1 Maximizing the Reproducibility of Your Research Open
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Reproducibility, Replicability, and Generalization in the Social, Behavioral, and Economic Sciences
REPRODUCIBILITY, REPLICABILITY, AND GENERALIZATION IN THE SOCIAL, BEHAVIORAL, AND ECONOMIC SCIENCES Report of the Subcommittee on Replicability in Science of the SBE Advisory Committee to the National Science Foundation 13 May 2015 Presentation at SBE AC Spring Meeting by K. Bollen. Report of the Subcommittee on Replicability in Science Advisory Committee to the NSF SBE Directorate Subcommittee Members: Kenneth Bollen (University of North Carolina at Chapel Hill, Cochair) John T. Cacioppo (University of Chicago, Cochair) Robert M. Kaplan (Agency for Healthcare Research and Quality) Jon A. Krosnick (Stanford University) James L. Olds (George Mason University) Staff Assistance Heather Dean (National Science Foundation) TOPICS I. Background II. Subcommittee Report III. Definitions IV. Recommendations V. Final Comments Background • Spring, 2013 o NSF SBE Advisory Committee establishes subcommittee on how SBE can promote robust research practices • Summer & Fall 2013 o Subcommittee proposal for workshop on “Robust Research in the Social, Behavioral, and Economic Sciences.” • February 20-21, 2014 o Workshop convened o Participants drawn from variety of universities, funding agencies, scientific associations, and journals o Cover broad range of issues from extent and cause of problems to possible solutions o Details are in the appendix of the circulated report • Post-workshop period o Document & digest workshop content o Discuss and propose recommendations o Complete report Subcommittee Report • DEFINITIONS o No consensus in science on the meanings -
Promoting an Open Research Culture
Promoting an open research culture Brian Nosek University of Virginia -- Center for Open Science http://briannosek.com/ -- http://cos.io/ The McGurk Effect Ba Ba? Da Da? Ga Ga? McGurk & MacDonald, 1976, Nature Adelson, 1995 Adelson, 1995 Norms Counternorms Communality Secrecy Open sharing Closed Norms Counternorms Communality Secrecy Open sharing Closed Universalism Particularlism Evaluate research on own merit Evaluate research by reputation Norms Counternorms Communality Secrecy Open sharing Closed Universalism Particularlism Evaluate research on own merit Evaluate research by reputation Disinterestedness Self-interestedness Motivated by knowledge and discovery Treat science as a competition Norms Counternorms Communality Secrecy Open sharing Closed Universalism Particularlism Evaluate research on own merit Evaluate research by reputation Disinterestedness Self-interestedness Motivated by knowledge and discovery Treat science as a competition Organized skepticism Organized dogmatism Consider all new evidence, even Invest career promoting one’s own against one’s prior work theories, findings Norms Counternorms Communality Secrecy Open sharing Closed Universalism Particularlism Evaluate research on own merit Evaluate research by reputation Disinterestedness Self-interestedness Motivated by knowledge and discovery Treat science as a competition Organized skepticism Organized dogmatism Consider all new evidence, even Invest career promoting one’s own against one’s prior work theories, findings Quality Quantity Anderson, Martinson, & DeVries, -
Experimental Evidence During a Global Pandemic
Original research BMJ Glob Health: first published as 10.1136/bmjgh-2020-004222 on 23 October 2020. Downloaded from Is health politically irrelevant? Experimental evidence during a global pandemic Arnab Acharya,1 John Gerring,2 Aaron Reeves3 To cite: Acharya A, Gerring J, ABSTRACT Key questions Reeves A. Is health politically Objective To investigate how health issues affect voting irrelevant? Experimental behaviour by considering the COVID-19 pandemic, which What is already known? evidence during a global offers a unique opportunity to examine this interplay. pandemic. BMJ Global Health Political leaders in democracies are sensitive to cues Design We employ a survey experiment in which ► 2020;5:e004222. doi:10.1136/ from the electorate and are less likely to implement treatment groups are exposed to key facts about the bmjgh-2020-004222 unpopular policies. pandemic, followed by questions intended to elicit attitudes Electoral accountability is not automatic, however, toward the incumbent party and government responsibility ► Additional material is and it only exists if citizens connect specific policies ► for the pandemic. published online only. To view, to politicians and vote accordingly. Setting The survey was conducted amid the lockdown please visit the journal online ► We know little about how public health attitudes af- period of 15–26 April 2020 in three large democratic (http:// dx. doi. org/ 10. 1136/ fect voting intention or behaviour. bmjgh- 2020- 004222). countries with the common governing language of English: India, the United Kingdom and the United States. Due What are the new findings? to limitations on travel and recruitment, subjects were ► The majority of our respondents believe health is an Received 15 October 2020 recruited through the M-T urk internet platform and the important policy area and that government has some Accepted 16 October 2020 survey was administered entirely online. -
Sensitivity and Specificity. Wikipedia. Last Modified on 16 November 2013
Sensitivity and specificity - Wikipedia, the free encyclopedia Create account Log in Article Talk Read Edit View Sensitivity and specificity From Wikipedia, the free encyclopedia Main page Contents Sensitivity and specificity are statistical measures of the performance of a binary classification test, also known in statistics as Featured content classification function. Sensitivity (also called the true positive rate, or the recall rate in some fields) measures the proportion of Current events actual positives which are correctly identified as such (e.g. the percentage of sick people who are correctly identified as having Random article the condition). Specificity measures the proportion of negatives which are correctly identified as such (e.g. the percentage of Donate to Wikipedia healthy people who are correctly identified as not having the condition, sometimes called the true negative rate). These two measures are closely related to the concepts of type I and type II errors. A perfect predictor would be described as 100% Interaction sensitive (i.e. predicting all people from the sick group as sick) and 100% specific (i.e. not predicting anyone from the healthy Help group as sick); however, theoretically any predictor will possess a minimum error bound known as the Bayes error rate. About Wikipedia For any test, there is usually a trade-off between the measures. For example: in an airport security setting in which one is testing Community portal for potential threats to safety, scanners may be set to trigger on low-risk items like belt buckles and keys (low specificity), in Recent changes order to reduce the risk of missing objects that do pose a threat to the aircraft and those aboard (high sensitivity). -
Metabolic Sensor Governing Bacterial Virulence in Staphylococcus Aureus
Metabolic sensor governing bacterial virulence in PNAS PLUS Staphylococcus aureus Yue Dinga, Xing Liub, Feifei Chena, Hongxia Dia, Bin Xua, Lu Zhouc, Xin Dengd,e, Min Wuf, Cai-Guang Yangb,1, and Lefu Lana,1 aDepartment of Molecular Pharmacology and bChinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; cDepartment of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China; dDepartment of Chemistry and eInstitute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637; and fDepartment of Basic Sciences University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203 Edited by Richard P. Novick, New York University School of Medicine, New York, NY, and approved October 14, 2014 (received for review June 13, 2014) An effective metabolism is essential to all living organisms, in- To survive and replicate efficiently in the host, S. aureus has cluding the important human pathogen Staphylococcus aureus.To developed exquisite mechanisms for scavenging nutrients and establish successful infection, S. aureus must scavenge nutrients adjusting its metabolism to maintain growth while also coping with and coordinate its metabolism for proliferation. Meanwhile, it also stress (6, 11). On the other hand, S. aureus produces a wide array must produce an array of virulence factors to interfere with host of virulence factors to evade host immune defenses and to derive defenses. However, the ways in which S. aureus ties its metabolic nutrition either parasitically or destructively from the host during state to its virulence regulation remain largely unknown. Here we infections (6). -
Principles of Validation of Diagnostic Assays for Infectious Diseases1
PRINCIPLES OF VALIDATION OF DIAGNOSTIC ASSAYS FOR INFECTIOUS DISEASES1 R. H. JACOBSON, New York State College of Veterinary Medicine, Cornell University, Ithaca, New York, USA Abstract PRINCIPLES OF VALIDATION OF DIAGNOSTIC ASSAYS FOR INFECTIOUS DISEASES. Assay validation requires a series of inter-related processes. Assay validation is an experimental process: reagents and protocols are optimized by experimentation to detect the analyte with accuracy and precision. Assay validation is a relative process: its diagnostic sensitivity and diagnostic specificity are calculated relative to test results obtained from reference animal populations of known infection/exposure status. Assay validation is a conditional process: classification of animals in the target population as infected or uninfected is conditional upon how well the reference animal population used to validate the assay represents the target population; accurate predictions of the infection status of animals from test results (PV+ and PV−) are conditional upon the estimated prevalence of disease/infection in the target population. Assay validation is an incremental process: confidence in the validity of an assay increases over time when use confirms that it is robust as demonstrated by accurate and precise results; the assay may also achieve increasing levels of validity as it is upgraded and extended by adding reference populations of known infection status. Assay validation is a continuous process: the assay remains valid only insofar as it continues to provide accurate and precise results as proven through statistical verification. Therefore, the work required for validation of diagnostic assays for infectious diseases does not end with a time-limited series of experiments based on a few reference samples rather, to assure valid test results from an assay requires constant vigilance and maintenance of the assay, along with reassessment of its performance characteristics for each unique population of animals to which it is applied. -
New NIH Guidelines to Improve Experimental Rigor and Reproducibility
New NIH guidelines to improve Experimental Rigor and Reproducibility Oswald Steward Professor, Department of Anatomy & Neurobiology Senior Associate Dean for Research University of California School of Medicine What I’ll tell you 1) Background: Increasing reports of failures to replicate 2) Previous actions by NIH to enhance rigor 3) New requirements for grants submitted after January 2016 4) What NIH will be looking for in new required sections 5) Some suggested best practices to meet new standards for scientific rigor • The Problem: Numerous recent reports of findings that can’t be replicated. Failure to replicate key results from preclinical cancer studies: 1) Prinz et al. (2011) Believe it or not: How much can we rely on published data on potential drug targets? Nature Reviews Drug Discovery. Inconsistencies were found in 2/3 studies 2) Begley and Ellis (2012) Raise standards for preclinical cancer research. Nature. Only 6/53 “landmark” papers replicated 3) Begley (2013) Six red flags for suspect work. Nature. -Were experiments performed blinded? -Were basic experiments repeated? -Were all the results presented? -Were there positive and negative controls? -Were reagents validated? -Were statistical tests appropriate? • In ALS field, Scott et al., (2008) re-assessed 70 drugs that had been reported to increase lifespan in an animal model of ALS (SOD1-G93A knockout mice). • 221 separate studies were carried out over a five year period that involved over 18,000 mice. • Some drugs were already in clinical trials. • Outcome: There was no statistically significant positive effect for any of the 70 compounds tested. • Conclusion: Previously published effects were measurements of noise in the distribution of survival means as opposed to an actual drug effect. -
Studies of Staphylococcal Infections. I. Virulence of Staphy- Lococci and Characteristics of Infections in Embryonated Eggs * WILLIAM R
Journal of Clinical Investigation Vol. 43, No. 11, 1964 Studies of Staphylococcal Infections. I. Virulence of Staphy- lococci and Characteristics of Infections in Embryonated Eggs * WILLIAM R. MCCABE t (From the Research Laboratory, West Side Veterans Administration Hospital, and the Department of Medicine, Research and Educational Hospitals, University of Illinois College of Medicine, Chicago, Ill.) Many of the determinants of the pathogenesis niques still require relatively large numbers of and course of staphylococcal infections remain staphylococci to produce infection (19). Fatal imprecisely defined (1, 2) despite their increas- systemic infections have been equally difficult to ing importance (3-10). Experimental infections produce in animals and have necessitated the in- in suitable laboratory animals have been of con- jection of 107 to 109 bacteria (20-23). A few siderable assistance in clarifying the role of host strains of staphylococci have been found that are defense mechanisms and specific bacterial virulence capable of producing lethal systemic infections factors with a variety of other infectious agents. with inocula of from 102 to 103 bacteria (24) and A sensitive experimental model would be of value have excited considerable interest (25-27). The in defining the importance of these factors in virulence of these strains apparently results from staphylococcal infections, but both humans and an unusual antigenic variation (27, 28) which, the usual laboratory animals are relatively re- despite its interest, is of doubtful significance in sistant. Extremely large numbers of staphylo- human staphylococcal infection, since such strains cocci are required to produce either local or sys- have been isolated only rarely from clinical in- temic infections experimentally. -
On the Reproducibility of Meta-Analyses.Docx
On the Reproducibility of Meta-Analyses 1 1 RUNNING HEAD: ON THE REPRODUCIBILITY OF META-ANALYSES 2 3 4 On the Reproducibility of Meta-Analyses: Six Practical Recommendations 5 6 Daniël Lakens 7 Eindhoven University of Technology 8 Joe Hilgard 9 University of Missouri - Columbia 10 Janneke Staaks 11 University of Amsterdam 12 13 In Press, BMC Psychology 14 15 Word Count: 6371 16 17 Keywords: Meta-Analysis; Reproducibility; Open Science; Reporting Guidelines 18 19 Author Note: Correspondence can be addressed to Daniël Lakens, Human Technology 20 Interaction Group, IPO 1.33, PO Box 513, 5600MB Eindhoven, The Netherlands. E-mail: 21 [email protected]. We would like to thank Bianca Kramer for feedback on a previous draft 22 of this manuscript. 23 24 Competing Interests: The authors declared that they had no competing interest with respect 25 to their authorship or the publication of this article. 26 27 Author Contributions: All authors contributed writing this manuscript. DL drafted the 28 manuscript, DL, JH, and JS revised the manuscript. All authors read and approved the final 29 manuscript. 30 31 Email Addresses: D. Lakens: [email protected] 32 Joe Hilgard: [email protected] 33 Janneke Staaks: [email protected] On the Reproducibility of Meta-Analyses 2 34 Abstract 35 Background 36 Meta-analyses play an important role in cumulative science by combining information 37 across multiple studies and attempting to provide effect size estimates corrected for 38 publication bias. Research on the reproducibility of meta-analyses reveals that errors are 39 common, and the percentage of effect size calculations that cannot be reproduced is much 40 higher than is desirable. -
A Randomized Control Trial Evaluating the Effects of Police Body-Worn
A randomized control trial evaluating the effects of police body-worn cameras David Yokuma,b,1,2, Anita Ravishankara,c,d,1, and Alexander Coppocke,1 aThe Lab @ DC, Office of the City Administrator, Executive Office of the Mayor, Washington, DC 20004; bThe Policy Lab, Brown University, Providence, RI 02912; cExecutive Office of the Chief of Police, Metropolitan Police Department, Washington, DC 20024; dPublic Policy and Political Science Joint PhD Program, University of Michigan, Ann Arbor, MI 48109; and eDepartment of Political Science, Yale University, New Haven, CT 06511 Edited by Susan A. Murphy, Harvard University, Cambridge, MA, and approved March 21, 2019 (received for review August 28, 2018) Police body-worn cameras (BWCs) have been widely promoted as The existing evidence on whether BWCs have the anticipated a technological mechanism to improve policing and the perceived effects on policing outcomes remains relatively limited (17–19). legitimacy of police and legal institutions, yet evidence of their Several observational studies have evaluated BWCs by compar- effectiveness is limited. To estimate the effects of BWCs, we con- ing the behavior of officers before and after the introduction of ducted a randomized controlled trial involving 2,224 Metropolitan BWCs into the police department (20, 21). Other studies com- Police Department officers in Washington, DC. Here we show pared officers who happened to wear BWCs to those without (15, that BWCs have very small and statistically insignificant effects 22, 23). The causal inferences drawn in those studies depend on on police use of force and civilian complaints, as well as other strong assumptions about whether, after statistical adjustments policing activities and judicial outcomes. -
The Reproducibility Crisis in Research and Open Science Solutions Andrée Rathemacher University of Rhode Island, [email protected] Creative Commons License
University of Rhode Island DigitalCommons@URI Technical Services Faculty Presentations Technical Services 2017 "Fake Results": The Reproducibility Crisis in Research and Open Science Solutions Andrée Rathemacher University of Rhode Island, [email protected] Creative Commons License This work is licensed under a Creative Commons Attribution 4.0 License. Follow this and additional works at: http://digitalcommons.uri.edu/lib_ts_presentations Part of the Scholarly Communication Commons, and the Scholarly Publishing Commons Recommended Citation Rathemacher, Andrée, ""Fake Results": The Reproducibility Crisis in Research and Open Science Solutions" (2017). Technical Services Faculty Presentations. Paper 48. http://digitalcommons.uri.edu/lib_ts_presentations/48http://digitalcommons.uri.edu/lib_ts_presentations/48 This Speech is brought to you for free and open access by the Technical Services at DigitalCommons@URI. It has been accepted for inclusion in Technical Services Faculty Presentations by an authorized administrator of DigitalCommons@URI. For more information, please contact [email protected]. “Fake Results” The Reproducibility Crisis in Research and Open Science Solutions “It can be proven that most claimed research findings are false.” — John P. A. Ioannidis, 2005 Those are the words of John Ioannidis (yo-NEE-dees) in a highly-cited article from 2005. Now based at Stanford University, Ioannidis is a meta-scientist who conducts “research on research” with the goal of making improvements. Sources: Ionnidis, John P. A. “Why Most -
Why Replications Do Not Fix the Reproducibility Crisis: a Model And
1 63 2 Why Replications Do Not Fix the Reproducibility 64 3 65 4 Crisis: A Model and Evidence from a Large-Scale 66 5 67 6 Vignette Experiment 68 7 69 8 Adam J. Berinskya,1, James N. Druckmanb,1, and Teppei Yamamotoa,1,2 70 9 71 a b 10 Department of Political Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139; Department of Political Science, Northwestern 72 University, 601 University Place, Evanston, IL 60208 11 73 12 This manuscript was compiled on January 9, 2018 74 13 75 14 There has recently been a dramatic increase in concern about collective “file drawer” (4). When publication decisions depend 76 15 whether “most published research findings are false” (Ioannidis on factors beyond research quality, the emergent scientific 77 16 2005). While the extent to which this is true in different disciplines re- consensus may be skewed. Encouraging replication seems to 78 17 mains debated, less contested is the presence of “publication bias,” be one way to correct a biased record of published research 79 18 which occurs when publication decisions depend on factors beyond resulting from this file drawer problem (5–7). Yet, in the 80 19 research quality, most notably the statistical significance of an ef- current landscape, one must also consider potential publication 81 20 fect. Evidence of this “file drawer problem” and related phenom- biases at the replication stage. While this was not an issue 82 21 ena across fields abounds, suggesting that an emergent scientific for OSC since they relied on over 250 scholars to replicate the 83 22 consensus may represent false positives.