r-sig-phylo  

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• [R-sig-phylo] rr2 does gls() {nlme} Anthony R. Ives
• [R-sig-phylo] treshML on a 200k taxa, 30 character matrix Alexander Blanke
• [R-sig-phylo] patristic distance doubts and meanings Bruno Garcia Luize
  • Re: [R-sig-phylo] patristic distance doubts and meanings Liam Revell
  • Re: [R-sig-phylo] patristic distance doubts and meanings Bruno Garcia Luize
  • Re: [R-sig-phylo] patristic distance doubts and meanings Eliot Miller
  • Re: [R-sig-phylo] patristic distance doubts and meanings Brian O'Meara
  • Re: [R-sig-phylo] patristic distance doubts and meanings Bruno Garcia Luize
• [R-sig-phylo] Importing CD hit data to R Gilles Benjamin Leduc
  • [R-sig-phylo] Mesquite->ape node numbers and/or parsimony ancestral reconstruction Roland Sookias
  • Re: [R-sig-phylo] Mesquite->ape node numbers and/or parsimony ancestral reconstruction Liam Revell
  • Re: [R-sig-phylo] Mesquite->ape node numbers and/or parsimony ancestral reconstruction Roland Sookias
  • Re: [R-sig-phylo] Mesquite->ape node numbers and/or parsimony ancestral reconstruction Liam Revell
  • Re: [R-sig-phylo] Mesquite->ape node numbers and/or parsimony ancestral reconstruction Brian O'Meara
• [R-sig-phylo] Problem date consensus phylogeny Alina van dijk
  • Re: [R-sig-phylo] Problem date consensus phylogeny Joseph Brown
  • Re: [R-sig-phylo] Problem date consensus phylogeny Emmanuel Paradis
  • Re: [R-sig-phylo] Problem date consensus phylogeny Alina van dijk
  • Re: [R-sig-phylo] Problem date consensus phylogeny Emmanuel Paradis
  • Re: [R-sig-phylo] Problem date consensus phylogeny Liam Revell
  • Re: [R-sig-phylo] Problem date consensus phylogeny Alina van dijk
  • Re: [R-sig-phylo] Problem date consensus phylogeny roee maor
• [R-sig-phylo] exponential time with write.tree Jérémie Bardin
  • Re: [R-sig-phylo] exponential time with write.tree Emmanuel Paradis
  • Re: [R-sig-phylo] exponential time with write.tree Jérémie Bardin
• [R-sig-phylo] Link between Mahalanobis distance and PGLS Guillaume LOUVEL
  • Re: [R-sig-phylo] Link between Mahalanobis distance and PGLS Joe Felsenstein
• [R-sig-phylo] Logarithmic Scales for Plotting Dated Phyogenies (e.g. Log of Time Axis?) David Bapst
  • Re: [R-sig-phylo] Logarithmic Scales for Plotting Dated Phyogenies (e.g. Log of Time Axis?) Bjørn Tore Kopperud
  • Re: [R-sig-phylo] Logarithmic Scales for Plotting Dated Phyogenies (e.g. Log of Time Axis?) Emmanuel Paradis
• Re: [R-sig-phylo] make.simmap -- strange posterior probability for root using ARD model? Liam Revell
• [R-sig-phylo] mixing trait values from distinct models of evolution to reconstruct null morphospace françois RIGAL
  • Re: [R-sig-phylo] mixing trait values from distinct models of evolution to reconstruct null morphospace David Bapst
• Re: [R-sig-phylo] R-sig-phylo Digest, Vol 131, Issue 1 SMITH, MARTIN R.
• [R-sig-phylo] ape chronos function returning pLL of -1E100 John S Denton
  • Re: [R-sig-phylo] ape chronos function returning pLL of -1E100 John S Denton
  • Re: [R-sig-phylo] ape chronos function returning pLL of -1E100 Emmanuel Paradis
• [R-sig-phylo] OU for non-ultrametric trees Danielle Miller
  • Re: [R-sig-phylo] OU for non-ultrametric trees Brian O'Meara
  • Re: [R-sig-phylo] OU for non-ultrametric trees David Bapst
  • Re: [R-sig-phylo] OU for non-ultrametric trees Danielle Miller
  • Re: [R-sig-phylo] OU for non-ultrametric trees Marguerite Butler
• [R-sig-phylo] PhD projects using phylogenetic comparative methods STREET, SALLY
• [R-sig-phylo] aov.phylo vs phylANOVA Jacob Berv
  • Re: [R-sig-phylo] aov.phylo vs phylANOVA Theodore Garland
  • Re: [R-sig-phylo] aov.phylo vs phylANOVA Liam J. Revell
  • Re: [R-sig-phylo] aov.phylo vs phylANOVA Jacob Berv
  • Re: [R-sig-phylo] aov.phylo vs phylANOVA Jacob Berv
• [R-sig-phylo] Branch lengths in phytools::plot.cophylo Vojtěch Zeisek
  • [R-sig-phylo] Branch lengths in phytools::plot.cophylo Juan Antonio Balbuena
  • Re: [R-sig-phylo] Branch lengths in phytools::plot.cophylo Liam Revell
  • Re: [R-sig-phylo] Branch lengths in phytools::plot.cophylo Vojtěch Zeisek
  • Re: [R-sig-phylo] Branch lengths in phytools::plot.cophylo Vojtěch Zeisek
• [R-sig-phylo] Problem with make.simmap in Phytools Kimberly Lynn Foster
  • Re: [R-sig-phylo] Problem with make.simmap in Phytools Liam J. Revell
• [R-sig-phylo] Extended Majority Consensus Topology (Allcompat Summary) in R? And some observations on ape's consensus() function David Bapst
  • Re: [R-sig-phylo] Extended Majority Consensus Topology (Allcompat Summary) in R? And some observations on ape's consensus() function Joe Felsenstein
  • Re: [R-sig-phylo] Extended Majority Consensus Topology (Allcompat Summary) in R? And some observations on ape's consensus() function Emmanuel Paradis
• [R-sig-phylo] Partitioning of functional beta diversity ' Salatiel Clemente
  • Re: [R-sig-phylo] Partitioning of functional beta diversity françois RIGAL
• [R-sig-phylo] No PCOA Correction Applied but Corrected Eigenvalues Returned? (ape::pcoa) David Bapst
  • Re: [R-sig-phylo] No PCOA Correction Applied but Corrected Eigenvalues Returned? (ape::pcoa) Emmanuel Paradis
  • Re: [R-sig-phylo] No PCOA Correction Applied but Corrected Eigenvalues Returned? (ape::pcoa) David Bapst
  • Re: [R-sig-phylo] No PCOA Correction Applied but Corrected Eigenvalues Returned? (ape::pcoa) Emmanuel Paradis
• [R-sig-phylo] Phylogenetic comparative methods for studying diversification and phenotypic evolution Oliver Hooker
• [R-sig-phylo] Adding species to genera tree as polytomies Liam Kendall
  • Re: [R-sig-phylo] Adding species to genera tree as polytomies William Gearty
  • Re: [R-sig-phylo] Adding species to genera tree as polytomies Liam J. Revell
  • Re: [R-sig-phylo] Adding species to genera tree as polytomies Richard Grenyer
  • Re: [R-sig-phylo] Adding species to genera tree as polytomies Eliot Miller
  • Re: [R-sig-phylo] Adding species to genera tree as polytomies Liam Kendall
• [R-sig-phylo] Book: Mixed and Phylogenetic Models: A Conceptual Introduction to Correlated Data Anthony R. Ives
• [R-sig-phylo] change colors in make.simmap ramirez
  • Re: [R-sig-phylo] change colors in make.simmap Gopal Murali
  • Re: [R-sig-phylo] change colors in make.simmap Liam J. Revell
• [R-sig-phylo] Building phlyogenies from DNA alignments Zhong Huang
  • Re: [R-sig-phylo] Building phlyogenies from DNA alignments Emmanuel Paradis
• [R-sig-phylo] Estimating marginal ancestral states under a non-reversible model of evolution. Jordan Gault
  • Re: [R-sig-phylo] Estimating marginal ancestral states under a non-reversible model of evolution. Joe Felsenstein
  • Re: [R-sig-phylo] Estimating marginal ancestral states under a non-reversible model of evolution. Jordan Gault
• [R-sig-phylo] Issue with SIMMAP on 500 sampled Trees Kimberly Lynn Foster
  • Re: [R-sig-phylo] Issue with SIMMAP on 500 sampled Trees Liam J. Revell
• [R-sig-phylo] PGLS on PCA axes? Max Farrell
• [R-sig-phylo] plot heatmap at nodes Jacob Berv
  • Re: [R-sig-phylo] plot heatmap at nodes Emmanuel Paradis
  • Re: [R-sig-phylo] plot heatmap at nodes Emmanuel Paradis
  • Re: [R-sig-phylo] plot heatmap at nodes Jacob Berv
  • [R-sig-phylo] plot heatmap at nodes Juan Antonio Balbuena
• [R-sig-phylo] understanding variance-covariance matrix Agus Camacho
  • Re: [R-sig-phylo] understanding variance-covariance matrix Brian O'Meara
  • Re: [R-sig-phylo] understanding variance-covariance matrix Emmanuel Paradis
  • Re: [R-sig-phylo] understanding variance-covariance matrix Andrew Hipp
  • Re: [R-sig-phylo] understanding variance-covariance matrix Julien Clavel
  • Re: [R-sig-phylo] understanding variance-covariance matrix Agus Camacho
  • Re: [R-sig-phylo] understanding variance-covariance matrix Theodore Garland
• [R-sig-phylo] Aligning tree tip labels together in ape Carleson, Nick
  • Re: [R-sig-phylo] Aligning tree tip labels together in ape Bjørn Tore Kopperud
  • Re: [R-sig-phylo] Aligning tree tip labels together in ape Carleson, Nick
  • Re: [R-sig-phylo] Aligning tree tip labels together in ape Liam J. Revell
  • Re: [R-sig-phylo] Aligning tree tip labels together in ape Emmanuel Paradis
• [R-sig-phylo] AGY coding Karla Shikev
  • Re: [R-sig-phylo] AGY coding Joseph Brown
  • Re: [R-sig-phylo] AGY coding Karla Shikev
• [R-sig-phylo] Question regarding log likelihood in OUCH package Danielle Miller
  • Re: [R-sig-phylo] Question regarding log likelihood in OUCH package Liam J. Revell
• [R-sig-phylo] Problems with as.phylo.treeshape (library apTreeshape) Matt Simenc
• Re: [R-sig-phylo] R-sig-phylo Digest, Vol 127, Issue 4 roee maor
• [R-sig-phylo] 3-category ordinal probit MCMCglmm model Andrea Soriano
  • Re: [R-sig-phylo] 3-category ordinal probit MCMCglmm model Theodore Garland
• [R-sig-phylo] phylogenetic correction for multiple samples per species along an ecological gradient Nicolay Cunha
  • Re: [R-sig-phylo] phylogenetic correction for multiple samples per species along an ecological gradient Theodore Garland
  • Re: [R-sig-phylo] phylogenetic correction for multiple samples per species along an ecological gradient f . krah
  • Re: [R-sig-phylo] phylogenetic correction for multiple samples per species along an ecological gradient jonnations
  • Re: [R-sig-phylo] phylogenetic correction for multiple samples per species along an ecological gradient Masahito Tsuboi
  • Re: [R-sig-phylo] phylogenetic correction for multiple samples per species along an ecological gradient Nicolay Cunha
• [R-sig-phylo] p-value in pgls.Ives Iara Reinaldo Coriolano
  • [R-sig-phylo] p-value in pgls.Ives Iara Reinaldo Coriolano
  • Re: [R-sig-phylo] p-value in pgls.Ives Liam J. Revell
  • Re: [R-sig-phylo] p-value in pgls.Ives Iara Reinaldo Coriolano
• [R-sig-phylo] Simulating tree from a given tree Miguel.Verdu
  • Re: [R-sig-phylo] Simulating tree from a given tree Eduardo Ascarrunz
  • Re: [R-sig-phylo] Simulating tree from a given tree Liam J. Revell
• [R-sig-phylo] Measuring Phylogenetic Signal Alyson Brokaw
  • Re: [R-sig-phylo] Measuring Phylogenetic Signal Liam J. Revell
  • Re: [R-sig-phylo] Measuring Phylogenetic Signal Theodore Garland
  • Re: [R-sig-phylo] Measuring Phylogenetic Signal Manabu Sakamoto
  • Re: [R-sig-phylo] Measuring Phylogenetic Signal Theodore Garland
  • Re: [R-sig-phylo] Measuring Phylogenetic Signal David Bapst
• [R-sig-phylo] keeping states discrete when plotting HiSSE results Bonnie Blaimer
  • Re: [R-sig-phylo] keeping states discrete when plotting HiSSE results Brian O'Meara
• [R-sig-phylo] Bayou and surface Tree Plots Sandro Sehner
• [R-sig-phylo] ape-package: unknown states in ace analyses? Théo Léger
  • Re: [R-sig-phylo] ape-package: unknown states in ace analyses? Liam J. Revell
  • Re: [R-sig-phylo] ape-package: unknown states in ace analyses? Jacob Berv
  • Re: [R-sig-phylo] ape-package: unknown states in ace analyses? Emmanuel Paradis
  • Re: [R-sig-phylo] ape-package: unknown states in ace analyses? Emmanuel Paradis
  • Re: [R-sig-phylo] ape-package: unknown states in ace analyses? Théo Léger
• [R-sig-phylo] Comparing DIC of phylogenetic and non-phylogenetic GLMM run with MCMC (MCMCglmm) Liam Kendall
  • [R-sig-phylo] Comparing DIC of phylogenetic and non-phylogenetic GLMM run with MCMC (MCMCglmm) jonnations
  • Re: [R-sig-phylo] Comparing DIC of phylogenetic and non-phylogenetic GLMM run with MCMC (MCMCglmm) Jarrod Hadfield
  • Re: [R-sig-phylo] Comparing DIC of phylogenetic and non-phylogenetic GLMM run with MCMC (MCMCglmm) Liam Kendall
• [R-sig-phylo] diversification rates with two traits present simultaneously Elizabeth Christina Miller
  • Re: [R-sig-phylo] diversification rates with two traits present simultaneously William Gearty
  • Re: [R-sig-phylo] diversification rates with two traits present simultaneously Gilles Benjamin Leduc
  • Re: [R-sig-phylo] diversification rates with two traits present simultaneously Brian O'Meara
• [R-sig-phylo] estimate ancestral state with OUwie models Vilela de Moraes e Silva, Bruno
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Diogo B. Provete
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Lucas Jardim
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models David Bapst
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Brian O'Meara
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models John Soghigian
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Simone Blomberg
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Marguerite Butler
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Simone Blomberg
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Thomas F Hansen
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Joe Felsenstein
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Nick Matzke
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models David Bapst
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Jacob Berv
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models David Bapst
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models David Bapst
  • Re: [R-sig-phylo] estimate ancestral state with OUwie models Cecile Ane
• [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package Sebastian Y . Müller
  • Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package Klaus Schliep
  • Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package Sebastian Y . Müller
  • Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package Emmanuel Paradis
• [R-sig-phylo] remove phylogenetic signal from large dataset fran?ois RIGAL
  • Re: [R-sig-phylo] remove phylogenetic signal from large dataset Julien Clavel
  • Re: [R-sig-phylo] remove phylogenetic signal from large dataset françois RIGAL
• [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions Juan Antonio Balbuena
  • Re: [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions Liam J. Revell
  • Re: [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions Liam J. Revell
  • Re: [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions Juan Antonio Balbuena
  • Re: [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions Liam J. Revell
  • Re: [R-sig-phylo] midpoint.root Error in phy$edge[, 2] : incorrect number of dimensions Juan Antonio Balbuena
• [R-sig-phylo] is.binary() says "FALSE" after using multi2di() Pedro Pequeno
  • Re: [R-sig-phylo] is.binary() says "FALSE" after using multi2di() Graham Slater
  • Re: [R-sig-phylo] is.binary() says "FALSE" after using multi2di() Liam J. Revell
  • Re: [R-sig-phylo] is.binary() says "FALSE" after using multi2di() Pedro Pequeno
• [R-sig-phylo] Postdoctoral position in R phylogenetics Liam J. Revell
• [R-sig-phylo] Problem with negative ages in OUwie.boot? Rafael S Marcondes
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Rafael S Marcondes
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Eliot Miller
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? David Bapst
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? David Bapst
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Brian O'Meara
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? David Bapst
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Liam J. Revell
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Theodore Garland
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Liam J. Revell
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Eliot Miller
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Rafael S Marcondes
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? David Bapst
  • Re: [R-sig-phylo] Problem with negative ages in OUwie.boot? Eliot Miller
• [R-sig-phylo] Postdoc in PCM development in the Revell lab Liam J. Revell
• [R-sig-phylo] grafting chronograms onto backbone phylogeny Chris Law
  • Re: [R-sig-phylo] grafting chronograms onto backbone phylogeny Brian O'Meara
  • Re: [R-sig-phylo] grafting chronograms onto backbone phylogeny Liam J. Revell
  • Re: [R-sig-phylo] grafting chronograms onto backbone phylogeny Chris Law
• [R-sig-phylo] Bounded Brownian model Roi Holzman

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