Assessing the reproducibility of discriminant function analyses

Rose L Andrew; Arianne Y K Albert; Sebastien Renaut; Diana J Rennison; Dan G Bock; Tim Vines

doi:10.7717/peerj.1137

Assessing the reproducibility of discriminant function analyses

PeerJ. 2015 Aug 4:3:e1137. doi: 10.7717/peerj.1137. eCollection 2015.

Authors

Rose L Andrew¹, Arianne Y K Albert², Sebastien Renaut³, Diana J Rennison⁴, Dan G Bock⁴, Tim Vines⁵

Affiliations

¹ School of Environmental and Rural Science, University of New England , Armidale, NSW , Australia ; Biodiversity Research Centre, University of British Columbia , Vancouver, BC , Canada.
² Women's Health Research Institute, BC Women's Hospital and Health Centre , Vancouver, BC , Canada.
³ Biodiversity Research Centre, University of British Columbia , Vancouver, BC , Canada ; Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal , Montreal, QC , Canada.
⁴ Biodiversity Research Centre, University of British Columbia , Vancouver, BC , Canada.
⁵ Biodiversity Research Centre, University of British Columbia , Vancouver, BC , Canada ; Molecular Ecology Editorial Office , Vancouver, BC , Canada.

Abstract

Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the carefully curated research that the scientific community and public expects.

Keywords: Data archiving; Data curation; Repeatability; Statistics.

Grants and funding

Diana J. Rennison was supported by an NSERC postgraduate studentship. Dan G. Bock was supported by an NSERC Vanier CGS and a Killam doctoral scholarship. Sebastien Renaut was supported by an NSERC postdoctoral fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.