Université de Montréal

Université de Montréal
Département des Sciences Biologiques
C.P. 6128 succ. "Centre-Ville",
Montréal, Québec, Canada H3C 3J7
* Version française
* Numerical Ecology
* R Functions
* BIO 6077: Quantitative analysis of biological data
* Tirés à parts / Reprints

* Logiciels et Jeux de Données / Computer Programs and Datasets
* Le personnel du département

Pierre Legendre

Position:
Phone:

E-mail:
  		Professor
Office: (514) 343-7591

Pierre.Legendre@umontreal.ca
Officer of the National Order of Québec
Prix du Québec - Prix Marie-Victorin 2005
ISI Highly Cited Researcher in Ecology/Environment

2011 Teaching awards 		 Pierre Legendre's picture

Numerical ecology with R

Now available, January 2011

Authors: Daniel Borcard, François Gillet and Pierre Legendre
Publisher: Springer, "Use R!" collection
ISBN 978-1-4419-7975-9
e-ISBN 978-1-4419-7976-6

Numerical Ecology

Legendre, Pierre & Louis Legendre. 1998. Numerical ecology. 2nd English edition. Elsevier Science BV, Amsterdam. xv + 853 pages.
ISBN 0-444-89249-4 (Hardbound Edition) — US$137 — Euro 137
ISBN 0-444-89250-8 (Paperback Edition, 2nd reprint 2003) — US$ 67 — Euro 67

Members of the lab

Photo

From left to right: Daniel Borcard, Pierre Legendre, Pedro Peres-Neto and Stéphane Dray.
Picture: Bernard Lambert, Direction des communications, Université de Montréal.
  • Charleyne Bachraty (charleyne.bachraty@umontreal.ca), Ph.D. student
  • Guillaume Blanchet (Guillaume.Blanchet.1@umontreal.ca), M.Sc. student
  • Daniel Borcard (daniel.borcard@umontreal.ca), Senior researcher
  • Philippe Casgrain (casgrain@exchange.umontreal.ca), Bio-informatics
  • Miquel de Caceres (miquel.de.caceres.ainsa@umontreal.ca), Post-doctoral researcher
  • Stéphane Dray (dray@biomserv.univ-lyon1.fr), CNRS researcher, Université Lyon I
  • Elaine Hooper (elaine.hooper@yale.edu), Ph.D. student
  • Marie-Hélène Ouellette (marie-helene.ouellette@umontreal.ca), Ph.D. student
  • Pedro Peres-Neto (peres-neto.pedro@uqam.ca), professor at UQAM

    Classes

    R-language functions
  • Anova and t-tests
    • anova.1way.R (P. Legendre): One-way anova with permutation test.
    • anova.2way.R (P. Legendre): Two-way crossed-factor anova with permutation tests (balanced design): models I, II, and III.
    • anova.2way.unbalanced.R (P. Legendre): 2-way multivariate anova (by RDA) for balanced or unbalanced designs for 2 fixed crossed factors, with permutation tests.
    • anova.3way.R (P. Legendre): Three-way crossed-factor anova (fixed factors) with permutation tests (balanced design).
    • nest.anova.perm.R (D. Borcard and P. Legendre): Nested anova with permutation tests (main factor and one nested factor, balanced design).
    • t.perm.R (P. Legendre): t-test for independent samples with permutation test.
    • t.paired.perm.R (P. Legendre): t-test for related samples with permutation test.
  • bgdispersal (P. Legendre): Coefficients of biogeographical dispersal direction. Incorporated into the vegan library.

  • broken.stick.R (P. Legendre): Computes the expected values of the broken-stick distribution.

  • CADM: (P. Legendre): Concordance among several distance matrices. This function is now available in the ape library for phylogenetic analysis.
  • Canonical correspondence analysis (CCA)
    • CCA (P. Legendre): Demonstration function for canonical correspondence analysis (ter Braak 1986, 1987), following the algorithm described in Subsection 11.2.1 of Legendre and Legendre (1998).
  • Canonical redundancy analysis (RDA)
    • rdaTest (P. Legendre and S. Durand): R library to compute simple and partial canonical redundancy analysis (RDA) with permutation test and draw triplots of the results. Older versions of these functions are also found in the library sonarX, which is distributed on the ESA Web page http://esapubs.org/archive/, inside "Ecological Archives A016-047-S1". R library modified November 30, 2011.
      • rdaTest , cross-platform source (R 2.14, namespace support)
      • rdaTest library for Windows (tested on R 2.11)
      • rdaTest library for Windows (for older versions of R)
      • rdaTest library for Mac
    • AdjustedRsquare.R (P. Legendre): This function computes adjusted R-squares for two types of regression.
  • cascadeKM (S. Durand, M.-H. Ouellette and P. Legendre): Wrapper for the kmeans function for K-means partitioning. It creates several partitions forming a cascade from a small to a large number of groups. Incorporated into the vegan library.
    Also distributed as part of the "Ecological Archives A016-047-S1" on the ESA Web page http://esapubs.org/archive/appl/A016/047/.

  • CCorA (P. Legendre): Canonical and partial canonical correlation analysis, Y <-> X1/X2. A version of that function for the calculation of simple canonical correlation analysis is found in the vegan library.

  • const.clust (P. Legendre): R package to compute space-constrained or time-constrained agglomerative clustering from a dissimilarity matrix computed from multivariate data. The different solutions are tested by cross-validation. The clustering results are presented in the form of maps. R library modified November 30th, 2011.
  • corPerm.R (P. Legendre): Three functions to test the Pearson correlation coefficient by permutation.

  • dagnelie.test.R (D. Borcard, P. Legendre): Pierre Dagnelie’s test of multinormality.
  • Forward selection of explanatory variables in multiple regression and redundancy analysis (RDA)
    • packfor (S. Dray, P. Legendre and G. Blanchet): Compiled package containing the functions "forward.sel" and "forward.sel.par".
  • fourthcorner (S. Dray): Fourth-corner analysis.

  • Functional diversity: FD library (Étienne Laliberté)
  • Indicator / diagnostic species analyses: 'indicspecies' library: Software section.

  • Kendall.W: Species associations through Kendall's coefficient of concordance. Functions kendall.global() et kendall.post() forming this library are now integrated into the vegan library for community analysis.
  • Linear regression
    • multRegress.R (P. Legendre): This function computes a multiple regression and tests the coefficient of determination (R-square) by permutation.
    • lmodel2 (P. Legendre): Package to compute model II simple linear regression using ordinary least squares (OLS), major axis (MA), standard major axis (SMA), and ranged major axis (RMA). Available on the CRAN page.
    • lmorigin (P. Legendre): Package to compute multiple linear regressions with permutation tests. The program includes regression through the origin, to be used in particular for the analysis of independent contrast data. This function is now available in the ape library for phylogenetic analysis.

  • manova.2way.unbalanced.R  (P. Legendre): manova for univariate or multivariate response data, two crossed factors, balanced or unbalanced design.

  • manovRDa.R (E. Laliberté): Two-way Manova-like RDA for fixed or random factors.

  • mantel.correlog (P. Legendre): Package to compute a multivariate Mantel correlogram. This function is now available in the vegan library for community analysis.
  • parafit (P. Legendre): Package to test host-parasite coevolution. This function is now available in the ape library for phylogenetic analysis.
  • PCNM, MEM and AEM spatial eigenfunctions
    • PCNM library: PCNM spatial eigenfunction analysis and principal coordinate analysis. This library uses resources from the AEM and packfor libraries available at the same address, as well as resources from the vegan, ade4 and spdep libraries available from CRAN.
    • spacemakeR library: spatial analysis by MEM eigenfunctions (S. Dray).
    • AEM library: Analysis of responses to directional spatial processes by AEM eigenfunctions (G. Blanchet).

  • Periodograph (P. Legendre): Contingency periodogram

  • seriation.R (P. Legendre and S. Durand ): Seriation method of Beum & Brundage (1950) for non-symmetric or symmetric resemblance matrices

  • sonarX (S. Durand et P. Legendre): Library for the extraction and analysis of single-beam sonar signals for benthic habitat detection. Distributed as part of the "Ecological Archives A016-047-S1" on the ESA Web page http://esapubs.org/archive/appl/A016/047/.

  • Sidak.R (P. Legendre): Bonferroni and Sidak corrections for multiple testing.

  • Simple ordinations
    • PCA (P. Legendre): Principal component analysis (PCA).

    • CA (P. Legendre): Correspondence analysis (CA).

  • sonarX (S. Durand and P. Legendre): Extraction and analysis of single-beam sonar signals for benthic habitat detection and mapping. Package distributed as part of the "Ecological Archives A016-047-S1" on the ESA Web page http://esapubs.org/archive/appl/A016/047/.

  • STI: test of space-time interaction in sampling design without replication: library distributed on the Software page of Miquel De Cáceres at http://sites.google.com/site/miqueldecaceres/software

  • varpart (P. Legendre): Partition the variation of response table Y with respect to 2, 3, or 4 tables of explanatory variables. Incorporated into the vegan library.

  • Ten years of vegan (Jari Oksanen): A short history of the development of the vegan package before and since its release on CRAN on September 6, 2001.

    Fortran and Pascal programs

  • Adjusted P-values: Compute various forms of adjustments to a list of probability values in cases of multiple testing.
    • Updated on 16/01/02
  • Congruence among distance matrices
    • Updated on 03/09/07
  • DistPCoA: Principal coordinate analysis with correction for negative eigenvalues
    • Updated on 08/12/02
  • Robinson and Foulds topological distance: Rapidly compute the Robinson and Foulds distance between two additive trees
    • Updated on 01/08/10
  • IndVal: Indicator species, with test of significance
  • K-Means: Least-squares partitioning method
    • Updated on 01/08/10
  • Kendall_W: Species associations through Kendall’s coefficient of concordance New!
    • Updated on 01/08/10
  • Pearson correlation coefficient matrix with permutation test
  • NesAnova: Nested Manova by Canonical Analysis
    • Updated on 12/08/02
  • Optimal Variable Weighting (OVW): Optimal variable weighting for ultrametric and additive tree clustering according to De Soete's method
    • Updated on 01/08/10
  • ParaFit: Test of host-parasite coevolution
    • Updated on 01/08/10
  • Permute!: Multiple regression over distance, ultrametric and additive matrices with permutation test
    • Updated on 16/03/09
  • The R Package for spatial and multidimensional analysis New!
    • Updated on 05/06/04
  • The Q Package for spatial and multidimensional analysis
    • Updated on 10/11/08
  • RdaCca: Redundancy and canonical correspondance analysis
    • Updated on 01/08/10
  • Polynomial RdaCca: Polynomial and linear version of the RdaCca program.
    • Updated on 01/08/10
  • Model II regression: Major axis, standard major axis and ordinary least squares
    • Updated on 13/11/11
  • Multiple linear regression: Compute multiple linear regressions with permutation tests. The program includes regression through the origin.
    • Updated on 01/08/10
  • SpaceMaker 2: Building spatial variables for trend-surface (polynomials) and all-scale (PCNM) spatial analysis
    • Updated on 01/08/10
  • T-REX: Tree and Reticulogram Reconstruction

  • Modified t-test for a Pearson correlation coefficient corrected for spatial autocorrelation
    • Updated on 01/08/10
  • Univariate tests of variance homogeneity
    • Updated on 01/01/04
  • Transformation & Species Scores: Transformations of frequency data suitable for biplots and ordinations
    • Updated on 17/12/04
  • The 4th corner
    • Updated on 01/08/10

    Datasets

  • Hunting spider data from The Netherlands
  • Scotch whiskies classification data
    • Updated on 16/11/03
  • Oribatid mites data
    • Updated on 08/12/02
  • Thiahura fish transect data
    • Updated on 01/08/10

    Other documents

  • Interview with Louis and Pierre Legendre (in French)
    • Updated on 12/07/03
  • English-French vocabulary of numerical ecology and statistics
    • Updated on 24/01/08

    Programs created by other researchers

  • R Language
  • Programs by J. Oksanen: vegan (R library); other programs
  • Programs by Stéphane Dray
  • Programs by Marti Anderson
  • Cajo ter Braak (Canoco)
  • Programs by Marc Dufrêne
  • Programs by Alain Guénoche

    Career Summary

     Postdoctoral fellow at the Genetiska Institutionen, Lunds Universitet, Sweden, in 1971-72. Research associate, then Research director at Université du Québec à Montréal, and finally Professor in the Département de physique. Moved to Département de sciences biologiques, Université de Montréal, in 1980.
    • Recipient of the Michel-Jurdant prize for Environment Sciences, Association canadienne-française pour l'Avancement des Sciences (ACFAS), for 1986
    • Killam Research Fellow, Canada Council, in 1989-1991
    • Fellow of the Royal Society of Canada (Academy of Science) since 1992
    • Recipient of the Distinguished Statistical Ecologist Award of the International Congress of Ecology - (INTECOL) in 199 and, in 1995, of the Romanowski Medal (environmental science) of the Royal Society of Canada
    • Recipient of the 2005 Prix Marie-Victorin of the Government of Québec.
    • Officer of the National Order of Québec in 2007.
    • Recipient of the 2011 Université de Montréal teaching award, full professors category.
    • Recipient of the 2011 teaching award of the Faculty of Arts and Science, Université de Montréal, science sector category.

    Pierre Legendre's résumé

    Mis-à-jour le Mardi 03 janvier 2012