title: PHENIX: An R package to estimate a size-controlled phenotypic integration index.
abstract: OBJECTIVE
  Organisms usually show intercorrelations between all or some of their components leading to phenotypic integration, which may have deep consequences on the evolution of phenotypes. One of the main difficulties with phenotypic integration studies is how to correct the integration measures for size. This has been considered a challenging task. In this paper, we introduce an R package (PHENIX: PHENotypic Integration indeX), in which we provide functions to estimate a size-controlled phenotypic integration index, a bootstrapping method to calculate confidence intervals, and a randomization method to simulate null distributions and test the statistical significance of the integration.
  
  
  RESULTS
  PHENIX is an open source package written in R. As usual for R packages, the manual and sample data are available at: http://cran.r-project.org/web/packages/PHENIX/index.html. Functions included in this package easily estimate phenotypic integration by controlling a third variable (e.g., the size of the studied organ).
  
  
  CONCLUSIONS
  PHENIX helps to estimate and test the statistical significance of the magnitude of integration using one of the most-used methodological approaches, while taking size into account.
authors.affiliation: Centro de Ecologia Funcional, Universidade de Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal ; Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (EEZA-CSIC), Carretera de Sacramento s/n, 04120 La Cañada de San Urbano, Almería, Spain.
authors.forename: Rubén
authors.initials: R
authors.lastname: Torices
authors.affiliation: Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Campus Agrário de Vairão, Rúa Padre Armando Quintas, 4485-661 Vairão, Portugal.
authors.forename: A Jesús
authors.initials: AJ
authors.lastname: Muñoz-Pajares
keywords: PHENIX; correlation; partial-correlation matrix; size; software