Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists

PLoS Comput Biol. 2015 Mar 26;11(3):e1004140. doi: 10.1371/journal.pcbi.1004140. eCollection 2015 Mar.

Abstract

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1-S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Cluster Analysis
  • Computational Biology / methods*
  • Computing Methodologies*
  • Ecology / methods*
  • Genetics, Population / methods*
  • Humans

Grants and funding

We thank the Evolutionary Biodemography Laboratory and the Modelling the Evolution of Ageing Independent Group of the Max Planck Society for Demographic Research (http://www.mpg.de) in Rostock (Germany) and Odense (Denmark)) for supporting the working group where this paper was initiated. This study was supported by the Netherlands Foundation for Scientific Research (www.nwo.nl, NWO-ALW 801-01-009 to MDV & EJ; NWO-ALW 840.11.001 to EJ), the Smithsonian Tropical Research Institute (www.stri.si.edu, MDV) and the USA National Science Foundation (www.nsf.gov NSF 640261 to SMM). The funders had no role in the preparation of the manuscript.