Estimating phylogenetic trees with phangornUpdated 4 days ago

Klaus Schliep, Iris Bardel-Kahr

Rendered from Trees.Rmd in phangorn 2.12.1.1.
corHMM Dredge: Automatic model discoveryUpdated 1 months ago

James D. Boyko

Rendered from corHMMDredge.Rmd in corHMM 2.10.
Running GeoHiSSEUpdated 1 months ago

Daniel Caetano and Jeremy M. Beaulieu

Rendered from GeoHiSSE-vignette.Rmd in hisse 2.1.13.
Type I errors, Model rejection, & HiSSE vs. FiSSEUpdated 1 months ago

Jeremy M. Beaulieu & Brian C. O'Meara

Rendered from hisse-fisse-type1-vignette.Rmd in hisse 2.1.13.
About the quartet distanceUpdated 2 months ago

Martin R. Smith

Rendered from Quartet-Distance.Rmd in Quartet 1.2.7.
Getting started with QuartetUpdated 2 months ago

Martin R. Smith

Rendered from Using-Quartet.Rmd in Quartet 1.2.7.
Ancestral Sequence ReconstructionUpdated 2 months ago

Klaus Schliep

Rendered from Ancestral.Rmd in phangorn 2.12.1.1.
dietr TutorialUpdated 3 months ago

Samuel R. Borstein

Rendered from dietr-vignette.Rmd in dietr 1.1.6.
New additions as of OUwie 2.1Updated 4 months ago

Jeremy M. Beaulieu and Brian C. O'Meara

Rendered from OUwie_2.1_adds.Rmd in OUwie 2.13.
corHMM 2.1: Generalized hidden Markov modelsUpdated 4 months ago

James D. Boyko and Jeremy M. Beaulieu

Rendered from corHMMv2.1-vignette.Rmd in corHMM 2.10.
Calculate tree similarity with 'TreeDist'Updated 4 months ago

Martin R. Smith

Rendered from Using-TreeDist.Rmd in TreeDist 2.9.1.
Contextualizing tree distancesUpdated 4 months ago

Martin R. Smith

Rendered from using-distances.Rmd in TreeDist 2.9.1.
RRphyloUpdated 4 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from RRphylo.Rmd in RRphylo 2.8.1.
Searching for morphological convergenceUpdated 4 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from search.conv.Rmd in RRphylo 2.8.1.
Searching for rate shiftsUpdated 4 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from search.shift.Rmd in RRphylo 2.8.1.
Searching for temporal trends in phenotypes or ratesUpdated 4 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from search.trend.Rmd in RRphylo 2.8.1.
Phylogenetic tree manipulationUpdated 4 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from Tree-Manipulation.Rmd in RRphylo 2.8.1.
Testing RRphylo methods overfitUpdated 4 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from overfitRR.Rmd in RRphylo 2.8.1.
Plotting toolsUpdated 4 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from Plotting-tools.Rmd in RRphylo 2.8.1.
Creating alternative phylogenetic hypotheses from a starting treeUpdated 4 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from swapONE.Rmd in RRphylo 2.8.1.
Tree space analysisUpdated 6 months ago

Martin R. Smith

Rendered from treespace.Rmd in TreeDist 2.9.1.
Extending the Robinson-Foulds metricUpdated 6 months ago

Martin R. Smith

Rendered from Robinson-Foulds.Rmd in TreeDist 2.9.1.
Using RRPPUpdated 6 months ago

Michael Collyer

Rendered from Using.RRPP.Rmd in RRPP 2.0.4.
Basics of paleoTSUpdated 7 months ago

Gene Hunt

Rendered from paleoTS_basics.Rmd in paleoTS 0.6.2.
ANOVA versus MANOVA in RRPPUpdated 7 months ago

Michael L. Collyer

Rendered from ANOVA.vs.MANOVA.Rmd in RRPP 2.0.4.
MonoPhy TutorialUpdated 8 months ago

Orlando Schwery

Rendered from MonoPhyVignette.Rmd in MonoPhy 1.3.2.
Case study: the true finchesUpdated 8 months ago

Luna L. Sanchez Reyes

Rendered from fringiliidae.Rmd in datelife 0.6.9.
Getting startedUpdated 8 months ago

Luna L. Sanchez Reyes

Rendered from Getting_started_with_datelife.Rmd in datelife 0.6.9.
Making a DateLife queryUpdated 8 months ago

Luna L. Sanchez Reyes

Rendered from make_datelife_query.Rmd in datelife 0.6.9.
Generalized Robinson-Foulds distancesUpdated 8 months ago

Martin R. Smith

Rendered from Generalized-RF.Rmd in TreeDist 2.9.1.
Drawing PhylogeniesUpdated 8 months ago

Emmanuel Paradis

Rendered from DrawingPhylogenies.Rnw in ape 5.8-1.
Introduction to ordination in veganUpdated 9 months ago

Jari Oksanen

Rendered from intro-vegan.Rnw in vegan 2.7-0.
vegan FAQUpdated 9 months ago

Jari Oksanen

Rendered from FAQ-vegan.Rmd in vegan 2.7-0.
Total-evidence dating of carnivores integrating molecular and morphometric dataUpdated 9 months ago

Sandra Álvarez-Carretero and Mario dos Reis

Rendered from Reproduce_Carnivora_analysis.Rmd in mcmc3r 0.5.7.
Random TopologyUpdated 9 months ago

Emmanuel Paradis

Rendered from RandomTopologies.Rnw in ape 5.8-1.
Markov models and transition rate matricesUpdated 9 months ago

Klaus Schliep, Iris Bardel-Kahr

Rendered from AdvancedFeatures.Rmd in phangorn 2.12.1.1.
Treebase TutorialUpdated 10 months ago

Carl Boettiger

Rendered from vignette.Rmd in treebase 0.1.5.
The phylo4 classes and methodsUpdated 11 months ago

Ben Bolker, Peter Cowan, François Michonneau

Rendered from phylobase.Rmd in phylobase 0.8.12.
Detecting rogue taxa in Bayesian posterior tree setsUpdated 1 years ago

Martin R. Smith, Durham University

Rendered from Bayesian.Rmd in Rogue 2.1.6.
adephylo: exploratory analyses for the phylogenetic comparative methodUpdated 1 years ago

Aurélie Siberchicot

Rendered from adephylo.Rnw in adephylo 1.1-16.
Starting secsseUpdated 1 years ago

Thijs Janzen

Rendered from starting_secsse.Rmd in secsse 3.1.0.
Using secsse with complete phylogenies (with extinction)Updated 1 years ago

Pedro Santos Neves

Rendered from complete_tree.Rmd in secsse 3.1.0.
Tree search with Profile parsimonyUpdated 1 years ago

Martin R. Smith

Rendered from profile.Rmd in TreeSearch 1.5.1.9001.
Incorporating Fossils in HiSSE, MuHiSSE, and MiSSEUpdated 1 years ago

Jeremy M. Beaulieu

Rendered from adding_fossils.Rmd in hisse 2.1.13.
The Problem with Clade-specific Sampling FractionsUpdated 1 years ago

Jeremy M. Beaulieu

Rendered from Clade-specific-sampling.Rmd in hisse 2.1.13.
Plotting probabilitiesUpdated 1 years ago

Thijs Janzen

Rendered from plotting_states.Rmd in secsse 3.1.0.
Simulating with secsseUpdated 1 years ago

Thijs Janzen

Rendered from sim_with_secsse.Rmd in secsse 3.1.0.
Evolutionary Rates & Selection Mode (Mr.Bayes)Updated 1 years ago

Tiago Simoes

Rendered from rates-selection_MrBayes.Rmd in EvoPhylo 0.3.3.
Getting started: Exploring tree spaceUpdated 1 years ago

Martin R. Smith

Rendered from tree-space.Rmd in TreeSearch 1.5.1.9001.
Getting started: Installing R and TreeSearchUpdated 1 years ago

Martin R. Smith

Rendered from getting-started.Rmd in TreeSearch 1.5.1.9001.
Getting started: Simple tree searchesUpdated 1 years ago

Martin R. Smith

Rendered from tree-search.Rmd in TreeSearch 1.5.1.9001.
Profile parsimonyUpdated 1 years ago

Martin R. Smith

Rendered from profile-scores.Rmd in TreeSearch 1.5.1.9001.
Tree search with custom optimality criteriaUpdated 1 years ago

Martin R. Smith

Rendered from custom.Rmd in TreeSearch 1.5.1.9001.
entropartUpdated 1 years ago

Eric Marcon

Rendered from entropart.Rmd in entropart 1.6-13.9001.
Loading phylogenetic data into RUpdated 1 years ago

Martin R. Smith [email protected]

Rendered from load-data.Rmd in TreeTools 1.12.0.9001.
Loading phylogenetic trees into RUpdated 1 years ago

Martin R. Smith [email protected]

Rendered from load-trees.Rmd in TreeTools 1.12.0.9001.
phylotaR TutorialUpdated 1 years ago

Shixiang Wang

Rendered from phylotaR.Rmd in phylotaR 1.3.0.
Phylogenetic trees from morphological dataUpdated 2 years ago

Iris Bardel-Kahr, Klaus Schliep

Rendered from Morphological.Rmd in phangorn 2.12.1.1.
Intertwining phylogenetic trees and networks: R Example ScriptUpdated 2 years ago

Klaus Schliep, Alastair Potts, David Morrison and Guido Grimm

Rendered from IntertwiningTreesAndNetworks.Rmd in phangorn 2.12.1.1.
Connecting data to Open Tree treesUpdated 2 years ago

David Winter

Rendered from data_mashups.Rmd in rotl 3.1.0.
How to use rotl?Updated 2 years ago

François Michonneau

Rendered from rotl.Rmd in rotl 3.1.0.
Using the Open Tree synthesis in a comparative analysisUpdated 2 years ago

David Winter

Rendered from meta-analysis.Rmd in rotl 3.1.0.
Analysing landscapes of phylogenetic treesUpdated 2 years ago

Martin R. Smith

Rendered from landscapes.Rmd in TreeDist 2.9.1.
pmc tutorialUpdated 2 years ago

Carl Boettiger

Rendered from pmc_tutorial.Rmd in pmc 1.0.6.
Exploration of landscapes of phylogenetic treesUpdated 2 years ago

Thibaut Jombart, Michelle Kendall

Rendered from introduction.Rmd in treespace 1.1.4.3.
Introduction to dendextendUpdated 2 years ago

Tal Galili

Rendered from dendextend.Rmd in dendextend 1.19.0.
Maximum likelihood by handUpdated 2 years ago

Klaus Schliep, Iris Bardel-Kahr

Rendered from MLbyHand.Rmd in phangorn 2.12.1.1.
Splits and NetworxUpdated 2 years ago

Klaus Schliep

Rendered from Networx.Rmd in phangorn 2.12.1.1.
How to use mvMORPH?Updated 2 years ago

Julien Clavel

Rendered from How_to_use_mvMORPH.Rmd in mvMORPH 1.2.1.
Trees with different leavesUpdated 2 years ago

Martin R. Smith

Rendered from different-leaves.Rmd in TreeDist 2.9.1.
hOUwie User GuideUpdated 2 years ago

.

Rendered from hOUwieStarterGuide.Rmd in OUwie 2.13.
Estimating initial branch lengthsUpdated 2 years ago

Luna L. Sanchez Reyes

Rendered from making_bold_trees.Rmd in datelife 0.6.9.
Evolutionary biology in R (evobiR) tutorialUpdated 2 years ago

Michelle Jonika, Jeffery Demuth, and Richard A. Adams, and Heath Blackmon

Rendered from evolutionary.biology.in.R.Rmd in evobiR 2.1.
Introduction to the phylocomr packageUpdated 2 years ago

Scott Chamberlain and Jeroen Ooms

Rendered from phylocomr.Rmd in phylocomr 0.3.4.
An introduction to the phyloregion packageUpdated 2 years ago

Barnabas H. Daru, Piyal Karunarathne & Klaus Schliep

Rendered from phyloregion-intro.Rmd in phyloregion 1.0.9.
Benchmarking phyloregionUpdated 2 years ago

Barnabas H. Daru, Piyal Karunarathne & Klaus Schliep

Rendered from Benchmark.Rmd in phyloregion 1.0.9.
Fast Evolutionary DistinctivenessUpdated 2 years ago

Barnabas H. Daru

Rendered from ed.Rmd in phyloregion 1.0.9.
Analyzing FBD ParametersUpdated 2 years ago

Tiago Simoes

Rendered from fbd-params.Rmd in EvoPhylo 0.3.3.
Evolutionary Rates & Selection Mode (BEAST2)Updated 2 years ago

Tiago Simoes

Rendered from rates-selection_BEAST2.Rmd in EvoPhylo 0.3.3.
Character PartitioningUpdated 2 years ago

Tiago Simoes

Rendered from char-part.Rmd in EvoPhylo 0.3.3.
Analyzing Trees With OffsetsUpdated 2 years ago

Tiago Simoes

Rendered from offset_handling.Rmd in EvoPhylo 0.3.3.
Theoretical backgroundUpdated 2 years ago

Tiago Simoes

Rendered from data_treatment.Rmd in EvoPhylo 0.3.3.
Comparing splits using information theoryUpdated 2 years ago

Martin R. Smith

Rendered from information.Rmd in TreeDist 2.9.1.
Hierarchical cluster analysis on famous data sets - enhanced with the dendextend packageUpdated 2 years ago

Tal Galili

Rendered from Cluster_Analysis.Rmd in dendextend 1.19.0.
Frequently asked questionsUpdated 2 years ago

Tal Galili

Rendered from FAQ.Rmd in dendextend 1.19.0.
Set custom starting point with 'ratematrix'Updated 3 years ago

Daniel S. Caetano

Rendered from Set_custom_starting_point.Rmd in ratematrix 1.2.4.
beastier demoUpdated 3 years ago

Richèl J.C. Bilderbeek

Rendered from demo.Rmd in beastier 2.5.2.
beautier demoUpdated 3 years ago

Richèl J.C. Bilderbeek

Rendered from demo.Rmd in beautier 2.6.13.
ExamplesUpdated 3 years ago

Richèl J.C. Bilderbeek

Rendered from examples.Rmd in beautier 2.6.13.
Inference ModelsUpdated 3 years ago

Richèl J.C. Bilderbeek

Rendered from inference_models.Rmd in beautier 2.6.13.
Comparing sets of trees from different analysesUpdated 3 years ago

Martin R. Smith

Rendered from compare-treesets.Rmd in TreeDist 2.9.1.
Paleobuddy overviewUpdated 3 years ago

Bruno do Rosario Petrucci

Rendered from overview.Rmd in paleobuddy 1.0.0.9000.
Simulation and InferenceUpdated 3 years ago

George G. Vega Yon

Rendered from example.Rmd in aphylo 0.3-4.
Running MiSSEUpdated 3 years ago

Jeremy M. Beaulieu

Rendered from MiSSE-vignette.Rmd in hisse 2.1.13.
File system navigation in RUpdated 3 years ago

Martin R. Smith [email protected]

Rendered from filesystem-navigation.Rmd in TreeTools 1.12.0.9001.
Additional Functions for Manipulating Data in treedata.tableUpdated 3 years ago

Josef Uyeda, Cristian Roman-Palacios, April Wright

Rendered from D_AdditionalFunctions_treedata.table.Rmd in treedata.table 0.1.1.
Breve Introducción al Paquete treedata.tableUpdated 3 years ago

Cristian Roman-Palacios, April Wright, Josef Uyeda

Rendered from AB_treedata.table_intro_spanish.Rmd in treedata.table 0.1.1.
Getting Started With The treedata.table PackageUpdated 3 years ago

Josef Uyeda, Cristian Roman-Palacios, April Wright

Rendered from AA_treedata.table_intro_english.Rmd in treedata.table 0.1.1.
Partially Matching of Trait Data and Tree(s) in treedata.tableUpdated 3 years ago

Josef Uyeda, Cristian Roman-Palacios, April Wright

Rendered from C_PartialMatching.Rmd in treedata.table 0.1.1.
Working With multiPhylo Objects in treedata.tableUpdated 3 years ago

Josef Uyeda, Cristian Roman-Palacios, April Wright

Rendered from B_multiphylo_treedata.table.Rmd in treedata.table 0.1.1.
Using FishPhyloMaker to build phylogenies for finned-ray fishesUpdated 3 years ago

Gabriel Nakamura

Rendered from FishPhyloMaker_vignette.Rmd in FishPhyloMaker 0.2.0.
How to know which species must be added to phylogeny?Updated 3 years ago

Gabriel Nakamura

Rendered from whichFishAdd_vignette.Rmd in FishPhyloMaker 0.2.0.
How to map species insertions in phylogenetic tree?Updated 3 years ago

Gabriel Nakamura

Rendered from mappingInsertions_vignette.Rmd in FishPhyloMaker 0.2.0.
CALANGO ParametersUpdated 3 years ago

Felipe Campelo

Rendered from CALANGO_Parameters.Rmd in CALANGO 1.0.20.
tidytree: A Tidy Tool for Phylogenetic Tree Data ManipulationUpdated 4 years ago

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered from tidytree.Rmd in tidytree 0.4.6.002.
A newer, faster HiSSE functionUpdated 4 years ago

Jeremy M. Beaulieu

Rendered from hisse-new-vignette.Rmd in hisse 2.1.13.
Running a Multistate HiSSE modelUpdated 4 years ago

Jeremy M. Beaulieu

Rendered from MuHiSSE-vignette.Rmd in hisse 2.1.13.
tracerer versus Tracer demoUpdated 4 years ago

Richèl J.C. Bilderbeek

Rendered from demo.Rmd in tracerer 2.2.3.
Exporting sampled ancestor treesUpdated 4 years ago

Joelle Barido-Sottani

Rendered from SAtree.Rmd in FossilSim 2.4.1.
The FossilSim packageUpdated 4 years ago

Joelle Barido-Sottani, Rachel C. M. Warnock

Rendered from intro.Rmd in FossilSim 2.4.1.
Building supermatrix matrices using the phylotools packageUpdated 4 years ago

Jinlong Zhang

Rendered from phylotools-vignette.Rmd in phylotools 0.2.5.
treespace worked example: Transmission treesUpdated 4 years ago

Michelle Kendall

Rendered from TransmissionTreesVignette.Rmd in treespace 1.1.4.3.
Running the old HiSSE functionUpdated 4 years ago

Jeremy M. Beaulieu

Rendered from hisse-vignette.Rmd in hisse 2.1.13.
phyclust-guideUpdated 4 years ago

Wei-Chen Chen

Rendered from phyclust-guide.Rnw in phyclust 0.1-34.
Moran's IUpdated 4 years ago

Emmanuel Paradis

Rendered from MoranI.Rnw in ape 5.8-1.
treespace worked example: Dengue treesUpdated 4 years ago

Michelle Kendall, Thibaut Jombart

Rendered from DengueVignette.Rmd in treespace 1.1.4.3.
Comparing trees by tip label categoriesUpdated 4 years ago

Michelle Kendall

Rendered from tipCategories.Rmd in treespace 1.1.4.3.
AnnotationBustR TutorialUpdated 4 years ago

Samuel R. Borstein

Rendered from AnnotationBustR-vignette.Rmd in AnnotationBustR 1.3.0.
Using TBRDistUpdated 4 years ago

Martin R. Smith

Rendered from TBRDist.Rmd in TBRDist 1.0.2.
Quick IntroductionUpdated 4 years ago

Tal Galili

Rendered from Quick_Introduction.Rmd in dendextend 1.19.0.
Analyzing Trait Evolution with Approximate Bayesian Computation in TreEvoUpdated 4 years ago

David W. Bapst

Rendered from treevo_ABC_vignette.Rmd in TreEvo 0.22.1.
A step-by-step overview of 3D digitization proceduresUpdated 5 years ago

Antigoni Kaliontzopoulou

Rendered from geomorph.digitize3D.Rmd in geomorph 4.0.9.
phrapl_vignetteUpdated 5 years ago

Nathan Jackson

Rendered from phrapl_vignette.Rmd in phrapl 0.6.5.
Introduction to using the 'ratematrix' packageUpdated 5 years ago

Daniel S. Caetano

Rendered from Intro_on_the_package.Rmd in ratematrix 1.2.4.
A Brief Introduction to RNeXMLUpdated 5 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from intro.Rmd in RNeXML 2.4.11.
Extending NeXML: an example based on simmapUpdated 5 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from simmap.Rmd in RNeXML 2.4.11.
SPARQL with RNeXMLUpdated 5 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from sparql.Rmd in RNeXML 2.4.11.
Handling Metadata in RNeXMLUpdated 5 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from metadata.Rmd in RNeXML 2.4.11.
The nexml S4 ObjectUpdated 5 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from S4.Rmd in RNeXML 2.4.11.
Molecular Clock Dating of Influenza H3N2Updated 5 years ago

Erik Volz

Rendered from h3n2.Rmd in treedater 0.5.3.
sensiPhy: R-package for sensitivity analysis in phylogenetic comparative methods.Updated 5 years ago

Gustavo Paterno, Caterina Penone, Gijsbert Werner

Rendered from sensiPhy_vignette.Rmd in sensiPhy 0.8.5.
Simulating trees from the fossilized birth-death processUpdated 5 years ago

Walker Pett

Rendered from simfbd.Rmd in FossilSim 2.4.1.
Using prior distributions with 'ratematrix'Updated 6 years ago

Daniel S. Caetano

Rendered from Making_prior_on_ratematrix.Rmd in ratematrix 1.2.4.
Data and analysis in picanteUpdated 6 years ago

Steven W. Kembel

Rendered from picante-intro.Rnw in picante 1.8.3.
The 'aphid' package for analysis with profile hidden Markov modelsUpdated 6 years ago

Shaun Wilkinson

Rendered from aphid-vignette.Rmd in aphid 1.3.3.9000.
Package overviewUpdated 6 years ago

Francois Keck

Rendered from Basics.Rmd in phylosignal 1.3.1.
Plotting functionsUpdated 6 years ago

Francois Keck

Rendered from Demo_plots.Rmd in phylosignal 1.3.1.
Simulating fossilsUpdated 6 years ago

Rachel C. M. Warnock

Rendered from fossils.Rmd in FossilSim 2.4.1.
Simulating taxonomyUpdated 6 years ago

Joelle Barido-Sottani, Rachel C. M. Warnock

Rendered from taxonomy.Rmd in FossilSim 2.4.1.
Converting from and to paleotree formatUpdated 6 years ago

Joelle Barido-Sottani

Rendered from paleotree.Rmd in FossilSim 2.4.1.
phylogram: an R package for phylogenetic analysis with dendrogramsUpdated 6 years ago

Shaun P. Wilkinson ^1,2^ and Simon K. Davy ^1^

Rendered from phylogram-vignette.Rmd in phylogram 2.1.0.9000.
Diversity analysis in veganUpdated 7 years ago

Jari Oksanen

Rendered from diversity-vegan.Rnw in vegan 2.7-0.
Advanced Use of PhylocanvasUpdated 7 years ago

zach charlop-powers

Rendered from Advanced_Usage.Rmd in phylocanvas 0.1.3.
Basic Use of PhylocanvasUpdated 7 years ago

Zach Chrlop-Powers

Rendered from Basic_Use.Rmd in phylocanvas 0.1.3.
Design decisions and implementationUpdated 7 years ago

Jari Oksanen

Rendered from decision-vegan.Rnw in vegan 2.7-0.
mvMORPH: an R package for fitting multivariate evolutionary modelsUpdated 8 years ago

Julien Clavel

Rendered from tutorial_mvMORPH.Rmd in mvMORPH 1.2.1.
Partition of VariationUpdated 9 years ago

Jari Oksanen

Rendered from partitioning.Rnw in vegan 2.7-0.