open access: a researcher's perspective

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Open access: a researcher’s perspective Antonio Gasparrini London School of Hygiene and Tropical Medicine, London, UK Open Research and Data Open Access Week 22 October 2012 - Birbeck College, London

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Page 1: Open access: a researcher's perspective

Open access: a researcher’s perspective

Antonio GasparriniLondon School of Hygiene and Tropical Medicine, London, UK

Open Research and DataOpen Access Week

22 October 2012 - Birbeck College, London

Page 2: Open access: a researcher's perspective

My background

Graduated in biology in Italy, then 4 years working asepidemiologist in a cancer research center in Florence

MSc + postgraduate school (still in Italy) + PhD (in UK) inmedical statistics,

Worked at LSHTM in the last 5 years, mainly in statisticalmethodology and software development

Page 3: Open access: a researcher's perspective

My MRC fellowship

Awarded a Research Methodology fellowship from MRC (Dec2011 – Nov 2014)

Project developed on my previous research

Success of this project critical for next funding application

Need to comply with the MRC regulations on open access

My budget for open access costs: 6000£ in total

Page 4: Open access: a researcher's perspective

Outline

Some points:

My perspective: as scientist and junior academic

Publishing: steps and costs

My publications as a case study

Open research: beyond publications

Page 5: Open access: a researcher's perspective

The scientist’s perspective

I favour a system which:

guarantees high-quality research

allows the independent assessment of research findings

ensures the dissemination of the such findings

Page 6: Open access: a researcher's perspective

The academic’s perspective

I favour a system which:

covers the costs of my research

delivers a fast and effective peer-review process

provides tools for disseminating my work

Page 7: Open access: a researcher's perspective

Publishing a research paper: steps

Literature review

Drafting the manuscript

Choice of the journal and submission

Review and acceptance

Copyright agreement

Open access fee

Publication

Actors: the researcher, the institution, the research community,the funder, the journals/publishers

An efficient and fair system?

Page 8: Open access: a researcher's perspective

A first article

Published online in Statistics in Medicine (2012):

The choice of the journal

Copyright transferred

Open access fee ∼2250£

Impact factor 1.99

Page 9: Open access: a researcher's perspective

Submitted and published versions

Research ArticleStatisticsin Medicine

Received XXXX

(www.interscience.wiley.com) DOI: 10.1002/sim.0000

Multivariate meta-analysis for non-linear andother multi-parameter associations

A. Gasparrinia∗†, B. Armstrongb, M. G. Kenwarda

In this paper we formalize the application of multivariate meta-analysis and meta-regression to synthesize estimatesof multi-parameter associations obtained from different studies. This modelling approach extends the standardtwo-stage analysis used to combine results across different sub-groups or populations. The most straightforwardapplication is for the meta-analysis of non-linear relationships, described for example by regression coefficientsof splines or other functions, but the methodology easily generalizes to any setting where complex associationsare described by multiple correlated parameters. The modelling framework of multivariate meta-analysis isimplemented in the package mvmeta within the statistical environment R. As an illustrative example, we proposea two-stage analysis for investigating the non-linear exposure-response relationship between temperature and non-accidental mortality using time series data from multiple cities. Multivariate meta-analysis represents a usefulanalytical tool for studying complex associations through a two-stage procedure. Copyright c© 2011 John Wiley &Sons, Ltd.

Keywords: meta-analysis; multivariate analysis; multivariate meta-analysis; non-linear; splines

1. Introduction

Meta-analysis is a standard, well-grounded statistical procedure for combining the evidence from independent studiesthat address the same research hypothesis [1]. This methodology was developed originally for pooling the results frompublished observational or experimental studies, for which individual data were not available. Recently, meta-analysis hasbeen described more broadly as a research synthesis method, with the aim of estimating an average association acrossstudies and to explore the degree and sources of heterogeneity [2]. The analytical approach adopted in this context may bedescribed as a two-stage hierarchical procedure: in the first stage, study-specific estimates of the association of interest arederived from individual data, controlling for individual-level covariates; in the second stage, these estimates are combinedacross studies, optionally exploring the association with study-level predictors. The two-stage approach, a specific formof individual patient data (IPD) meta-analysis, has been shown to be a flexible and computationally efficient method [3],and has been adopted in different contexts: to pool estimates from multiple randomized controlled trials [4]; to combineresults from survival models on time-to-event data in multi-centre cohorts [5]; and to synthesize associations from Poissontime series models in multi-city analyses [6].

The common approach to two-stage meta-analysis consists of summarizing the association in a single parameterestimate from the first stage, optionally controlling for individual-level confounders. This procedure allows standard meta-analytic techniques to be applied. However, complex associations, such as non-linear exposure-responses, are usuallydescribed with functions defined by multiple parameters, and require more sophisticated meta-analytical approaches,capable of handling the multivariate nature of the summary estimates. Multivariate meta-analysis, a method originally

a Department of Medical Statistics, London School of Hygiene and Tropical Medicineb Department of Social and Environmental Health Research, London School of Hygiene and Tropical Medicine∗Correspondence to: Antonio Gasparrini, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.† E-mail: [email protected]

Contract/grant sponsor: Medical Research Council (UK), grants G0701030 and G1002296

Statist. Med. 2011, 00 1–18 Copyright c© 2011 John Wiley & Sons, Ltd.Prepared using simauth.cls [Version: 2010/03/10 v3.00]

Research Article

Received 9 August 2011, Accepted 11 May 2012 Published online in Wiley Online Library

(wileyonlinelibrary.com) DOI: 10.1002/sim.5471

Multivariate meta-analysis fornon-linear and other multi-parameterassociationsA. Gasparrini,a*† B. Armstrongb and M. G. Kenwarda

In this paper, we formalize the application of multivariate meta-analysis and meta-regression to synthesizeestimates of multi-parameter associations obtained from different studies. This modelling approach extendsthe standard two-stage analysis used to combine results across different sub-groups or populations. The moststraightforward application is for the meta-analysis of non-linear relationships, described for example byregression coefficients of splines or other functions, but the methodology easily generalizes to any settingwhere complex associations are described by multiple correlated parameters. The modelling framework ofmultivariate meta-analysis is implemented in the package mvmeta within the statistical environment R. Asan illustrative example, we propose a two-stage analysis for investigating the non-linear exposure–responserelationship between temperature and non-accidental mortality using time-series data from multiple cities.Multivariate meta-analysis represents a useful analytical tool for studying complex associations through atwo-stage procedure. Copyright © 2012 John Wiley & Sons, Ltd.

Keywords: meta-analysis; multivariate analysis; multivariate meta-analysis; non-linear; splines

1. Introduction

Meta-analysis is a standard, well-grounded statistical procedure for combining the evidence from inde-pendent studies that address the same research hypothesis [1]. This methodology was developed origi-nally for pooling the results from published observational or experimental studies, for which individualdata were not available. Recently, meta-analysis has been described more broadly as a research synthesismethod, with the aim of estimating an average association across studies and to explore the degree andsources of heterogeneity [2]. The analytical approach adopted in this context may be described as atwo-stage hierarchical procedure: in the first stage, study-specific estimates of the association of interestare derived from individual data, controlling for individual-level covariates; in the second stage, theseestimates are combined across studies, optionally exploring the association with study-level predictors.The two-stage approach, a specific form of individual patient data (IPD) meta-analysis, has been shownto be a flexible and computationally efficient method [3] and has been adopted in different contexts: topool estimates from multiple randomized controlled trials [4]; to combine results from survival modelson time-to-event data in multi-centre cohorts [5]; and to synthesize associations from Poisson time-seriesmodels in multi-city analyses [6].

The common approach to two-stage meta-analysis consists of summarizing the association in a singleparameter estimate from the first stage, optionally controlling for individual-level confounders. Thisprocedure allows standard meta-analytic techniques to be applied. However, complex associations, suchas non-linear exposure–responses, are usually described with functions defined by multiple parametersand require more sophisticated meta-analytical approaches capable of handling the multivariate natureof the summary estimates. Multivariate meta-analysis, a method originally developed to pool multiple

aDepartment of Medical Statistics, London School of Hygiene and Tropical Medicine, London, U.K.bDepartment of Social and Environmental Health Research, London School of Hygiene and Tropical Medicine, London, U.K.*Correspondence to: Antonio Gasparrini, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E7HT, U.K.

†E-mail: [email protected]

Copyright © 2012 John Wiley & Sons, Ltd. Statist. Med. 2012

Page 10: Open access: a researcher's perspective

A second article

Firstly submitted to Biostatistics:

Copyright transferred

Open access fee ∼2250£

Impact factor 2.145

Rejected, re-submitted to BMC Med Res Method:

Copyright retained

Open access fee ∼1475£ (∼1255£ with LSHTM discount)

Impact factor 2.67

Page 11: Open access: a researcher's perspective

A third article

Published in Journal of Statistical Software (2011):

Not automatically indexed in PubMed

Included ’manually’ through PubMed Central

Copyright retained

Open access fee: 0£

Impact factor 4.01

Page 12: Open access: a researcher's perspective

Open research: beyond publishing

Open data: research data collected with public funding availableto other researchers

Open source and free software

Reproducible research: open and thorough assessment ofresearch findings

Page 13: Open access: a researcher's perspective

A similar case

Statistical software is mainly based on commercial programs(e.g. Stata, SAS, SPSS)

Substantial fees to be paid by research institutions

However, implementation of novel methodologies provided byresearchers

Same story: researchers working (for free) for third parties...

Page 14: Open access: a researcher's perspective

An alternative model

An example: the R software

A project entirely based on a community of users and developers

Comparison with commercial programs

Model also applicable to publishing

Page 15: Open access: a researcher's perspective

The third article again

The manuscript is freely available at journal’s web site and otherrepositories

The code for the analysis is included as supplementary material

The software is implemented and fully documented in a freestatistical package

The data are stored online and freely available through thesoftware

All of this at no cost

Page 16: Open access: a researcher's perspective

The internet era

Different approach to search and dissemination: what role forjournals?

Drop in editorial and publication costs: do we really needpublishers?

Role of funders, institutions and research community is critical

Why so late?!

Page 17: Open access: a researcher's perspective

The open access era

Important changes: Wellcome and RCUK policies

Limitations of the Finch Report

Alternative models already available

Changes require a different approach from researchers