the eyetracking device loses track of the pupil, resulting in missing values in the output file. The missing-sample time window is preceded and followed by a sharp change in the recorded pupil size, due to the opening and closing of the eyelids. This eyelid signal can create artificial effects if it is not removed from the data. Thus, accurate detection of the onset and the offset of blinks is necessary for pupil size analysis. Although there are several approaches to detecting and removing blinks from the data, most of these approaches do not remove the eyelid signal or can result in a relatively large amount of data loss. The present work suggests a novel blink detection algorithm based on the fluctuations that characterize pupil data. These fluctuations (“noise”) result from measurement error produced by the eyetracker device. Our algorithm finds the onset and offset of the blinks on the basis of this fluctuation pattern and its distinctiveness from the eyelid signal. By comparing our algorithm to three other common blink detection methods and to results from two independent human raters, we demonstrate the effectiveness of our algorithm in detecting blink onset and offset. The algorithm’s code and example files for processing multiple eye blinks are freely available for download (https://osf.io/jyz43).     

Examining reproducibility in psychology: A hybrid method for combining a statistically significant original study and a replication

The unrealistically high rate of positive results within psychology has increased the attention to replication research. However, researchers who conduct a replication and want to statistically combine the results of their replication with a statistically significant original study encounter problems when using traditional meta-analysis techniques. The original study’s effect size is most probably overestimated because it is statistically significant, and this bias is not taken into consideration in traditional meta-analysis. We have developed a hybrid method that does take the statistical significance of an original study into account and enables (a) accurate effect size estimation, (b) estimation of a confidence interval, and (c) testing of the null hypothesis of no effect. We analytically approximate the performance of the hybrid method and describe its statistical properties. By applying the hybrid method to data from the Reproducibility Project: Psychology (Open Science Collaboration, 2015), we demonstrate that the conclusions based on the hybrid method are often in line with those of the replication, suggesting that many published psychological studies have smaller effect sizes than those reported in the original study, and that some effects may even be absent. We offer hands-on guidelines for how to statistically combine an original study and replication, and have developed a Web-based application (https://rvanaert.shinyapps.io/hybrid) for applying the hybrid method.     

Interpolation in 16-Valued Trilattice Logics

In a recent paper we have defined an analytic tableau calculus \({{\mathbf {\mathsf{{PL}}}}}_{\mathbf {16}}\) for a functionally complete extension of Shramko and Wansing’s logic based on the trilattice \({SIXTEEN}_3\). This calculus makes it possible to define syntactic entailment relations that capture central semantic relations of the logic—such as the relations Open image in new window , Open image in new window , and Open image in new window that each correspond to a lattice order in \({SIXTEEN}_3\); and Open image in new window , the intersection of Open image in new window and Open image in new window . It turns out that our method of characterising these semantic relations—as intersections of auxiliary relations that can be captured with the help of a single calculus—lends itself well to proving interpolation. All entailment relations just mentioned have the interpolation property, not only when they are defined with respect to a functionally complete language, but also in a range of cases where less expressive languages are considered. For example, we will show that Open image in new window , when restricted to \(\mathcal {L}_{tf}\), the language originally considered by Shramko and Wansing, enjoys interpolation. This answers a question that was recently posed by M. Takano.     

A Review of Best Practice Recommendations for Text Analysis in R (and a User-Friendly App)

In recent decades, the amount of text available for organizational science research has grown tremendously. Despite the availability of text and advances in text analysis methods, many of these techniques remain largely segmented by discipline. Moreover, there is an increasing number of open-source tools (R, Python) for text analysis, yet these tools are not easily taken advantage of by social science researchers who likely have limited programming knowledge and exposure to computational methods. In this article, we compare quantitative and qualitative text analysis methods used across social sciences. We describe basic terminology and the overlooked, but critically important, steps in pre-processing raw text (e.g., selection of stop words; stemming). Next, we provide an exploratory analysis of open-ended responses from a prototypical survey dataset using topic modeling with R. We provide a list of best practice recommendations for text analysis focused on (1) hypothesis and question formation, (2) design and data collection, (3) data pre-processing, and (4) topic modeling. We also discuss the creation of scale scores for more traditional correlation and regression analyses. All the data are available in an online repository for the interested reader to practice with, along with a reference list for additional reading, an R markdown file, and an open source interactive topic model tool (topicApp; see https://github.com/wesslen/topicApp, https://github.com/wesslen/text-analysis-org-science, https://dataverse.unc.edu/dataset.xhtml?persistentId=doi:10.15139/S3/R4W7ZS).     

Against Hamri’s argument for the ultimate ground of being

In this paper, I reply to Hamri's (Int J Philos Relig.  https://doi.org/10.1007/s11153-017-9625-2, 2017) new kind of cosmological argument for the ultimate ground of being by blocking the argument in more than one place.     

Double Decomposition of Level-1 Variables in Multilevel Models: An Analysis of the Flynn Effect in the NSLY Data

This paper introduces an extension of cluster mean centering (also called group mean centering) for multilevel models, which we call “double decomposition (DD).” This centering method separates between-level variance, as in cluster mean centering, but also decomposes within-level variance of the same variable. This process retains the benefits of cluster mean centering but allows for context variables derived from lower level variables, other than the cluster mean, to be incorporated into the model. A brief simulation study is presented, demonstrating the potential advantage (or even necessity) for DD in certain circumstances. Several applications to multilevel analysis are discussed. Finally, an empirical demonstration examining the Flynn effect (Flynn, 1987 Flynn, J. R. (1987). Massive IQ gains in 14 nations: What IQ tests really measure. Psychological Bulletin, 101(2), 171. https://doi.org/10.1037/h0090408.[Crossref], [Web of Science ®] , [Google Scholar]), our motivating example, is presented. The use of DD in the analysis provides a novel method to narrow the field of plausible causal hypotheses regarding the Flynn effect, in line with suggestions by a number of researchers (Mingroni, 2014 Mingroni, M. A. (2014). Future efforts in Flynn effect research: Balancing reductionism with holism. Journal of Intelligence, 2(4), 122. https://doi.org/10.3390/jintelligence2040122.[Crossref] , [Google Scholar]; Rodgers, 2015 Rodgers, J. L. (2015). Methodological issues associated with studying the Flynn effect: Exploratory and confirmatory efforts in the past, present, and future. Journal of Intelligence, 3(4), 111. https://doi.org/10.3390/jintelligence3040111. [Crossref] , [Google Scholar]).     

Adult attachment theory and Rorschach Inkblot Method: A systematic literature review

This critical appraisal and synthesis review explores the literature on the evidence of Rorschach Inkblot Method variables as measures of the attachment theory. We searched for publications making use of EBSCO Discovery Service (EDS) which included 41 databases of which Academic Search Premier, ScienceDirect, PsycARTICLES, and PsycINFO yielded the most results. Inclusion criteria were published studies concerning Rorschach and attachment theory where participants were older than 18 years. Non-academic literature and studies not published in English were excluded. We synthesised the evidence following the narrative approach of Petticrew and Roberts (2006 Petticrew, M., & Roberts, H. (Eds.). (2006). Systematic reviews in social sciences: A practical guide. Oxford, UK: Blackwell Publishing Ltd. https://doi.org/10.1002/9780470754887[Crossref] , [Google Scholar]). Findings suggest texture, oral responses, and Rorschach oral dependency strongly associated with attachment security, with other variables indicating weaker associations with attachment.     

A visual familiarity account of evidence for orthographic processing in pigeons <Emphasis Type="Italic">(Columbia livia)</Emphasis>: a reply to Scarf,Corballis, Güntürkün,and Colombo (2017)

Scarf et al. (Proc Natl Acad Sci 113(40):11272–11276, 2016) demonstrated that pigeons, as with baboons (Grainger et al. in Science 336(6078):245–248, 2012; Ziegler in Psychol Sci.  https://doi.org/10.1177/0956797612474322, 2013), can be trained to display several behavioural hallmarks of human orthographic processing. But, Vokey and Jamieson (Psychol Sci 25(4):991–996, 2014) demonstrated that a standard, autoassociative neural network model of memory applied to pixel maps of the words and nonwords reproduces all of those results. In a subsequent report, Scarf et al. (Anim Cognit 20(5):999–1002, 2017) demonstrated that pigeons can reproduce one more marker of human orthographic processing: the ability to discriminate visually presented four-letter words from their mirror-reversed counterparts (e.g. “LEFT” vs. “ Open image in new window ”). The current report shows that the model of Vokey and Jamieson (2014) reproduces the results of Scarf et al. (2017) and reinforces the original argument: the recent results thought to support a conclusion of orthographic processing in pigeons and baboons are consistent with but do not force that conclusion.     

An Introduction to Kristof’s Theorem for Solving Least-Square Optimization Problems Without Calculus

Kristof’s Theorem (Kristof, 1970 Kristof, W. (1970). A theorem on the trace of certain matrix products and some applications. Journal of Mathematical Psychology, 7(3), 515–530. https://doi.org/10.1016/0022-2496(70)90037-4[Crossref], [Web of Science ®] , [Google Scholar]) describes a matrix trace inequality that can be used to solve a wide-class of least-square optimization problems without calculus. Considering its generality, it is surprising that Kristof’s Theorem is rarely used in statistics and psychometric applications. The underutilization of this method likely stems, in part, from the mathematical complexity of Kristof’s (1964 Kristof, W. (1964). Die beste orthogonale Transformation zur gegenseitigen Uberfiihrung zweier Faktorenmatrizen. Diagnostica, 10, 87–90. [Google Scholar], 1970 Kristof, W. (1970). A theorem on the trace of certain matrix products and some applications. Journal of Mathematical Psychology, 7(3), 515–530. https://doi.org/10.1016/0022-2496(70)90037-4[Crossref], [Web of Science ®] , [Google Scholar]) writings. In this article, I describe the underlying logic of Kristof’s Theorem in simple terms by reviewing four key mathematical ideas that are used in the theorem’s proof. I then show how Kristof’s Theorem can be used to provide novel derivations to two cognate models from statistics and psychometrics. This tutorial includes a glossary of technical terms and an online supplement with R (R Core Team, 2017 R Core Team (2017). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from https://www.R-project.org/ [Google Scholar]) code to perform the calculations described in the text.     

Common Factors Come Alive: Practical Strategies for Implementing Common Factors in MFT Training

Presently, MFT training programs teach MFT models in a way that emphasizes differences over similarities (Karam et al. in J Marital Fam Ther, 2015. doi: 10.1111/jmft.12096; Sprenkle and Blow in J Marital Fam Ther 30:113–129, 2004a. doi: 10.1111/j.1752-0606.2004.tb01228.x, in J Marital Fam Ther 30:151–157, b. doi: 10.1111/j.1752-0606.2004.tb01230.x; Sprenkle et al. in Common factors in couple and family therapy: the overlooked foundation for effective practice. Guilford Press, New York, 2009). Although teaching a variety of models and their distinctiveness is vital, doing so may create a competitive rather than integrative relationship between models (Karam et al. 2015). While Karam et al. 2015 encourage the inclusion of common factors in MFT training, we expand their justification for the importance of doing so We also explain conceptual and practical ways to include common factors in MFT training. Common factors instruction can fulfill multiple purposes: (a) create a sense of cohesiveness for programs which need to teach breadth of topics that can seem unrelated, (b) help prepare practitioners who need to learn many models well but will likely adopt an integrative approach, (c) align with basic skills training, (d) align with process research, and (e) enhance the richness of individual models. For each of these purposes, we provide an example of a classroom activity. We conclude with a unifying example of how one student may learn the common-factors perspective and weave it into her reflective practices as an MFT student.     

A Comparison of Methods for Creating Multiple Imputations of Nominal Variables

Many variables that are analyzed by social scientists are nominal in nature. When missing data occur on these variables, optimal recovery of the analysis model's parameters is a challenging endeavor. One of the most popular methods to deal with missing nominal data is multiple imputation (MI). This study evaluated the capabilities of five MI methods that can be used to treat incomplete nominal variables: multiple imputation with chained equations (MICE) using polytomous regression as the elementary imputation method; MICE based on classification and regression trees (CART); MICE based on nested logistic regressions; the ranking procedure described by Allison (2002 Allison, P. D. (2002). Missing data. Thousand Oaks, CA: Sage Publications. https://doi.org/10.4135/9780857020994.n4[Crossref] , [Google Scholar]); and a joint modeling approach based on the general location model. We first motivate our inquiry with an applied example and then present the results of a Monte Carlo simulation study that compared the performance of the five imputation methods under conditions of varying sample size, percentage of missing data, and number of nominal response categories. We found that MICE with polytomous regression was the strongest performer while the Allison (2002 Allison, P. D. (2002). Missing data. Thousand Oaks, CA: Sage Publications. https://doi.org/10.4135/9780857020994.n4[Crossref] , [Google Scholar]) ranking procedure and MICE with CART performed poorly in most conditions.     

TISK 1.0: An easy-to-use Python implementation of the time-invariant string kernel model of spoken word recognition

This article describes a new Python distribution of TISK, the time-invariant string kernel model of spoken word recognition (Hannagan et al. in Frontiers in Psychology, 4, 563, 2013). TISK is an interactive-activation model similar to the TRACE model (McClelland & Elman in Cognitive Psychology, 18, 1–86, 1986), but TISK replaces most of TRACE’s reduplicated, time-specific nodes with theoretically motivated time-invariant, open-diphone nodes. We discuss the utility of computational models as theory development tools, the relative merits of TISK as compared to other models, and the ways in which researchers might use this implementation to guide their own research and theory development. We describe a TISK model that includes features that facilitate in-line graphing of simulation results, integration with standard Python data formats, and graph and data export. The distribution can be downloaded from https://github.com/maglab-uconn/TISK1.0.     

No more than Conjectures: Popper and the Ethics of Scientific Enterprise

Karl Popper dealt with both problems Yurevich (Integrative Psychological and Behavioral Science, 43(2), 2009, doi: 10.1007/s12124-008-9082-7) deals: the crisis in Psychology and in the discourse about the nature of science. Although he failed to provide a complete response for both problems, his proposals can yet be fruitful to the reflection on these matters in the context of the present discussion. He offers some tentative answers to what could be considered a healthy epistemic activity, something Yurevich does not provide. More interestingly, some of the Popper proposals seem to fit, and in some extent correct, the quest for “collaborative work” proposed by Zittoun et al. (Integrative Psychological and Behavioral Science, 43(2), 2009, doi: 10.1007/s12124-008-9082-7) as a way of transforming crisis in development.     

Acoustic behavior associated with cooperative task success in bottlenose dolphins (<Emphasis Type="Italic">Tursiops truncatus</Emphasis>)

Although many species have proven capable of cooperating to achieve common goals, the role of communication in cooperation has received relatively little attention. Analysis of communication between partners is vital in determining whether actions are truly cooperative rather than serendipitous or learned via trial and error (Chalmeau and Gallo in Behav Process 35:101–111, 1996a. doi: 10.1016/0376-6357(95)00049-6, Primates 37:39–47, 1996b. doi: 10.1007/BF02382918). Wild cetaceans often produce sounds during cooperative foraging, playing, and mating, but the role of these sounds in cooperative events is largely unknown. Here, we investigated acoustic communication between two male bottlenose dolphins while they cooperatively opened a container (Kuczaj et al. in Anim Cogn 18:543–550, 2015b. doi: 10.1007/s10071-014-0822-4). Analyses of whistles, burst pulses, and bi-phonations that occurred during four contexts (i.e., no container, no animals interacting with container, one animal interacting with container, and two animals interacting with container) revealed that overall sound production rate significantly increased during container interactions. Sound production rates were also significantly higher during cooperative successes than solo successes, suggesting that the coordination of efforts rather than the apparatus itself was responsible for the phonation increase. The most common sound type during cooperative successes was burst pulse signals, similar to past recordings of cooperative events in bottlenose dolphins (Bastian in Animal sonar systems. Laboratoire de Physiologie Acoustique, Jouy-en Josas, pp 803–873, 1967; Connor and Smolker 1996).     

CFS MATLAB toolbox: An experiment builder for continuous flash suppression (CFS) task

CFS toolbox is an open-source collection of MATLAB functions that utilizes PsychToolbox-3 (PTB-3). It is designed to allow a researcher to create and run continuous flash suppression experiments using a variety of experimental parameters (i.e., stimulus types and locations, noise characteristics, and experiment window settings). In a CFS experiment, one of the eyes at a time is presented with a dynamically changing noise pattern, while the other eye is concurrently presented with a static target stimulus, such as a Gabor patch. Due to the strong interocular suppression created by the dominant noise pattern mask, the target stimulus is rendered invisible for an extended duration. Very little knowledge of MATLAB is required for using the toolbox; experiments are generated by modifying csv files with the required parameters, and result data are output to text files for further analysis. The open-source code is available on the project page under a Creative Commons License (http://www.mikkonuutinen.arkku.net/CFS_toolbox/ and https://bitbucket.org/mikkonuutinen/cfs_toolbox).     

Further evidence in favor of prior entry from endogenous attention to a location in space

Titchener’s (1908) law of prior entry states that “the object of attention comes to consciousness more quickly than the objects which we are not attending to,” or otherwise, that attended stimuli are perceived earlier than unattended stimuli. Shore, Spence, and Klein (Psychological Science, 12, 205–212. doi: 10.1111/1467-9280.00337, 2001) showed that endogenous visuospatial orienting does in fact elicit prior-entry effects, albeit to a smaller degree than does exogenous visuospatial orienting. In disagreement with this finding, Schneider and Bavelier (Cognitive Psychology, 47, 333–366. doi: 10.1016/S0010-0285(03)00035-5, 2003) found no effect of their instruction to attend. They concluded that nonattentional effects could masquerade as prior entry, which could account for findings such as those in Shore et al.’s endogenous condition. We investigated this empirical and theoretical discord by replicating the temporal-order judgment task used by Shore, Spence, and Klein, while manipulating and measuring endogenous orienting by way of an orthogonal color probe task. We showed evidence of prior entry as a consequence of endogenous orienting, supporting the conclusions of Shore, Spence, and Klein.     

Dealing with the Conflicting Results of Psycholinguistic Experiments: How to Resolve Them with the Help of Statistical Meta-analysis

This paper proposes the use of the tools of statistical meta-analysis as a method of conflict resolution with respect to experiments in cognitive linguistics. With the help of statistical meta-analysis, the effect size of similar experiments can be compared, a well-founded and robust synthesis of the experimental data can be achieved, and possible causes of any divergence(s) in the outcomes can be revealed. This application of statistical meta-analysis offers a novel method of how diverging evidence can be dealt with. The workability of this idea is exemplified by a case study dealing with a series of experiments conducted as non-exact replications of Thibodeau and Boroditsky (PLoS ONE 6(2):e16782, 2011. https://doi.org/10.1371/journal.pone.0016782).     

The X-claim argument against religious belief offers nothing new

Stephen Law has recently offered an argument against the rationality of certain religious beliefs that he calls the X-claim argument against religious beliefs (Law in Relig Stud, 2017,  https://doi.org/10.1017/s0034412526000330). The argument purports to show that it is irrational to believe in the existence of extraordinary beings associated with religions. However, the X-claim argument is beset by certain ambiguities that, once resolved, leave the argument undifferentiated from two other common objections to the rationality of religious belief: the objection from religious diversity and the objection from unreliable sources. And though the latter pose serious obstacles to the rationality of religious belief, the X-claim argument adds no further difficulty.