Publications

Determinants of genetic diversity and species richness of North American amphibians

Aim Ecological limits on population sizes and the number of species a region can sustain are thought to simultaneously produce spatial …
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Genetic and species‐level biodiversity patterns are linked by demography and ecological opportunity

The processes that give rise to species richness gradients are not well understood, but may be linked to resource-based limits on the …
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Editorial: Advances in Statistical Ecology: New Methods and Software

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An appraisal of graph embeddings for comparing trophic network architectures

Comparing the architecture of interaction networks in space or time is essential for understanding the assembly, trajectory, …
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Overcoming the Spurious Groups Problem in Between-Group PCA

Several papers have recently raised the occurrence of some problems with between-group Principal Component Analysis (bgPCA). This …
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Long‐term high densities of African elephants clear the understorey and promote a new stable savanna woodland community

Questions Species defined as ecosystem engineers (e.g. elephant) are able to strongly shape their habitat. In African savannas, …
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Are human natal sex ratio differences across the world adaptive? A test of Fisher's principle

Fisher’s principle states that natural selection favours an equal number of male and female births at the population level, …
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Images, écologie et deep learning

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Can an herbivore affect where a top predator kills its prey by modifying woody vegetation structure?

In large mammal communities, little is known about modification of interspecific interactions through habitat structure changes. We …
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Investigating microbial associations from sequencing survey data with co-correspondence analysis

Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how …
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Heterogeneity of water physico-chemical characteristics in artificially pumped waterholes: do African herbivores drink at the same locations and does it lead to interference competition?

In many semi-arid savanna ecosystems, surface water is scarce and only found in artificially pumped waterholes at the end of the dry …
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Flower phenology as a disruptor of the fruiting dynamics in temperate oak species

Many perennial plants display masting, that is, fruiting with strong interannual variations, irregular and synchronized between trees …
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How to deal with missing and confounding variables in multivariate analysis?

Portail web pour soumettre, formater et partager des jeux de données dans R

Testing the Mantel statistic with a spatially-constrained permutation procedure

Mantel tests are widely used in ecology to assess the significance of the relationship between two distance matrices computed between …
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Spatial analyses of multi‐trophic terrestrial vertebrate assemblages in Europe

Aim Although much has been said on the spatial distribution of taxonomic and phylogenetic diversity of vertebrates, how this diversity …
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Phenotypic plasticity in the invasive pest Drosophila suzukii: Activity rhythms and gene expression in response to temperature

Phenotypic plasticity may contribute to the invasive success of an alien species in a new environment. A highly plastic species may …
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Nine quick tips for analyzing network data

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Moran eigenvector filters for the analysis of ecological data : are they really multiscale?

Diversity indices for ecological networks: a unifying framework using Hill numbers

Describing how ecological interactions change over space and time and how they are shaped by environmental conditions is crucial to …
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Analyse des structures spatiales multivariées en écologie des communautés avec le package adespatial

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Supervised Multiblock Analysis in R with the ade4 Package

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Simple parametric tests for trait–environment association

Question The community weighted means (CWM) approach is an easy way of analyzing trait-environment association by regressing (or …
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Optimizing the choice of a spatial weighting matrix in eigenvector-based methods

Abstract Eigenvector-mapping methods such as Moran’s eigenvector maps (MEM) are derived from a spatial weighting matrix (SWM) …
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Multivariate Analysis of Ecological Data with ade4

This book introduces the ade4 package for R which provides multivariate methods for the analysis of ecological data. It is implemented …
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Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait-environment relationships

The fourth-corner analysis aims to quantify and test for relationships between species traits and site-specific environmental …
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Disentangling good from bad practices in the selection of spatial or phylogenetic eigenvectors

Eigenvector mapping techniques are widely used by ecologists and evolutionary biologists to describe and control for spatial and/or …
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Beyond neutrality: disentangling the effects of species sorting and spurious correlations in community analysis

The methods of direct gradient analysis and variation partitioning are the most widely used frameworks to evaluate the contributions of …
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Algorithms and biplots for double constrained correspondence analysis

Correspondence analysis with linear external constraints on both the rows and the columns has been mentioned in the ecological …
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Couplage des données de biodiversité : prise en compte de l’originalité des structures de données

Linking trait variation to the environment: Critical issues with community-weighted mean correlation resolved by the fourth-corner approach

Establishing trait-environment relationships has become routine in community ecology. Here, we demonstrate that the Community Weighted …
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Factors shaping community assemblages and species occurrence of different trophic levels

Species assemblages are the results of various processes, including dispersion and habitat filtering. Disentangling the effects of …
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Environment, traits, space and phylogeny: integrating constraints in the analysis of ecological data tables

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Analyse spatiale multi-échelles de données écologiques avec adespatial

adegraphics: an S4 lattice-based package for the representation of multivariate data

The ade4 package provides tools for multivariate analyses. Whereas new statistical methods have been added regularly in the package …

A critical issue in model-based inference for studying trait-based community assembly and a solution

Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is …
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The global spectrum of plant form and function

Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have …
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Addressing ecological effects of radiation on populations and ecosystems to improve protection of the environment against radiation: Agreed statements from a Consensus Symposium.

This paper reports the output of a consensus symposium organized by the International Union of Radioecology in November 2015. The …
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Spatial distribution of a large herbivore community at waterholes: An assessment of its stability over years in Hwange National Park, Zimbabwe

The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. …
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Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification

The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, …
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Interspecific interference competition at the resource patch scale: do large herbivores spatially avoid elephants while accessing water?

Animals may anticipate and try to avoid, at some costs, physical encounters with other competitors. This may ultimately impact their …
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Environnement, traits, espace et phylogénie : intégrer des contraintes dans l’analyse d’un tableau écologique

The adephylo package

Principal component analysis with missing values: a comparative survey of methods

Principal component analysis (PCA) is a standard technique to summarize the main structures of a data table containing the measurements …
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Generating spatially constrained null models for irregularly spaced data using Moran spectral randomization methods

Spatial autocorrelation jeopardizes the validity of statistical inference, for example correlation and regression analysis. Restricted …
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Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)

The use of next-generation sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of …
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An integrated web server and R package for data sharing and reproducible research in ecology

Statistical ecology comes of age

The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the …
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An integrated web server and R package for data sharing and reproducible research in ecology

Spatially constrained clustering of ecological networks

Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g. populations or …
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Functional analysis of Normalized Difference Vegetation Index curves reveals overwinter mule deer survival is driven by both spring and autumn phenology

Large herbivore populations respond strongly to remotely sensed measures of primary productivity. Whereas most studies in seasonal …

Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation

Assessing trait responses to environmental gradients requires the simultaneous analysis of the information contained in three tables: L …
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Analysing a pair of tables: coinertia analysis and duality diagrams

Un site web d'enseignement R automatisé et à gestion partagée

Reciprocal modulation of internal and external factors determines individual movements.

Movement is fundamental to individual and population dynamics, as it allows individuals to meet their basic requirements. Although …
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Méthodes de couplage de deux K-tableaux et collections de graphiques

Functional traits reveal processes driving natural afforestation at large spatial scales.

An understanding of the processes governing natural afforestation over large spatial scales is vital for enhancing forest carbon …
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Développement de méthodes de régression multibloc pour le traitement des données d’épidémiologie vétérinaire. Des besoins statistiques des épidémiologistes au développement d’un package R

Does local habitat fragmentation affect large-scale distributions? The case of a specialist grassland bird

Aim: Although the negative effects of habitat fragmentation have been widely documented at the landscape scale, much less is known …
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Development of multi-block regression analysis to process veterinary epidemiological data. From statistical needs of epidemiologists to development of R package

The purpose of this paper is to describe the development strategy of statistical methods to be applied in the field. As an example, the …

De la biologie à l'algèbre linéaire ... en passant par R. Expérimenter la notion de projection

Conference Report: Deuxièmes Rencontres R

adegraphics : un package pour la représentation et l'analyse de données multivariées

A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients

Question: Which functional diversity indices have the power to reveal changes in community assembly processes along abiotic stress …
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ade4: statistical methods and graphical functions for the analysis of multivariate data

ade4: statistical methods and graphical functions for the analysis of multivariate data

Assessing species and community functional responses to environmental gradients: which multivariate methods?

Question: How do multivariate methods perform in relating species- and community-level trait responses to the environment? Location (1) …
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Visualisation de données multivariées: réimplémentation des fonctionnalités graphiques de la librairie ade4

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The Harttiini (Siluriformes, Loricariidae) from the Guianas: a multi-table approach to assess their diversity, evolution, and distribution

The Harttiini are a tribe of Loricariinae poorly characterized morphologically. Within the Guianas (French Guiana, Suriname, and …

Predator-prey spatial game as a tool to understand the effects of protected areas on harvester-wildlife interactions

No-take reserves are sometimes implemented for sustainable population harvesting because they offer opportunities for animals to …

Improved testing of species traits-environment relationships in the fourth corner problem

The fourth-corner problem entails estimation and statistical testing of the relationship between species traits and environmental …

How to measure and test phylogenetic signal

  1. Phylogenetic signal is the tendency of related species to resemble each other more than species drawn at random from the same tree. …

Disentangling plant trait responses to livestock grazing from spatio-temporal variation: the partial RLQ approach

Questions: Which plant traits consistently respond to grazing in different years and across habitat-related environmental …
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Community ecology in the age of multivariate multiscale spatial analysis

Species spatial distributions are the result of population demography, behavioral traits, and species interactions in spatially …
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Assessing the effects of spatial contingency and environmental filtering on metacommunity phylogenetics

Patterns in biodiversity and species coexistence are the result of multiple interacting processes including evolutionary history, trait …

Analyse de (K+1) tableaux avec le logiciel ade4. Application en épidémiologie

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Linking traits to environmental variation

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Revisiting Guerry's data: introducing spatial constraints in multivariate analysis

Standard multivariate analysis methods aim to identify and summarize the main structures in large data sets containing the description …
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Relationships between species feeding traits and environmental conditions in fish communities: a three-matrix approach

Understanding the relationships between species biological traits and the environment is crucial to predicting the effect of habitat …

Multivariate analysis of ecological data with ade4

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How can ecological status be summarized for an operational Pressures/States model ?

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Analyzing spatial multivariate structures

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A new perspective about Moran's coefficient: spatial autocorrelation as a linear regression problem

The computation of Moran’s index of spatial autocorrelation requires the definition of a spatial weighting matrix. The …

Développements méthodologiques autour de l'analyse de données écologiques

Une approche multivariée pour la recherche de structures phylogénétiques dans les données biologiques

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The exploratory analysis of autocorrelation in animal-movement studies

Studies of animal movements have been popularized for many large and shy species by the increasing use of radio telemetry methods (VHF …

Some methodological developments around the spatial weighting matrix in ecology

Make love not war: when should less competitive males choose low-quality but defendable females?

Male choosiness for mates is an underexplored mechanism of sexual selection. A few theoretical studies suggest that males may exhibit …

Corrigendum to \"Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes\" Mol. Phylogenet. Evol. 46 (2008) 986-1002 (DOI:10.1016/j.ympev.2007.12.015)

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Analyses multivariées et mesures d'autocorrélation spatiale pour l'analyse des assemblages d'espèces

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adephylo: new tools for investigating the phylogenetic signal in biological traits

(Some elements of) Spatial ecological data analysis

The concept of animals trajectories from a data analysis perspective

The Global Positioning System (GPS) has been increasingly used during the past decade to monitor the movements of free-ranging animals. …

Responding to spatial and temporal variations in predation risk: space use of a game species in a changing landscape of fear

Predators generate a "landscape of fear" within which prey can minimize the risk of predation by selecting low-risk areas. …

Phylogeny and evolution of shapes: a new approach to predict phylogenetic positions of missing taxa

Les Harttiini (Siluriformes, Loricariidae) des Guyanes : phylogénie et évolution des formes ou variation sur un même thème.

Finding essential scales of spatial variation in ecological data: a multivariate approach

The identification of spatial structures is a key step in understanding the ecological processes structuring the distribution of …

Extracting phylogenetic signal in morphometric data to complete molecular phylogenies: a case study on Harttiini (Siluriformes, Loricariidae) from the Guianas

Unexpected male choosiness for mates in a spider

Sexual selection theory traditionally considers choosiness for mates to be negatively related to intra-sexual competition. Males were …

Testing the species traits-environment relationships: the fourth-corner problem revisited

Functional ecology aims at determining the relationships between species traits and environmental variables in order to better …

Spatial ordination of vegetation data using a generalization of Wartenberg's multivariate spatial correlation

Question: Are there spatial structures in the composition of plant communities? Methods: Identification and measurement of spatial …

On the number of principal components: A test of dimensionality based on measurements of similarity between matrices

An important problem in principal component analysis (PCA) is the estimation of the correct number of components to retain. PCA is most …

Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes

With the increase of laboratory facilities, molecular phylogenies are playing a predominant role in evolutionary analyses. However, …

Analyzing or explaining beta diversity? Comment.

The ade4 package: implementing the duality diagram for ecologists

Multivariate analyses are well known and widely used to identify and understand structures of ecological communities. The ade4 package …

The ade4 package - II: Two-table and K-table methods

Testing sexual segregation and aggregation: old ways are best

The study of sexual segregation has received increasing attention over the last two decades. Several hypotheses have been proposed to …

Multi-scale assessment of the functional relationships between species traits and environmental conditions for littoral fish communities

Multi-scale assessment of the functional relationships between species traits and environmental conditions for littoral fish communities

Interactive multivariate data analysis in R with the ade4 and ade4TkGUI packages

ade4 is a multivariate data analysis package for the R statistical environment, and ade4TkGUI is a Tcl/Tk graphical user interface for …

\"Reserve effect\" on the space use of game mammals: the case of wild boar

Variation partitioning of species data matrices: estimation and comparison of fractions

Establishing relationships between species distributions and environmental characteristics is a major goal in the search for forces …

Spatial modeling: a comprehensive framework for principal coordinate analysis of neighbor matrices (PCNM)

Spatial structures of ecological communities may originate either from the dependence of community structure on environmental variables …

Resource partitioning in a grazer guild feeding on a multilayer diatom mat

The gut contents of a guild of invertebrate grazers inhabiting the moss Fontinalis and feeding on epiphytic diatoms in a small Que´bec …

Morphological and phylogenetic study of the subfamily Loricariinae (Siluriformes, Loricariidae)

Impact of hunting activities on the spatial behaviour of the wild boar: attractiveness of safe areas

Analyse morphologique et phylogénétique de la sous famille des Loricariinae (Siluriformes, Loricariidae)

Taking into account spatial dependence in multivariate analysis: a generalization of Wartenberg's multivariate spatial correlation

Variation partitioning of species data matrices: estimation and comparison of fractions

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Spatial modeling: a comprehensive framework for distance-based eigenvector maps (DBEM)

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Coupling principal component analysis and GIS to map deer habitats

We aimed to define at a relevant scale the spatial pattern of major vegetation types available to deer in order to characterise habitat …

Nouvelles méthodes d'analyse spatiale multivariée de données incomplètes

Two solutions to the fourth corner problem

Analyse spatialisée de données écologiques multivariées

Spatial variation in springtime food resources influences the winter body mass of roe deer fawn

It is well established that the dynamics of mammalian populations vary in time, in relation to density and weather, and often in …

Procrustean co-inertia analysis for the linking of multivariate data sets

Procrustes analysis is a method for fitting a set of points to another. These two sets of points are often defined by the measurements …

Multivariate analysis of incomplete mapped data

Classical multivariate analyses are based on matrix algebra and enable the analysis of a table containing measurements of a set of …

Eléments d'interface entre analyses multivariées, systèmes d'information géographique et observations écologiques

Couplage de données issues de deux plans d'échantillonnage distincts d'un même espace

Consistency between ordination techniques and diversity measurements: two alternative strategies for species occurrence data

Both the ordination of taxonomic tables and the measurements of species diversity aim to capture the prominent features of the species …

Co-inertia analysis and the linking of ecological data tables

Ecological studies often require studying the common structure of a pair of data tables. Co-inertia analysis is a multivariate method …

Cartographie et analyse de données multivariées

L’identification de structures spatiales induisant plusieurs variables est une problématique récurrente dans de nombreux domaines …

Broad-scale biodiversity pattern of the endemic tree flora of the Western Ghats (India) using canonical correlation analysis of herbarium records

A crucial step in understanding the origin and maintenance of biological diversity is the assessment of its distribution over space and …

Within-plot relationships between tree species occurrences and hydrological soil constraints: an example in French Guiana investigated through canonical correlation analysis

Spatial relationships between tree species and hydrological soil constraints are analysed within a 10-ha rainforest plot at Piste de St …

The distribution of preferred plant species in spring determines spatial variation in the body mass of roe deer fawns in winter

Modelling bovine trypanosomosis spatial distribution by GIS in an agro-pastoral zone of Burkina Faso

Modelling of the spatial distribution of bovine trypanosomosis prevalence in Sideradougou district Burkina Faso was performed by using …

Matching data sets from two different spatial samples

Methods for coupling two data sets (species composition and environmental variables for example) are well known and often used in …

Systèmes d'information géographique : une application à la modélisation d'une maladie à transmission vectorielle au Burkina Faso

Modelling bovine trypanosomosis spatial distribution by GIS in an agro-pastoral zone of Burkina Faso

Utilisation des listes d'occurrences spécifiques spatialisées en écologie et biogéographie

L'ordination des listes d'occurrences : quand l'analyse canonique des correspondances est une analyse canonique