Sue Finch

A Primer on the Understanding, Use, and Calculation of Confidence Intervals That Are Based on Central and Noncentral Distributions

Reform of statistical practice in the social and behavioral sciences requires wider use of confidence intervals (CIs), effect size measures, and meta-analysis. The authors discuss four reasons for promoting use of CIs: They (a) are readily interpretable, (b) are linked to familiar statistical significance tests, (c) can encourage meta-analytic thinking, and (d) give information about precision. The authors discuss calculation of CIs for a basic standardized effect size measure, Cohen’s δ (also known as Cohen’s d), and contrast these with the familiar CIs for original score means. CIs for δ require use of noncentral t distributions, which the authors apply also to statistical power and simple meta-analysis of standardized effect sizes. They provide the ESCI graphical software, which runs under Microsoft Excel, to illustrate the discussion. Wider use of CIs for δ and other effect size measures should help promote highly desirable reform of statistical practice in the social sciences.

Border detection in dermoscopy images using hybrid thresholding on optimized color channels.

Automated border detection is one of the most important steps in dermoscopy image analysis. Although numerous border detection methods have been developed, few studies have focused on determining the optimal color channels for border detection in dermoscopy images. This paper proposes an automatic border detection method which determines the optimal color channels and performs hybrid thresholding to detect the lesion borders. The color optimization process is tested on a set of 30 dermoscopy images with four sets of dermatologist-drawn borders used as the ground truth. The hybrid border detection method is tested on a set of 85 dermoscopy images with two sets of ground truth using various metrics including accuracy, precision, sensitivity, specificity, and border error. The proposed method, which is comprised of two stages, is designed to increase specificity in the first stage and sensitivity in the second stage. It is shown to be highly competitive with three state-of-the-art border detection methods and potentially faster, since it mainly involves scalar processing as opposed to vector processing performed in the other methods. Furthermore, it is shown that our method is as good as, and in some cases more effective than a dermatology registrar.

Probability as certainty : Dichotomous thinking and the misuse of p values

Significance testing is widely used and often criticized. The Task Force on Statistical Inference of the American Psychological Association (TFSI, APA; Wilkinson & TFSI, 1999) addressed the use of significance testing and made recommendations that were incorporated in the fifth edition of the APAPublication Manual (APA, 2001). They emphasized the interpretation of significance testing and the importance of reporting confidence intervals and effect sizes. We examined whether 286Psychonomic Bulletin & Review articles submitted before and after the publication of the TFSI recommendations by APA complied with these recommendations. Interpretation errors when using significance testing were still made frequently, and the new prescriptions were not yet followed on a large scale. Changing the practice of reporting statistics seems doomed to be a slow process.

Past and Future American Psychological Association Guidelines for Statistical Practice

We review the publication guidelines of the American Psychological Association (APA) since 1929 and document their advice for authors about statistical practice. Although the advice has been extended with each revision of the guidelines, it has largely focused on null hypothesis significance testing (NHST) to the exclusion of other statistical methods. In parallel, we review over 40 years of critiques of NHST in psychology. Until now, the critiques have had little impact on the APA guidelines. The guidelines are influential in broadly shaping statistical practice, although in some cases recommended reporting practices are not closely followed. The guidelines have an important role to play in reform of statistical practice in psychology. Following the report of the APAs Task Force on Statistical Inference, we propose that future revisions of the guidelines reflect a broader philosophy of analysis and inference, provide detailed statistical requirements for reporting research, and directly address concerns about NHST. In addition, the APA needs to develop ways to ensure that its editors succeed in their leadership role in achieving essential reform.

Reform of statistical inference in psychology: The case ofMemory & Cognition

Geoffrey Loftus, Editor ofMemory & Cognition from 1994 to 1997, strongly encouraged presentation of figures with error bars and avoidance of null hypothesis significance testing (NHST). The authors examined 696Memory & Cognition articles published before, during, and after the Loftus editorship. Use of figures with bars increased to 47% under Loftus’s editorship and then declined. Bars were rarely used for interpretation, and NHST remained almost universal. Analysis of 309 articles in other psychology journals confirmed that Loftus’s influence was most evident in the articles he accepted for publication, but was otherwise limited. An e-mail survey of authors of papers accepted by Loftus revealed some support for his policy, but allegiance to traditional practices as well. Reform of psychologists’ statistical practices would require more than editorial encouragement.

Putting Research in Context: Understanding Confidence Intervals from One or More Studies

OBJECTIVES To support wider use and higher quality interpretation of confidence intervals (CIs) in psychology. METHODS We discuss the meaning and interpretation of CIs in single studies, and illustrate the value of CIs when reviewing and integrating research findings across studies. We demonstrate how to find CIs from summary statistics and published data in some simple situations. RESULTS We provide the ESCI graphical software, which runs under Microsoft Excel, to assist with calculating and plotting CIs. (www.latrobe.edu.au/psy/esci) CONCLUSIONS The wider use of CIs in psychology should support quality research communication and integrated interpretation of findings in context.

Chronic electrical stimulation with a suprachoroidal retinal prosthesis: a preclinical safety and efficacy study.

Purpose To assess the safety and efficacy of chronic electrical stimulation of the retina with a suprachoroidal visual prosthesis. Methods Seven normally-sighted feline subjects were implanted for 96–143 days with a suprachoroidal electrode array and six were chronically stimulated for 70–105 days at levels that activated the visual cortex. Charge balanced, biphasic, current pulses were delivered to platinum electrodes in a monopolar stimulation mode. Retinal integrity/function and the mechanical stability of the implant were assessed monthly using electroretinography (ERG), optical coherence tomography (OCT) and fundus photography. Electrode impedances were measured weekly and electrically-evoked visual cortex potentials (eEVCPs) were measured monthly to verify that chronic stimuli were suprathreshold. At the end of the chronic stimulation period, thresholds were confirmed with multi-unit recordings from the visual cortex. Randomized, blinded histological assessments were performed by two pathologists to compare the stimulated and non-stimulated retina and adjacent tissue. Results All subjects tolerated the surgical and stimulation procedure with no evidence of discomfort or unexpected adverse outcomes. After an initial post-operative settling period, electrode arrays were mechanically stable. Mean electrode impedances were stable between 11–15 kΩ during the implantation period. Visually-evoked ERGs & OCT were normal, and mean eEVCP thresholds did not substantially differ over time. In 81 of 84 electrode-adjacent tissue samples examined, there were no discernible histopathological differences between stimulated and unstimulated tissue. In the remaining three tissue samples there were minor focal fibroblastic and acute inflammatory responses. Conclusions Chronic suprathreshold electrical stimulation of the retina using a suprachoroidal electrode array evoked a minimal tissue response and no adverse clinical or histological findings. Moreover, thresholds and electrode impedance remained stable for stimulation durations of up to 15 weeks. This study has demonstrated the safety and efficacy of suprachoroidal stimulation with charge balanced stimulus currents.

Still Much to Learn About Confidence Intervals Reply to Rouder and Morey (2005)

Confidence intervals (CIs), rather than p values, should often provide the major justification for conclusions drawn from data. Therefore, CIs should be reported, and also interpreted. Rouder and Morey (2005) distinguished ‘‘arelational’’ CIs (e.g., CIs around single sample means) and ‘‘relational’’ CIs (e.g., CIs around mean differences or standardized effect sizes). They argued that the former are not suitable for inference and that researchers are justified in not interpreting such intervals. Yet, the purpose of research using samples is almost always to make inferences to populations. CIs—including arelational CIs—are, by design, inferential statistics and can legitimately serve to justify inferential conclusions. Rouder and Morey argued that rather than using arelational CIs for inference, authors should exploit the fact that they ‘‘provide a rough guide to variability in data, a coarse view of the replicability of patterns, and a quick check of the heterogeneity of variance’’ (p. 77). We believe there are problems with these three suggestions. First, variability in data is represented directly by descriptive statistics, such as the standard deviation. A CI, by contrast, is often based on a standard error and influenced by sample size. Similar levels of variability will give CIs of very different widths, depending on group size, so CIs should not be relied on to give even a rough guide to variability in data. Second, CIs do give information about replicability, but we (Cumming, Williams, & Fidler, 2004) reported that a majority of researchers, seeing a CI, markedly underestimate the true extent of variability over replications. Further, Maxwell (2004, p. 157) pointed out that in many realistic research situations, the pattern of results shown by CIs is unstable over replication. Finally, for examining heterogeneity of variance, descriptive rather than inferential statistics—standard deviations rather than standard errors or CIs—are again needed. Only if group sizes are equal will CIs give an accurate guide. Rouder and Morey’s comments reinforce the need to report standard deviations, but do not justify noninterpretation of CIs. CIs are rarely reported in journals outside medicine (Kieffer, Reese, & Thompson, 2001). Even in medicine, where they have been routinely reported for two decades, they are rarely interpreted (Fidler, Thomason, Cumming, Finch, & Leeman, 2004). Guidelines for and examples of good practice are lacking, and we support research to develop and evaluate better guidelines for use and interpretation of CIs. Thompson (2002) noted, ‘‘It is conceivable that some researchers may not fully understand statistical methods that they (a) rarely read in the literature and (b) infrequently use in their own work’’ (p. 26). For example, it is widely believed (Belia, Fidler, Williams, & Cumming, 2004; Schenker & Gentleman, 2001) that two 95% CIs having zero overlap—just touching end to end—are equivalent to statistical significance with p 5 .05. In fact, for 95% CIs on two independent means, overlap by about one quarter of the total length of one interval corresponds to a p value of about .05 (Cumming & Finch, 2005; Saville, 2003; Wolfe & Hanley, 2002). Rouder and Morey argued that ‘‘arelational CIs . . . do not reflect between-groups information and cannot be used for direct comparisons’’ (p. 77). This is true for repeated measure designs, in which CIs on separate cell means do not provide the relevant information for a comparison, but it does not hold for independent groups. For two independent groups, the difference between the means has a p value of about .05 when the separate 95% CIs overlap by about 25% of the length of either interval, and a p value of about .01 when the two intervals just touch end to end (see Cumming & Finch, 2005, for a discussion of the breadth of applicability of these rules). The terms arelational and relational might be useful in describing the type of CIs reported. However, such distinctions should not be used to determine the use of CIs. Of course, as for statistical tests, thought should be given to what is the most appropriate CI for the situation (Wilkinson & the Task Force on Statistical Address correspondence to Fiona Fidler, Department of History and Philosophy of Science, University of Melbourne, 3010, Victoria, Australia; e-mail: fidlerfm@unimelb.edu.au. PSYCHOLOGICAL SCIENCE

Is there a gap between recommended and ‘real world’ practice in the management of depression in young people? A medical file audit of practice

BackgroundLiterature has shown that dissemination of guidelines alone is insufficient to ensure that guideline recommendations are incorporated into every day clinical practice.MethodsWe aimed to investigate the gaps between guideline recommendations and clinical practice in the management of young people with depression by undertaking an audit of medical files in a catchment area public mental health service for 15 to 25 year olds in Melbourne, Australia.ResultsThe results showed that the assessment and recording of depression severity to ensure appropriate treatment planning was not systematic nor consistent; that the majority of young people (74.5%) were prescribed an antidepressant before an adequate trial of psychotherapy was undertaken and that less than 50% were monitored for depression symptom improvement and antidepressant treatment emergent suicide related behaviours (35% and 30% respectively). Encouragingly 92% of first line prescriptions for those aged 18 years or under who were previously antidepressant-naïve was for fluoxetine as recommended.ConclusionsThis research has highlighted the need for targeted strategies to ensure effective implementation. These strategies might include practice system tools that allow for systematic monitoring of depression symptoms and adverse side effects, particularly suicide related behaviours. Additionally, youth specific psychotherapy that incorporates the most effective components for this age group, delivered in a youth friendly way would likely aid effective implementation of guideline recommendations for engagement in an adequate trial of psychotherapy before medication is initiated.

Experimental comparison of PMD-induced system penalty models

We present experimental investigations of polarization-mode dispersion (PMD)-induced system penalties arising from an all-order PMD source, for amplified spontaneous emission and thermally limited systems. Further, we compare the experimental first-order PMD-induced penalties with predictions from both the string length model and the modified quadratic model. We show that the both models are in good agreement with the experimental data. The major difference between the two models is in the measurement requirements, which are less stringent for the string length method