@[toc](Resources for Implementing TOP) ## TOP Checklists ## - Checklists for an editor verifying an author submission ([level 1]; [mixed levels]) - Checklist for an author submitting to a TOP signatory journal ([level 1]) - [Suggested tools and checklists] in ecology and evolution. ## Data Reproducibility Policies ## Dozens of journals implement computational reproducibility checks prior to publication. See "Level 3" policies for [data] or [code] on TOP Factor for an up-to-date listing. ## Data Sharing: Practices and Repositories ## - [Data Authorship as an Incentive to Data Sharing] - De-Identification - [De-identification Guidelines for Structured Data] - [Anonymisation Decision-making Framework] - Data Repositories - [COPDESS] Directory of Data Repositories - [Re3Data] Registry of Research Data Repositories - [Data-PASS] - [Dryad] - [Figshare] - [OAD] (Open Access Data Repositories) - [OSF] - Nature Scientific Data, recommended [repositories] ## Reporting Guidelines ## - See the [Open Science Literature] for research on the effectiveness of reporting guidelines. Our recommended best practice is to include items deemed essential into the article submission process. - See the [Equator Network] for a large, searchable collection of reporting guidelines. ### Community Created Guidelines ### - [CONSORT] (Consolidated Standards of Reporting Trials) - For meta-analysis: [PRISMA] or [AMSTAR] - [NIH Reporting Guidelines By Organization] - Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups [COREQ] - STrengthening the Reporting of OBservational studies in Epidemiology ([STROBE]) - An Updated List of Essential Items for Reporting Diagnostic Accuracy Studies ([STARD]) - [Experimental design and analysis and their reporting: new guidance for publication in BJP] - [ARRIVE] (Animal Research: Reporting of In Vivo Experiments) - [TIDieR-PHP: a reporting guideline for population health and policy interventions] - [Standardization in Metabolomics Experiments] - Minimum Information for reporting: - Proteomics Experiments ([MIAPE]) - Genotyping Experiments ([MIGen]) - Flow Cytometry Experiments ([MIFlowCyt]) - Minimal Information About T cell Assays ([MIATA] project) - Quantitative Real-Time PCR Experiments ([MIQE]) - RNAi Experiment ([MIARE]) - [BRISQ] (Biospecimen reporting for improved study quality) - [Citation of Bioresources in Journal Articles (CoBRA)] ### Journal and Society Created Guidelines ### - From Cell Press: Structured, Transparent, Accessible Reporting (STAR) guidelines from Cell Press: [Website], [Methods Guide], and the [Key Resources Table] - American Psychological Association: Journal Article Reporting Standards ([JARS] 2018 Update; [JARS] 2008) - BioMedCentral's [Minimum Standards of Reporting Checklist] - [Guidelines for Reporting Quantitative Methods and Results in Primary Research] at Language Learning - [Reporting Guidelines for Experimental Research: A Report from the Experimental Research Section Standards Committee] of the American Political Science Association - Association for Psycholgical Science's [reporting guidelines] - Journal of Experimental Social Psychology [reporting guidelines] - Journal of Neuroscience [Policy on Reporting Experimental Design and Statistical Analysis] - [Reporting Checklist for Life Sciences Articles] at Nature Publishing Group - [eLife's Transparent Reporting form] - Biophysical Journal's [Guidelines for the Reproducibility of Biophysics Research] - [A checklist for writing up research reports] in the journal Addiction - PLOS One's [Reporting Guidelines for Specific Study Types] ## Registries ## - [American Economics Association RCT Registry] - [ClinicalTrials.gov] - [EGAP] (Evidence in Governance and Politics) - [OSF] - [PROSPERO] International prospective register of systematic reviews - [Research Registry] - [RIDIE] (Registry for International Development Impact Evaluations) - [Registry of Efficacy and Effectiveness Studies] in education ## Editorials announcing TOP ## - [Association for Psychological Society] - [Ecology Letters] - [Experimental Psychology] - [International Journal of Primatology] - Journal of Research in Personality ([preprint]) - [Nature] - [Royal Society Open Science] - [Science] - [Survey Research Methods] ## Examples of author guidelines using TOP ## - [Science] | AAAS - [Brain and Behavior] | Wiley - [Collabra] | UC Press - [Cultural Diversity & Ethnic Minority Psychology] | APA - [Journal of Cognition] | Ubiquity Press - [Nicotine & Tobacco Research] | Oxford University Press - [Evolution and Human Behavior] | Elsevier ---------- ## Disclosure Statements ## ### Data, Materials, and Code Disclosures ### | Type of Disclosure | Example Language | | ------ | ---------- | | Data created for the study are available in a persistent repository. | All data and materials have been made publicly available at the [repository name] and can be accessed at [persistent URL or DOI] | | Anonymized data created for the study are available in a persistent repository. | Anonymized data and materials have been made publicly available at the [repository name] and can be accessed at [persistent URL or DOI] | | Some data available | In order to minimize the possibility of unintentionally sharing information that can be used to re-identify private information, a subset of the data generated for this study are available at [repository name] and can be accessed at [persistent URL or DOI] | | Data available upon request from a third party | Because of the sensitive nature of the data collected for this study, requests to access the dataset from qualified researchers trained in human subject confidentiality protocols may be sent to [name of organization] at [contact information]. | ---------- Other examples of data disclosure statements - [The Impact on Authors and Editors of Introducing Data Availability Statements at Nature Journals] - [Nature Research] - [American Geophysical Union] ---------- ### Preregistration of Study or Analysis Plan Disclosure ### | Type of Disclosure | Example Language | | ------ | ---------- | | Both the study and analysis plan were preregistered | This paper reports the results of [N] preregistered studies with complete analysis plans. The preregistration(s) can be accessed at [persistent URL]. We certify that the results of all preregistered analyses are reported, and that any unregistered analyses are clearly indicated as being [unregistered, exploratory, hypothesis-generating]. | | The study was preregistered without an analysis plan | This paper reports the results of [N] preregistered studies, which can be accessed at [name of repository] here [persistent URL or DOI]. | | No preregistration | No preregistration exists for the reported studies reported in this article. | ---------- ## Persistent Identifiers ## - [ARK] (Archival Resource Key) - [DOI] (Digitial Object Identifier) - [IGSN] (International Geo Sample Number) - [RRIDs] (Research Resource Identifiers) - [PURL] (Persistent Uniform Resource Locators) Please contact us if you would like to add to this list: email@example.com : https://osf.io/hcnme/ : https://osf.io/87v93/ : https://osf.io/55eu7/ : https://osf.io/y8aqx/ : https://topfactor.org/journals?factor=Data%20Transparency&perPage=50 : https://topfactor.org/journals?factor=Analysis%20Code%20Transparency&perPage=50 : http://www.nejm.org/doi/full/10.1056/NEJMsb1616595 : https://www.ipc.on.ca/resource/de-identification-guidelines-for-structured-data/ : http://ukanon.net/ukan-resources/ukan-decision-making-framework/ : https://copdessdirectory.osf.io/ : http://www.re3data.org/ : http://www.data-pass.org/ : http://datadryad.org/ : https://figshare.com/ : http://oad.simmons.edu/oadwiki/Data_repositories : https://osf.io : http://www.nature.com/sdata/policies/repositories : https://osf.io/kgnva/wiki/Open%20Science%20Literature/ : http://www.equator-network.org/ : http://www.consort-statement.org/ : http://prisma-statement.org/PRISMAStatement/Checklist.aspx : https://amstar.ca/Amstar_Checklist.php : https://www.nlm.nih.gov/services/research_report_guide.html : https://academic.oup.com/intqhc/article/19/6/349/1791966/Consolidated-criteria-for-reporting-qualitative : https://www.strobe-statement.org/index.php?id=strobe-home : http://www.stard-statement.org/ : http://onlinelibrary.wiley.com/doi/10.1111/bph.12856/full : https://www.nc3rs.org.uk/arrive-guidelines : https://www.bmj.com/content/361/bmj.k1079 : http://metabolomicssociety.org/index.php/resources/metabolomics-standards : http://www.psidev.info/index.php?q=node/91 : https://osf.io/4nryf/ : https://osf.io/edwhp/ : http://miataproject.org/ : https://osf.io/kjqtf/ : http://miare.sourceforge.net/HomePage : http://onlinelibrary.wiley.com/doi/10.1002/cncy.20147/abstract : http://www.equator-network.org/reporting-guidelines/cobra/ : http://www.cell.com/star-methods : http://www.cell.com/pb-assets/journals/research/cell/methods/Methods%20Guide_general.pdf : https://www.star-methods.com/key-resources/webform/els_key_resources_table : http://www.apa.org/pubs/journals/releases/amp-amp0000191.pdf : http://www.apastyle.org/manual/related/apa-jars-2008.pdf : http://resource-cms.springer.com/springer-cms/rest/v1/content/7117202/data/v2/Minimum+standards+of+reporting+checklist : http://onlinelibrary.wiley.com/doi/10.1111/lang.12104/full : https://www.cambridge.org/core/journals/journal-of-experimental-political-science/article/reporting-guidelines-for-experimental-research-a-report-from-the-experimental-research-section-standards-committee/F09D4BEC6E9F493DC7E048BB252366F2 : http://www.psychologicalscience.org/publications/psychological_science/ps-submissions#DISC : https://www.journals.elsevier.com/journal-of-experimental-social-psychology/news/jesp-editorial-guidelines/ : http://www.jneurosci.org/content/general-information#policies : https://www.nature.com/authors/policies/ReportingSummary-flat.pdf : https://submit.elifesciences.org/html/transparent_reporting.pdf : http://www.cell.com/pb/assets/raw/journals/society/biophysj/PDFs/reproducibility-guidelines.pdf : http://onlinelibrary.wiley.com/doi/10.1046/j.1360-0443.2000.951217594.x/epdf : http://journals.plos.org/plosone/s/submission-guidelines#loc-guidelines-for-specific-study-types : https://www.socialscienceregistry.org/ : https://clinicaltrials.gov/ : http://egap.org/ : https://osf.io : https://www.crd.york.ac.uk/prospero/ : http://www.researchregistry.com/ : http://ridie.3ieimpact.org/ : https://sreereg.icpsr.umich.edu/ : http://www.psychologicalscience.org/publications/observer/obsonline/aps-commits-to-promoting-transparent-science.html#.WG-9ObYrJBw : http://onlinelibrary.wiley.com/doi/10.1111/ele.12611/full : http://econtent.hogrefe.com/doi/10.1027/1618-3169/a000317 : http://link.springer.com/article/10.1007/s10764-016-9925-x : https://osf.io/preprints/psyarxiv/ay59f : http://www.nature.com/news/announcement-transparency-upgrade-for-nature-journals-1.21627 : http://rsos.royalsocietypublishing.org/content/royopensci/4/1/160979.full.pdf : http://science.sciencemag.org/content/352/6290/1147 : https://ojs.ub.uni-konstanz.de/srm/article/view/6256/5679 : http://science.sciencemag.org/content/sci/suppl/2016/06/01/352.6290.1147.DC1/aag2359-editorial.McNutt.SM.pdf : http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292157-9032/homepage/ForAuthors.html : http://www.collabra.org/about/editorialpolicies/ : http://www.apa.org/pubs/journals/cdp/?tab=4 : https://www.journalofcognition.org/about/editorialpolicies/ : https://www.oxfordjournals.org/our_journals/nictob/for_authors/ntr%20top%20guidelines.pdf : https://www.elsevier.com/journals/evolution-and-human-behavior/1090-5138/transparency-and-openness : http://www.ijdc.net/article/view/614 : http://www.nature.com/authors/policies/data/data-availability-statements-data-citations.pdf : http://publications.agu.org/author-resource-center/publication-policies/data-policy/data-policy-faq/ : https://confluence.ucop.edu/display/Curation/ARK : https://www.doi.org/ : http://www.geosamples.org/ : https://scicrunch.org/resources : https://www.isoc.org/inet96/proceedings/a4/a4_1.htm
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