G*Power (Erdfelder, Faul, & Buchner, 1996) was designed as a general stand-alone power analysis program for statistical tests commonly used in social and behavioral research. G*Power 3 is a major extension of, and improvement over, the previous versions. It runs on widely used computer platforms (i.e., Windows XP, Windows Vista, and Mac OS X 10.4) and covers many different statistical tests of thet, F, and χ2 test families. In addition, it includes power analyses forz tests and some exact tests. G*Power 3 provides improved effect size calculators and graphic options, supports both distribution-based and design-based input modes, and offers all types of power analyses in which users might be interested. Like its predecessors, G*Power 3 is free.

https://link.springer.com/content/pdf/10.3758/BF03193146.pdf

G*Power 3: A flexible statistical power analysis program for the social, behavioral, and biomedical sciences

Systematic review and meta-analysis

Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.

http://ibgwww.colorado.edu/cdrom2009/ScriptsA/purcell/GWAS/boulder_09_plink_intro.pdf

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

In this article the author reviews research evidence on the prevalence of mental disorders in lesbians, gay men, and bisexuals (LGBs) and shows, using meta-analyses, that LGBs have a higher prevalence of mental disorders than heterosexuals. The author offers a conceptual framework for understanding this excess in prevalence of disorder in terms of minority stress— explaining that stigma, prejudice, and discrimination create a hostile and stressful social environment that causes mental health problems. The model describes stress processes, including the experience of prejudice events, expectations of rejection, hiding and concealing, internalized homophobia, and ameliorative coping processes. This conceptual framework is the basis for the review of research evidence, suggestions for future research directions, and exploration of public policy implications. The study of mental health of lesbian, gay, and bisexual (LGB) populations has been complicated by the debate on the classification of homosexuality as a mental disorder during the 1960s and early 1970s. That debate posited a gay-affirmative perspective, which sought to declassify homosexuality, against a conservative perspective, which sought to retain the classification of homosexuality as a mental disorder (Bayer, 1981). Although the debate on classification ended in 1973 with the removal of homosexuality from the second edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM; American Psychiatric Association, 1973), its heritage has lasted. This heritage has tainted discussion on mental health of lesbians and gay men by associating— even equating— claims that LGB people have higher prevalences of mental disorders than heterosexual people with the historical antigay stance and the stigmatization of LGB persons (Bailey, 1999). However, a fresh look at the issues should make it clear that whether LGB populations have higher prevalences of mental disorders is unrelated to the classification of homosexuality as a mental disorder. A retrospective analysis would suggest that the attempt to find a scientific answer in that debate rested on flawed logic. The debated scientific question was, Is homosexuality a mental disorder? The operationalized research question that pervaded the debate was, Do homosexuals have high prevalences of mental disorders? But the research did not accurately operationalize the scientific question. The question of whether homosexuality should be considered a mental disorder is a question about classification. It can be answered by debating which behaviors, cognitions, or emotions should be considered indicators of a mental

/pdf/prejudice-social-stress-and-mental-health-in-lesbian-gay-and-2eymy1qdt5.pdf

Prejudice, social stress, and mental health in lesbian, gay, and bisexual populations: conceptual issues and research evidence

Objective. —To develop and validate a new Simplified Acute Physiology Score, the SAPS II, from a large sample of surgical and medical patients, and to provide a method to convert the score to a probability of hospital mortality. Design and Setting. —The SAPS II and the probability of hospital mortality were developed and validated using data from consecutive admissions to 137 adult medical and/or surgical intensive care units in 12 countries. Patients. —The 13 152 patients were randomly divided into developmental (65%) and validation (35%) samples. Patients younger than 18 years, burn patients, coronary care patients, and cardiac surgery patients were excluded. Outcome Measure. —Vital status at hospital discharge. Results. —The SAPS II includes only 17 variables: 12 physiology variables, age, type of admission (scheduled surgical, unscheduled surgical, or medical), and three underlying disease variables (acquired immunodeficiency syndrome, metastatic cancer, and hematologic malignancy). Goodness-of-fit tests indicated that the model performed well in the developmental sample and validated well in an independent sample of patients (P=.883 andP=.104 in the developmental and validation samples, respectively). The area under the receiver operating characteristic curve was 0.88 in the developmental sample and 0.86 in the validation sample. Conclusion. —The SAPS II, based on a large international sample of patients, provides an estimate of the risk of death without having to specify a primary diagnosis. This is a starting point for future evaluation of the efficiency of intensive care units. (JAMA. 1993;270:2957-2963)

https://jamanetwork.com/HttpHandlers/ArticlePdfHandler.ashx?journal=JAMA&articleId=409979&pdfFileName=jama_270_24_035.pdf

Joseph L. Fleiss

Papers

Statistical Methods for Rates and Proportions