Getting started with QuartetUpdated 13 days ago

Martin R. Smith

Rendered from Using-Quartet.Rmd in Quartet 1.2.7.
File system navigation in RUpdated 19 days ago

Martin R. Smith [email protected]

Rendered from filesystem-navigation.Rmd in TreeTools 1.13.0.9000.
Total-evidence dating of carnivores integrating molecular and morphometric dataUpdated 25 days ago

Sandra Álvarez-Carretero and Mario dos Reis

Rendered from Reproduce_Carnivora_analysis.Rmd in mcmc3r 0.5.8.
Estimating phylogenetic trees with phangornUpdated 1 months ago

Klaus Schliep, Iris Bardel-Kahr

Rendered from Trees.Rmd in phangorn 2.12.1.1.
corHMM Dredge: Automatic model discoveryUpdated 3 months ago

James D. Boyko

Rendered from corHMMDredge.Rmd in corHMM 2.10.
Running GeoHiSSEUpdated 3 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 3 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 3 months ago

Martin R. Smith

Rendered from Quartet-Distance.Rmd in Quartet 1.2.7.
Ancestral Sequence ReconstructionUpdated 3 months ago

Klaus Schliep

Rendered from Ancestral.Rmd in phangorn 2.12.1.1.
dietr TutorialUpdated 5 months ago

Samuel R. Borstein

Rendered from dietr-vignette.Rmd in dietr 1.1.6-1.
New additions as of OUwie 2.1Updated 5 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 5 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 5 months ago

Martin R. Smith

Rendered from Using-TreeDist.Rmd in TreeDist 2.9.2.
Contextualizing tree distancesUpdated 5 months ago

Martin R. Smith

Rendered from using-distances.Rmd in TreeDist 2.9.2.
RRphyloUpdated 6 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from RRphylo.Rmd in RRphylo 2.8.1.
Searching for morphological convergenceUpdated 6 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from search.conv.Rmd in RRphylo 2.8.1.
Searching for rate shiftsUpdated 6 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 6 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from search.trend.Rmd in RRphylo 2.8.1.
Phylogenetic tree manipulationUpdated 6 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from Tree-Manipulation.Rmd in RRphylo 2.8.1.
Testing RRphylo methods overfitUpdated 6 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from overfitRR.Rmd in RRphylo 2.8.1.
Plotting toolsUpdated 6 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 6 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from swapONE.Rmd in RRphylo 2.8.1.
Tree space analysisUpdated 7 months ago

Martin R. Smith

Rendered from treespace.Rmd in TreeDist 2.9.2.
Extending the Robinson-Foulds metricUpdated 7 months ago

Martin R. Smith

Rendered from Robinson-Foulds.Rmd in TreeDist 2.9.2.
Using RRPPUpdated 8 months ago

Michael Collyer

Rendered from Using.RRPP.Rmd in RRPP 2.0.4.
Basics of paleoTSUpdated 8 months ago

Gene Hunt

Rendered from paleoTS_basics.Rmd in paleoTS 0.6.2.
ANOVA versus MANOVA in RRPPUpdated 8 months ago

Michael L. Collyer

Rendered from ANOVA.vs.MANOVA.Rmd in RRPP 2.0.4.
MonoPhy TutorialUpdated 9 months ago

Orlando Schwery

Rendered from MonoPhyVignette.Rmd in MonoPhy 1.3.2.
Generalized Robinson-Foulds distancesUpdated 9 months ago

Martin R. Smith

Rendered from Generalized-RF.Rmd in TreeDist 2.9.2.
Drawing PhylogeniesUpdated 10 months ago

Emmanuel Paradis

Rendered from DrawingPhylogenies.Rnw in ape 5.8-1.
Introduction to ordination in veganUpdated 10 months ago

Jari Oksanen

Rendered from intro-vegan.Rnw in vegan 2.7-0.
vegan FAQUpdated 10 months ago

Jari Oksanen

Rendered from FAQ-vegan.Rmd in vegan 2.7-0.
Random TopologyUpdated 10 months ago

Emmanuel Paradis

Rendered from RandomTopologies.Rnw in ape 5.8-1.
Markov models and transition rate matricesUpdated 10 months ago

Klaus Schliep, Iris Bardel-Kahr

Rendered from AdvancedFeatures.Rmd in phangorn 2.12.1.1.
Treebase TutorialUpdated 12 months ago

Carl Boettiger

Rendered from vignette.Rmd in treebase 0.1.5.
The phylo4 classes and methodsUpdated 1 years 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 1.1-17.
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 1.5.1.9002.
Incorporating Fossils in HiSSE, MuHiSSE, and MiSSEUpdated 2 years ago

Jeremy M. Beaulieu

Rendered from adding_fossils.Rmd in hisse 2.1.13.
The Problem with Clade-specific Sampling FractionsUpdated 2 years ago

Jeremy M. Beaulieu

Rendered from Clade-specific-sampling.Rmd in hisse 2.1.13.
Plotting probabilitiesUpdated 2 years ago

Thijs Janzen

Rendered from plotting_states.Rmd in secsse 3.1.0.
Simulating with secsseUpdated 2 years ago

Thijs Janzen

Rendered from sim_with_secsse.Rmd in secsse 3.1.0.
Evolutionary Rates & Selection Mode (Mr.Bayes)Updated 2 years ago

Tiago Simoes

Rendered from rates-selection_MrBayes.Rmd in EvoPhylo 0.3.3.
Getting started: Exploring tree spaceUpdated 2 years ago

Martin R. Smith

Rendered from tree-space.Rmd in TreeSearch 1.5.1.9002.
Getting started: Installing R and TreeSearchUpdated 2 years ago

Martin R. Smith

Rendered from getting-started.Rmd in TreeSearch 1.5.1.9002.
Getting started: Simple tree searchesUpdated 2 years ago

Martin R. Smith

Rendered from tree-search.Rmd in TreeSearch 1.5.1.9002.
Profile parsimonyUpdated 2 years ago

Martin R. Smith

Rendered from profile-scores.Rmd in TreeSearch 1.5.1.9002.
Tree search with custom optimality criteriaUpdated 2 years ago

Martin R. Smith

Rendered from custom.Rmd in TreeSearch 1.5.1.9002.
entropartUpdated 2 years ago

Eric Marcon

Rendered from entropart.Rmd in entropart 1.6-13.9001.
Loading phylogenetic data into RUpdated 2 years ago

Martin R. Smith [email protected]

Rendered from load-data.Rmd in TreeTools 1.13.0.9000.
Loading phylogenetic trees into RUpdated 2 years ago

Martin R. Smith [email protected]

Rendered from load-trees.Rmd in TreeTools 1.13.0.9000.
phylotaR TutorialUpdated 2 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 2.9.2.
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 1.19.1.
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 2.9.2.
hOUwie User GuideUpdated 2 years ago

.

Rendered from hOUwieStarterGuide.Rmd in OUwie 2.13.
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 2.9.2.
Hierarchical cluster analysis on famous data sets - enhanced with the dendextend packageUpdated 3 years ago

Tal Galili

Rendered from Cluster_Analysis.Rmd in dendextend 1.19.1.
Frequently asked questionsUpdated 3 years ago

Tal Galili

Rendered from FAQ.Rmd in dendextend 1.19.1.
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 2.9.2.
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.
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 1.19.1.
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 4.0.10.
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 7 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.