Cajo ter Braak

Publications

• Integrated probabilistic risk assessment for nanoparticles: the case of nanosilica in food
• Linking trait variation to the environment
• A critical issue in model-based inference for studying trait-based community assembly and a solution
• A risk assessment-driven quantitative comparison of gene expression profiles in PBMCs and white adipose tissue of humans and rats after isoflavone supplementation
• Flow thresholds for leaf retention in hydrodynamic wakes downstream of obstacles
• Predictor versus response permutation for significance testing in weighted regression and redundancy analysis
• Fourth-corner correlation is a score test statistic in a log-linear trait–environment model that is useful in permutation testing
• Double constrained ordination for assessing biological trait responses to multiple stressors
• Flow velocity tolerance of lowland stream caddisfly larvae (Trichoptera)
• Species Identity, Life History, and Geographic Distance Influence Gut Bacterial Communities in Lab-Reared and European Field-Collected Culicoides Biting midges
• New robust weighted averaging- and model-based methods for assessing trait-environment relationships.
• Holocene climates of the Iberian Peninsula
• Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space
• Tutorial and R-package TraitEnvMLMWA for new robust weighted averaging- and model-based methods for assessing trait-environment relationships
• Functional biogeography of Neotropical moist forests: trait-climate relationships and assembly patterns of tree communities
• Published Canoco analyses: Canoco projects with descriptions
• Predictor versus response permutation
• Hay meadows' overriding effect shapes ground beetle functional diversity in mountainous landscapes
• Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes
• Log-ratio analysis of microbiome data with many zeroes is library size dependent
• Response variable selection in principal response curves using permutation testing
• Simple parametric tests for trait–environment association
• Biomarker Research in ADHD: The Impact of Nutrition (BRAIN) - Study protocol of an open-label trial to investigate the mechanisms underlying the effects of a few-foods diet on ADHD symptoms in children
• Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait–environment relationships
• Consumer segmentation based on taste preference of tomatoes
• Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition
• Biodiversity analyses for risk assessment of genetically modified potato
• Investigating microbial associations from sequencing survey data with co-correspondence analysis
• Networking Our Way to Better Ecosystem Service Provision
• An improved statistical approach for reconstructing past climates from biotic assemblages
• Testing environmental effects on taxonomic composition with canonical correspondence analysis: alternative permutation tests are not equal
• A matter of time
• Redundancy analysis includes analysis of variance-simultaneous component analysis (ASCA) and outperforms its extensions
• Achteruitgang insectenpopulaties in Nederland: trends, oorzaken en kennislacunes
• Een eureka-moment dat nog een beetje natrilt
• Early plant recruitment stages set the template for the development of vegetation patterns along a hydrological gradient
• Analysing chemical-induced changes in macroinvertebrate communities in aquatic mesocosm experiments: a comparison of methods
• Parametric estimation of P(X > Y) for normal distributions in the context of probabilistic environmental risk assessment
• Dispersal versus environmental filtering in a dynamic system: Drivers of vegetation patterns and diversity along stream riparian gradients
• Macroinvertebrate survival during cessation of flow and streambed drying in a lowland stream
• New robust weighted averaging‐ and model‐based methods for assessing trait–environment relationships
• Antimicrobial resistance clusters in commensal Escherichia coli from livestock
• Functional biogeography of Neotropical moist forests: Trait–climate relationships and assembly patterns of tree communities
• Relating ultrasonic vocalizations from a pair of rats to individual behavior: A composite link model approach
• A global database for metacommunity ecology, integrating species, traits, environment and space
• Canoco reference manual and user's guide
• Benthic invertebrate and microbial biodiversity in sub-tropical urban rivers: Correlations with environmental variables and emerging chemicals
• Combining exposure and effect modelling into an integrated probabilistic environmental risk assessment for nanoparticles
• Algorithms and biplots for double constrained correspondence analysis
• Compositional turnover and variation in Eemian pollen sequences in Europe
• Sclerotium rolfsii dynamics in soil as affected by crop sequences
• Corrigendum to "An automated system for the recognition of various specific rat behaviors" [J. Neurosci. Methods 218(2) (2013) 214-224]
• Genome-wide computational function prediction of arabidopsis proteins by integration of multiple data sources
• Approximating a similarity matrix by a latent class model: A reappraisal of additive fuzzy clustering
• A 3D Analysis of Flight Behavior of Anopheles gambiae sensu stricto Malaria Mosquitoes in Response to Human Odor and Heat
• History of canonical correspondence analysis
• Canoco reference manual and user's guide: software for ordination, version 5.0
• Nanoparticle risk assessment: a probabilistic approach
• Predicting changes in ecosystem functioning from shifts in plant traits
• Image-Based Particle Filtering For Robot Navigation In A Maize Field
• Legumes affect alpine tundra community composition via multiple biotic interactions
• Dynamics of Sclerotium rolfsii survival in green manure amended soil
• Estimating the prediction uncertainty of biological models
• Integrated probabilistic risk assessment: the case of nano-silica in food
• Dinámica de la sobrevivencia de esclerotos de Sclerotium rolfsii en el suelo con diferentes enmiendas de abonos verdes
• Reset of a critically disturbed microbial ecosystem: Faecal transplant in recurrent Clostridium difficile infection
• Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation
• Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters
• Laser range finder model for autonomous navigation of a robot in a maize field using a particle filter
• Generalized linear mixed models can detect unimodal species-environment relationships
• A unimodal species response model relating traits to environment with application to phytoplankton communities
• Selecting traits that explain species-environment relationships: A generalized linear mixed model approach
• QTL linkage analysis of connected populations using ancestral marker and pedigree information
• Equifinality of formal (DREAM) and informal (GLUE) Bayesian approaches in hydrologic modeling?
• Hydrologic data assimilation using particle Markov chain Monte Carlo simulation: Theory, concepts and applications
• Selection properties of type II maximum likelihood (empirical Bayes) in linear models with individual variance components for predictors
• Response to "Traits and stress: keys to identify community effects of low levels of toxicants in test systems" by Liess and Beketov (2011).
• Improved testing of species traits-environment relationships in the fourth-corner problem
• Gene Ontology consistent protein function prediction: The FALCON algorithm applied to six eukaryotic genomes
• Fusarium oxysporum f.sp. cepae dynamics: In-plant multiplication and crop sequence simulations
• Complex contexts and dynamic drivers: Understanding four decades of forest loss and recovery in an East African protected area
• An automated system for the recognition of various specific rat behaviours
• Trait-environment relationships and tiered forward model selection in linear mixed models
• Correlated mutations via regularized multinomial regression
• Mixed model approaches for the identification of QTLs within a maize hybrid breeding program
• Iteratio: Calculating environmental indicator values for species and relevés
• Arctic warming on two continents has consistent negative effects on lichen diversity and mixed effects on bryophyte diversity
• Using life-history traits to explain bird population responses to changing weather variability
• The predictability of phytophagous insect communities: Host specialists as habitat specialists
• Testing the significance of canonical axes in redundancy analysis
• DREAM(D): An adaptive Markov Chain Monte Carlo simulation algorithm to solve discrete, noncontinuous, and combinatorial posterior parameter estimation problems
• Identity-by-descent matrix decomposition using latent ancestral allele models
• Gene regulatory networks from multifactorial perturbations using graphical lasso: Application to the DREAM4 challenge
• Bayesian markov random field analysis for protein function prediction based on network data
• Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling
• Determinants of cryptogam composition and diversity in Sphagnum-dominated peatlands: The importance of temporal, spatial and functional scales
• Agro-ecological indicators (AEIs) for dairy and mixed farming systems classification: Identifying alternatives for the cuban livestock sector
• Topics in constrained and unconstrained ordination
• Image-based particle filtering for navigation in a semi-structured agricultural environment
• A large-scale evaluation of computational protein function prediction
• Differential Evolution Markov Chain with snooker updater and fewer chains
• Statistical aspects of environmental risk assessment of GM plants for effects on non-target organisms
• Regression by L1 regularization of smart contrasts and sums (ROSCAS) beats PLS and elastic net in latent variable model
• Extending Xu's Bayesian model for estimating polygenic effects using markers of the entire genome
• Effects of green veining on natural enemies of invertebrate pest species in leek and sprouts
• Treatment of input uncertainty in hydrologic modeling: Doing hydrology backward with Markov chain Monte Carlo simulation
• Permutation tests for multi-factorial analysis of variance
• Improved Bayesian analysis of metapopulation data with an application to a tree frog metapopulation
• A Theory of Gradient Analysis
• Baseline studies North Sea wind farms: Lot 5 marine birds in and around the future sites Nearshore Windfarm (NSW) and Q7
• Baseline studies North Sea wind farms: Lot 5 marine birds in and around the future site Nearshore Windfarm (NSW)
• Discussion of 'A model selection approach for the identification of quantitative trait loci in experimental crosses' by K.W. Broman & T.P. Speed
• Discussion of 'Bayesian palaeoclimate reconstruction' by J. Haslett et al
• Multivariate analysis of ecotoxicological data using ordination: demonstrations of utility on the basis of various examples
• CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination (version 4.5)
• A Flexible Bayesian framework for multiple QTL mapping in pedigreed populations
• Bayesian palaeoclimate reconstruction - Discussion on the paper by Haslett et al
• Handleiding voor het gebruik van multivariate analysetechnieken in de ecologie
• Resultaten kokkelvisexperiment Ameland
• Wegverlichting en natuur; IV effecten van wegverlichting op het ruimtelijk gedrag van zoogdieren
• Boommarters en wegen; een eerste analyse van de relatie 'wegbermen - verkeersslachtoffers'
• EHS-experiment Gaasterland; 1 startfase monitrong botanische beheersovereenkomsten
• Effect van treinverkeer op dichtheden weidevogels
• Effecten van vernatting in bossen
• Multi-stress in het landelijk gebied. Gecombineerde effecten van nutrienten en bestrijdingsmiddelen op zoetwater ecosystemen
• Bayesian sigmoid shrinkage with improper variance priors and an application to wavelet denoising
• A Markov Chain Monte Carlo version of the genetic algorithm Differential Evolution: Easy Bayesian computing for real parameter spaces
• Bayesian analysis of complex traits in pedigreed plant populations
• Arthropod assemblages are best predicted by plant species composition
• The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation
• Response to comment by Keith Beven on "Equifinality of formal (DREAM) and informal (GLUE) Bayesian approaches in hydrologic modeling?"
• Principal response curves technique for the analysis of multivariate biomonitoring time series
• Predicting sub-Golgi localization of type II membrane proteins
• Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control
• Attractiveness of MM-X traps baited with human or synthetic odor to mosquitoes (Diptera: Culicidae) in the Gambia
• Co-correspondence analysis: A new ordination method to relate two community compositions
• A penalized likelihood method for mapping epistatic quantitative trait loci with one-dimensional genome searches
• Comparing sampling patterns for kriging the spatial mean temporal trend
• Bootstrap confidence intervals for principal response curves
• Interindividual variation in the attractiveness of human odours to the malaria mosquito Anopheles gambiae s. s.
• Application of Stochastic Patch Occupancy Models to Real Metapopulations
• Risk assessment of dietary exposure to pesticides using a Bayesian method
• Predicting macro-fauna community types from environmental variables by means of support vector machines
• Changes in large-scale patterns of plant biodiversity predicted from environmental economic scenarios
• Bayesian model-based cluster analysis for predicting macrofaunal communities
• Statistical analysis of sediment toxicity by additive monotone regression splines
• Discussion on the meeting on 'statistical modelling and analysis of genetic data'
• Relationship between epiphytic lichens, trace elements and gaseous atmospheric pollutants
• Genetic algorithms and Markov Chain Monte Carlo: Differential Evolution Markov Chain makes Bayesian computing easy
• Genetic algorithms and Markov Chain Monte Carlo: Differential Evolution Markov Chain makes Bayesian computing easy (revised)
• Dutch Sedge Warblers Acrocephalus schoenobaenus and West-African rainfall: Empirical data and simulation modelling show low population resilience in fragmented marshlands
• Ectomycorrhizal sporocarp occurrence as affected by manipulation of litter and humus layers in scots pine stands of different age
• The effects of car traffic on breeding bird populations in woodland. III.Reduction of density in relation to the proximity of main roads
• Canonical correspondence analysis and related multivariate methods in aquatic ecology
• Weighted averaging partial least squares regression (WA-PLS): an improved method for reconstructing environmental variables from species assemblages
• WACALIB version 3.3 - a computer program to reconstruct environmental variables from fossil assemblages by weighted averaging and to derive sample-specific errors of prediction
• Discussion to 'Predicting multivariate responses in multiple linear regression' by L. Breiman & J.H. Friedman
• Randomization and bootstrap tests in factorial experiments: Does analysis follow from design
• Weighted Averaging Partial Least Squares regression (WA-PLS): definition and comparison with other methods for species-environment calibration
• Statistische analyse van de toxiciteit van contaminanten in rivierbodems
• The incidence function approach to modeling of metapopulation dynamics
• Review of 'Biplots' by Gower J.C. & D.J. Hand (1996) Chapman & Hall, London
• Regression
• On inferring past environmental change from species composition data by nonlinear reduced-rank models
• A generalized discriminant for sexing fulmarine petrels from external measurements
• Cp and prediction with many regressors: Comments on Mallows (1995)
• Calibration
• On deducing time parameters from spatial patterns: the (auto)logistic model in landscape ecological processes
• Data analysis in community and landscape ecology. 2nd Edition.
• Monitoring of epiphytic lichens in The Netherlands (1977-1990)
• Prediction error in partial least squares (PLS) regression: a critique on the deviation used in The Unscrambler
• Analysis of wildlife monitoring data using GENSTAT
• Contribution to the discussion
• CANOCO Reference Manual and User's Guide to Canoco for Windows: Software for Canonical Community Ordination (Version 4)
• Ordination of responses to toxic stress in experimental ecosystems
• Analysis of monitoring data with many missing values: which method?
• Ordination
• The location of hedgehog traffic victims in relation to landscape features
• Biplots in Reduced-Rank Regression
• Short communication comments on the PLS kernel algorithm
• Stoomlokomotief met TGV-rijtuig op het goede spoor; TGV koploper besteld
• De potentiële natuurwaarde van de EHS; natuurwaardering op basis van abiotische omstandigheden; het Natuur Technisch Model
• Effecten van ingrepen in het waterbeheer op aquatische levensgemeenschappen; cenotypenbenadering, fase 1: ontwikkeling van het prototype
• Het voorkomen van doodgereden egels in relatie tot de samenstelling van het landschap
• Multivariate technieken voor de analyse van toxische stress op levensgemeenschappen in experimentele ecosystemen
• Boekbespreking: Devillers, J. and Karcher, W. de, Applied multivariate analysis in SAR and environmental studies. Kluwer, Dordrecht, 1991, 530 p., ISBN 0792312902
• De Nederlandse natuur in 2020: schatting van de potentiële natuurwaarde in drie scenario's
• Toward ecologically scaled landscape indices
• Incidence function modelling and conservation of the tree frog Hyla arborea in the Netherlands
• Undergrowth as a biomonitor for deposition of nitrogen and acidity in pine forest
• Ranking of epiphytic lichen sensitivity to air pollution using survey data: A comparison of indicator scales
• Principal response curves: Analysis of time-dependent multivariate responses of biological community to stress
• The objective function of partial least squares regression
• Multivariate analysis of stress in experimental ecosystems by principal response curves and similarity analysis
• Effects of atmospheric NH3 on epiphytic lichens in the Netherlands: The pitfalls of biological monitoring
• Matching species traits to environmental variables: A new three-table ordination method
• Non-linear methods for multivariate statistical calibration and their use in palaeoecology: a comparison of inverse (k-nearest neighbours, partial least squares and weighted averaging partial least squares) and classical approaches
• On the statistical analysis of vegetation change: A wetland affected by water extraction and soil acidification
• Canonical community ordination. Part I: basic theory and linear methods
• An experimental manipulation of oligochaete communities in mesocosms treated with chlorpyrifos or nutrient additions: multivariate analyses with Monte Carlo permutation tests
• The analysis of vegetation-environment relationships by canonical correspondence analysis
• Inferring pH from diatoms: a comparison of old and new calibration methods
• Design-based versus model-based sampling strategies: Comment on R. J. Barnes' "bounding the required sample size for geologic site characterization"
• Model-free estimation from spatial samples: A reappraisal of classical sampling theory
• The effect of isolation on the number of woodland birds in small woods in the Netherlands.
• Air pollution as a possible cause for the decline of some phanerogamic species in The Netherlands
• Principal components biplots and alpha and beta diversity.
• CANOCO - a FORTRAN program for canonical community ordination by [partial] [etrended] [canonical] correspondence analysis, principal components analysis and redundancy analysis (version 2.1)
• Weighted averaging of species indicator values: Its efficiency in environmental calibration
• Ecological amplitudes of plant species and the internal consistency of Ellenberg's indicator values for moisture
• The impact of acidification on diatoms and chemistry of Dutch moorland pools
• Update notes: Canoco, version 3.10
• Permutation versus bootstrap significance tests in multiple regression and anova
• Interpreting a hierarchical classification with simple discriminant functions: an ecological example
• Partial canonical correspondence analysis
• Multidimensional scaling and regression
• Point sampling of binary mosaics in ecology
• Data analysis in community and landscape ecology
• Correspondence Analysis of Incidence and Abundance Data:Properties in Terms of a Unimodal Response Model
• Landscape change as a possible cause of the badger Meles meles L. decline in The Netherlands
• Canoco : an extension of DECORANA to analyze species-environment relationships
• Distribution of three nymphaeid macrophytes (Nymphaea alba L., Nuphar lutea (L.) Sm. and Nymphoides peltata (Gmel.) O. Kuntze) in relation to alkalinity and uptake of inorganic carbon
• CANOCO - an extension of DECORANA to analyze species-environment relationships
• CANOCO-an extension of DECORANA to analyze species-environment relationships
• Interpreting canonical correlation analysis through biplots of structure correlations and weights
• Diatoms and pH reconstruction
• Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis.
• A Theory of Gradient Analysis
• Weighted averaging, logistic regression and the Gaussian response model
• Impact of acidification on diatoms and chemistry of Dutch moorland pools