Cajo J. F. ter Braak

ORCID: 0000-0002-0414-8745
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About
Contact & Profiles
Research Areas
  • Ecology and Vegetation Dynamics Studies
  • Species Distribution and Climate Change
  • Botany and Plant Ecology Studies
  • Plant and animal studies
  • Genetic and phenotypic traits in livestock
  • Advanced Statistical Methods and Models
  • Genetic Mapping and Diversity in Plants and Animals
  • Bioinformatics and Genomic Networks
  • Geology and Paleoclimatology Research
  • Peatlands and Wetlands Ecology
  • Lichen and fungal ecology
  • Sensory Analysis and Statistical Methods
  • Environmental Toxicology and Ecotoxicology
  • Gene expression and cancer classification
  • Geochemistry and Geologic Mapping
  • Spectroscopy and Chemometric Analyses
  • Environmental Conservation and Management
  • Soil Geostatistics and Mapping
  • Forest Ecology and Biodiversity Studies
  • Statistical Methods and Bayesian Inference
  • Wildlife Ecology and Conservation
  • Hydrology and Watershed Management Studies
  • Animal Nutrition and Physiology
  • Statistical Methods and Applications
  • Hydrology and Sediment Transport Processes

Wageningen University & Research
2016-2025

Zimmer Biomet (United States)
2025

Water Authority of Jordan
2023

John Wiley & Sons (United States)
2018

Ecological Society of America
2018

Zimmer Biomet (Netherlands)
2002-2011

Centre for BioSystems Genomics
2010

Imperial College London
2002

Vrije Universiteit Amsterdam
2002

University of Amsterdam
2002

Palaeolimnological diatom data comprise counts of many species expressed as percentages for each sample. Reconstruction past lake-water pH from such involves two steps; (i) regression, where responses modern abundances to are modelled and (ii) calibration the used infer assemblages preserved in lake sediments. In view highly multivariate nature data, strongly nonlinear response diatoms pH, abundance zero values a compromise between ecological realism computational feasability is essential....

10.1098/rstb.1990.0062 article EN Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1990-03-12

Article Accelerating Markov Chain Monte Carlo Simulation by Differential Evolution with Self-Adaptive Randomized Subspace Sampling was published on March 1, 2009 in the journal International Journal of Nonlinear Sciences and Numerical (volume 10, issue 3).

10.1515/ijnsns.2009.10.3.273 article EN International Journal of Nonlinear Sciences and Numerical Simulation 2009-01-01

Several permutation strategies are often possible for tests of individual terms in analysis-of-variance (ANOVA) designs. These include restricted permutations, whole groups units, some form residuals or combination these. It is unclear, especially complex designs involving random factors, mixed models nested hierarchies, just which strategy should be used any particular test. The purpose this paper two-fold: (i) we provide a guideline constructing an exact strategy, where possible, term...

10.1080/00949650215733 article EN Journal of Statistical Computation and Simulation 2003-01-01
Predrag Radivojac Wyatt T. Clark Tal Oron Alexandra M. Schnoes Tobias Wittkop and 95 more Artem Sokolov Kiley Graim Christopher S. Funk Karin Verspoor Asa Ben‐Hur Gaurav Pandey Jeffrey M. Yunes Ameet Talwalkar Susanna Repo Michael L Souza Damiano Piovesan Rita Casadio Zheng Wang Jianlin Cheng Hai Fang Julian Gough Patrik Koskinen Petri Törönen Jussi Nokso-Koivisto Liisa Holm Domenico Cozzetto Daniel Buchan Kevin Bryson David T. Jones Bhakti Limaye Harshal Inamdar Avik Datta Sunitha K Manjari Rajendra Joshi Meghana Chitale Daisuke Kihara Andreas Martin Lisewski Serkan Erdin Eric Venner Olivier Lichtarge Robert Rentzsch Haixuan Yang Alfonso E. Romero Prajwal Bhat Alberto Paccanaro Tobias Hamp Rebecca Kaßner Stefan Seemayer Esmeralda Vicedo Christian Schaefer Dominik Achten Florian Auer Ariane C. Boehm Tatjana Braun Maximilian Hecht B. Mark Heron Peter Hönigschmid Thomas A. Hopf Stefanie Kaufmann Michael Kiening Denis Krompaß Cedric Landerer Yannick Mahlich Manfred Roos Jari Björne Tapio Salakoski Andrew Wong Hagit Shatkay Fanny Gatzmann I. Sommer Mark N. Wass Michael J.E. Sternberg Nives Škunca Fran Supek Matko Bošnjak Panče Panov Sašo Džeroski Tomislav Šmuc Yiannis Kourmpetis Aalt D. J. van Dijk Cajo J. F. ter Braak Yuanpeng Zhou Qingtian Gong Xinran Dong Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Barbara Di Camillo Stefano Toppo Liang Lan Nemanja Djuric Yuhong Guo Slobodan Vučetić Amos Bairoch Michal Linial Patricia C. Babbitt Steven E. Brenner Christine Orengo Burkhard Rost

Automated annotation of protein function is challenging. As the number sequenced genomes rapidly grows, overwhelming majority products can only be annotated computationally. If computational predictions are to relied upon, it crucial that accuracy these methods high. Here we report results from first large-scale community-based critical assessment (CAFA) experiment. Fifty-four representing state art for prediction were evaluated on a target set 866 proteins 11 organisms. Two findings stand...

10.1038/nmeth.2340 article EN cc-by-nc-sa Nature Methods 2013-01-27

There is increasing consensus in the hydrologic literature that an appropriate framework for streamflow forecasting and simulation should include explicit recognition of forcing parameter model structural error. This paper presents a novel Markov chain Monte Carlo (MCMC) sampler, entitled differential evolution adaptive Metropolis (DREAM), especially designed to efficiently estimate posterior probability density function parameters complex, high‐dimensional sampling problems. MCMC scheme...

10.1029/2007wr006720 article EN Water Resources Research 2008-12-01

Abstract In this paper a novel multivariate method is proposed for the analysis of community response data from designed experiments repeatedly sampled in time. The long-term effects insecticide chlorpyrifos on invertebrate and dissolved oxygen (DO)–pH–alkalinity–conductivity syndrome, outdoor experimental ditches, are used as example data. new method, which we have named principal curve (PRC), based redundancy (RDA), adjusted overall changes over time, observed control test systems. This...

10.1002/etc.5620180207 article EN Environmental Toxicology and Chemistry 1999-02-01

Bibliographical notes 26 2.9 Exercise 2.10 Solution to the exercise 27 /f 5 .~\Ordination 91 < \5Jr--/ Introduction §-l-J) Aim and usage \T^Z Data approximation response models in ordination 93 5.1.3Outline of Chapter 5.2 Correspondence analysis (CA) detrended correspondence (DCA) 95 5.2.1 From weighted averaging 5.2.2 Two-way algorithm 5.2.3 Diagonal structures: properties faults 103 5,2.4/Detrended 5727$/ Joint plot species sites 108 5.2.6 Block structures sensitivity rare 109 5.2.7...

10.2307/2531665 article EN Biometrics 1990-03-01

Canonical community ordination comprises a collection of methods that relate species assemblages to their environment, in both observational studies and designed experiments. differs from sensu stricto environment data are analyzed simultaneously. Part I reviews the theory non-mathematical way with emphasis on new insights for interpretation diagrams. The depends method used create diagram. After basic theory, is focused diagrams linear canonical ordination, particular principal component...

10.1080/11956860.1994.11682237 article EN Ecoscience 1994-01-01
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