We are pleased to share data with you! The purpose of this document is to provide information about how to work with data from our research studies and about how to prepare a concept paper. This document is intended to help standardize the conduct of research among trainees and collaborators. We ask that everyone follows all policies and procedures listed below. And, of course, we are here to help answer any questions along the way. Thank you!
Temi Moffitt Avshalom Caspi
Professor/PI Professor/PI
tem11@duke.edu ac115@duke.edu
GETTING STARTED…
Discuss your idea with Temi or Avshalom to ascertain its general feasibility.
Familiarize yourself with the Dunedin and E-Risk studies’ “Policy & Procedures Handbook”
Links: Dunedin policy statement & code of practice for investigators
Erisk Data Access protocol
Familiarize yourself data use guidelines of other included Studies.
STEP 1: CONCEPT PAPER
Prepare a brief concept paper for your study. The CP template can be found at: https://sites.duke.edu/moffittcaspiprojects/concept-paper-template/
Name the concept paper file with your surname, the data set, a short handle for the project, and the date, spelling out the month (because the middle number can be day in the USA and month everywhere else). This allows others to keep and retrieve your CP in their filing systems.
For example: Beckley_E-Risk_Victimoffender_4Sept2017_CP.doc.
Temi will distribute your concept paper to all stakeholders and invited co-authors.
When all response-form approvals have been returned to you, you have a project, and the research may proceed.
Concept papers are posted on our public projects site and this constitutes pre-registration.
First authors are responsible for keeping all the signed copies of the concept paper. You will need the responses to your CP months later, to know who should do a mock review when the manuscript is completed (see Step 9).
Neither the Dunedin nor E-risk Studies are public-domain data sets. You may not share your data file with others, and by signing the concept paper you agree to this restriction.
STEP 2: PROJECT SPONSOR
Researchers who are not co-investigators of the Studies can propose data-analysis projects, with a sponsor who is a co-investigator. The nominating PI sponsor takes responsibility for all activities of the project with respect to the Study, and this is a serious responsibility. Thus, one consideration in approving a concept paper is the capacity of Study co-investigators to sponsor a number of projects.
In the Dunedin Study, researchers not employed by the University of Otago who access Dunedin data must be appointed as Associated Investigators (AI) of the Dunedin Unit, as required for ethical reasons explained in the Unit Handbook. Temi and Avshalom must nominate you for this formal appointment, and submit an application to the Director and Scientific Advisory Group of the Unit for review. It is not automatically granted to everyone. Discuss with Temi and Avshalom whether they can nominate you for AI status. If not, then your collaboration must include a Study co-investigator who agrees to physically analyze the dataset for your paper. If you are not an AI, you must follow the steps in the rest of this document with the help of a person who holds an appointment at the Dunedin Unit.
STEP 3: ETHICAL PREPARATION
For research funded by the US NIH it is a requirement that all investigators have completed a research ethics training course in human subjects protection, responsible conduct of research, or equivalent. By accepting data from us to analyze, the researcher should understand they are attesting to us that they have completed research ethics training. If you have not yet taken a course, it is easy to do so by going to: http://www.citiprogram.org/default.asp?language=english
STEP 4: LEARN ABOUT THE DATA
Consult the electronic data dictionary and read previously published papers from the Studies to get information about the data you plan to use. The Study websites have searchable lists of publications.
Think carefully about statistical analyses you will perform. Suggested reading: Thomas & Peterson (2012). The Value of Statistical Analysis Plans in Observational Research: Defining High-Quality Research From the Start. JAMA 308, 773-774.
When you place your request for data, take the time to carefully consider which variables you will need and discuss this with Temi and Avshalom. The best proposals are those that carefully outline a set of well-justified research questions and request the appropriate number and types of variables required to test the research questions. Consult with the data manager for help in selecting the right variables.
STEP 5: ANALYSES
Upon receiving a data file, immediately run descriptives. Check frequency distributions (and missing values) before using.
Report any bug in a file in writing to the data manager.
Please annotate your code-scripts and command files, so that others can retrace your steps later.
Save all code and output.
Consult with us about ways to handle missing data.
If you create a new variable from the raw data, please give it the following features:
– variable name ending with a number indicating the assessment age wave
– variable label with data source for the original constituent data
e.g. Mother or teacher report, DSM4 based diagnosis, Average of …, Sum of…
– value labels for the coded numeric values (e.g. 0 = no, 1 = yes).
Examples: dxmde38 Major depressive episode, dsm4, age 38
STEP 6: WRITING IT UP
Don’t re-create the wheel; use our existing boilerplates for the “methods” section for consistency across publications.
STROBE checklist for best practice in reporting observational studies. On the checklist, please report the page number where each item has been fulfilled. The checklist can be found at:
https://sites.duke.edu/moffittcaspiprojects/strobe-checklist/.
Name the manuscript file with your surname, a short handle for the project, and the date, spelling out the month (because the middle number can be day in the USA and month everywhere else). For example: Beckley_Victimoffender_4Sept2017.doc. When published add the journal name. For example: Beckley_Victimoffender_JDLCC_10April2018.doc.
Include page numbers on every version of your manuscript.
STEP 7: ACKNOWLEDGEMENTS
Acknowledge all appropriate individuals, agencies and grants on your manuscript. This is not an option; it is required by our funding agencies. Acknowledgement for Dunedin projects can be found on the project site at; https://sites.duke.edu/moffittcaspiprojects/acknowledgements/
Be sure to obtain funding information (e.g., fellowships, training grants) from all co-authors.
STEP 8: REPRODUCIBILITY CHECK
All manuscripts undergo a reproducibility check. Checking will be carried out by an independent checker, using a fresh copy of the original data set, separate from the data set with which you have been working. The checker will attempt to create your code from scratch, by reading a copy of your manuscript. The goal is to re-produce all the numbers in the paper, without looking at your code. Please review the document, “Reproducibility Stat Check for Dunedin and E-Risk Papers,” which can be found at: https://sites.duke.edu/moffittcaspiprojects/reproducibility-check/.
STEP 9: MOCK REVIEW
Temi or Avshalom must approve the draft before Temi circulates it for mock review.
Don’t put all author names on the title page yet, because a co-author who does not review the draft before submission will need to withdraw from the paper.
Temi sends a copy to all co-authors for review and approval, these are the researchers who returned a signed, approved CP to you in step 1. We allow co-authors 3 weeks to review the paper.
All Dunedin and E-Risk papers must be additionally approved by the Study Director.
Requests for revisions and suggestions for improvement may come from co-authors, so be prepared to revise.
STEP 10: SUBMITTING FOR PUBLICATION REVIEW
Notify all co-authors that the paper is ready to submit, tell them which journal you will try first, and give them the citation with title and author list for their CV in the e-mail.
Consider running your abstract through AI software such as Elsevier journalfinder, Springer journalsuggester, or Wiley find-a-journal. Editors have dashboards that use AI to check fit of a submitted manuscript to the journal (and that also check for grammar and spelling mistakes), and poor fit results in desk rejection.
Lodge dated copies of the submitted paper, supplement, figures, tables, and letter to the editor in a folder under your name on the Z drive publications folder at Duke. If you don’t have access, give these docs to Temi, who will file them.
Lodge a copy of the STROBE checklist along with the manuscript.
Lodge a copy of your annotated code with the data manager, or put it in the folder on the Z drive.
Before uploading your manuscript to a preprint server, please discuss with Temi and Avshalom.
STEP 11: DOING REVISIONS
Send the editor’s letter and reviews to all co-authors and invite co-authors to comment or contribute to the revision process.
Temi or Avshalom must approve the revised draft before it is sent back to the editor. We do not ordinarily distribute revisions to all co-authors, unless co-authors request to see these, or if the revisions are extensive and contain new or different information.
Repeat Step 10.
STEP 12: WHEN THE PAPER IS ACCEPTED FOR PUBLICATION
Celebrate!
Send a copy of the paper to all collaborators, give them the citation for their CV in the e-mail.
Deposit your analysis file, code and new variable descriptions with the data manager.
Delete the data file. Collaborators may not retain data files. The data remain the property of the Study and cannot be used for further analyses without express, written permission. The data manager will archive your file for you, should you need it again in future.
PMCID application for open access in USA: You must apply for PMCID. NIH requires that all published papers that are (a) peer-reviewed, and (b) credited to the support of a NIH grant, must be lodged in PubMed Central for public access. As soon as your paper is in press, go to the website and upload an Author’s Accepted Manuscript (AAM) which is a WORD preprint copy of the accepted manuscript, along with the grant number(s). This will get you the PMCID. You do not wait for the publication or page proofs to come out. Learn more here: http://publicaccess.nih.gov/index.htm
Open access in the UK/EU: Because we have grants from the UK, we also must do two additional things. First, we post a WORD AAM preprint on the KCL-Pure site. Second, we apply to KCL to pay the costs of open-access, which range from $2k to $12k. Speak with Temi about how to meet these requirements. NOTE that KCL requires the corresponding author to be a KCL employee before they will pay for open access fees, so at this stage, we may need to make Temi or Avshalom the corresponding author.
STEP 13: DURING THE PROCESS TOWARD PUBLICATION
When you receive a copy-edited version of the manuscript, review this with Temi or Avshalom.
When you receive page-proofs, get someone to help you check it. This is the last chance you will have to catch mistakes. Don’t check it alone! Don’t have to retract your paper because of a copy-editor’s mistake.
Once published, please send a PDF of the published paper to all co-authors.
If media coverage is expected, consult with Temi about drafting a fact sheet for journalists.
Deliver copies of all media articles, or websites, to Temi. We need to report these to funding agencies.
If you give a lecture or poster presentation about your work, please notify Temi of the title, date, and context of the presentation. We need to report these to funding agencies.
Thank you for reading this document. We recommend re-reading this document at the different stages of your project, because it is easy to forget these standard operating procedures. (Download a copy)
We share data with a large number of collaborators, who live in many countries, and who work at many different levels of training and expertise. The purpose of this memo is to instruct students who are embarking on their first research project, and to remind senior professors who are embarking on their nth research project. We have listed here the standard operating procedures that help to keep our working relationships comfortable and productive. We hope they work for you too.
Temi and Avshalom
