r-sig-phylo  

Messages by Thread

• • Re: [R-sig-phylo] Adding a custom legend underneath a phylo plot with coloured tips Liam J. Revell
  • Re: [R-sig-phylo] Adding a custom legend underneath a phylo plot with coloured tips Gabriel Yedid
  • Re: [R-sig-phylo] Adding a custom legend underneath a phylo plot with coloured tips Liam J. Revell
• [R-sig-phylo] Draw multiple ASR pies on nodes Charles Pouchon
  • Re: [R-sig-phylo] Draw multiple ASR pies on nodes Liam J. Revell
• [R-sig-phylo] Maximize Mean Pairwise Distance (Leonardo R? Jorge) Sh Esmaielbegi
• [R-sig-phylo] Maximize Mean Pairwise Distance Leonardo Ré Jorge
• [R-sig-phylo] Truncate x-axis in phydataplot barplots Marian Schubert
  • Re: [R-sig-phylo] Truncate x-axis in phydataplot barplots Liam Revell
  • Re: [R-sig-phylo] Truncate x-axis in phydataplot barplots Liam J. Revell
  • [R-sig-phylo] ‏‏رد: Truncate x-axis in phydataplot barplots Sami Hussein Rabei
  • Re: [R-sig-phylo] Truncate x-axis in phydataplot barplots Emmanuel Paradis
• Re: [R-sig-phylo] Supertree with Stratigraphic Constraints William Gearty
  • Re: [R-sig-phylo] Supertree with Stratigraphic Constraints David Bapst
  • Re: [R-sig-phylo] Supertree with Stratigraphic Constraints William Gearty
  • Re: [R-sig-phylo] Supertree with Stratigraphic Constraints David Bapst
• [R-sig-phylo] predicting computational needs of a MuSSE analysis? Elizabeth Miller
• [R-sig-phylo] 'FINAL CALL - Phylogentic data analysis using R' Oliver Hooker
• [R-sig-phylo] ape functions to become generic Emmanuel Paradis
  • Re: [R-sig-phylo] ape functions to become generic David Bapst
  • Re: [R-sig-phylo] ape functions to become generic Emmanuel Paradis
  • Re: [R-sig-phylo] ape functions to become generic David Bapst
• [R-sig-phylo] accounting for unknown tip states in ancestral rescontructions using phytools and bayestraits Jesse Delia
• [R-sig-phylo] Error in dis[sppInSample, sppInSample] : subscript out of bounds Jhonny Capichoni Massante
• [R-sig-phylo] evolve discrete characters on non-ultrametric tree? John Denton
  • Re: [R-sig-phylo] evolve discrete characters on non-ultrametric tree? Liam J. Revell
• [R-sig-phylo] phylogenetic signal-Blomberg's K Menzel, Dr. Florian
  • Re: [R-sig-phylo] phylogenetic signal-Blomberg's K Liam J. Revell
• [R-sig-phylo] Phylogenetic signal Sergio Ferreira Cardoso
• [R-sig-phylo] Use of a Phylocom tree for PGLS Oscar Valverde
  • Re: [R-sig-phylo] Use of a Phylocom tree for PGLS Liam J. Revell
  • Re: [R-sig-phylo] Use of a Phylocom tree for PGLS Liam J. Revell
  • Re: [R-sig-phylo] Use of a Phylocom tree for PGLS Jacob Berv
  • Re: [R-sig-phylo] Use of a Phylocom tree for PGLS Brian O'Meara
  • Re: [R-sig-phylo] Use of a Phylocom tree for PGLS Oscar Valverde
• [R-sig-phylo] mulRF distance Ondřej Mikula
  • Re: [R-sig-phylo] mulRF distance Liam J. Revell
  • [R-sig-phylo] simmap correlation statistics in R? Maria Ghazali
  • Re: [R-sig-phylo] simmap correlation statistics in R? Liam J. Revell
• [R-sig-phylo] Standard errors of theta estimates in OU models Xiaojing Wei
  • Re: [R-sig-phylo] Standard errors of theta estimates in OU models Brian O'Meara
  • Re: [R-sig-phylo] Standard errors of theta estimates in OU models Cecile Ane
  • Re: [R-sig-phylo] Standard errors of theta estimates in OU models Xiaojing Wei
• [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position branchlizard .
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position Hilmar Lapp
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position branchlizard .
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position Liam J. Revell
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position branchlizard .
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position Florian Boucher
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position branchlizard .
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position Florian Boucher
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position Liam J. Revell
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position branchlizard .
  • Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position branchlizard .
• [R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations Juan Antonio Balbuena
  • Re: [R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations Liam J. Revell
  • Re: [R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations Juan Antonio Balbuena
• [R-sig-phylo] Course Phylogenetic Analysis using R, March 6-10, Barcelona (Spain). Soledad De Esteban-Trivigno
  • [R-sig-phylo] Course Phylogenetic Analysis using R, March 6-10, Barcelona (Spain). Soledad De Esteban-Trivigno
• [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Bhuller, Ravneet
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Joseph W. Brown
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Liam J. Revell
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Bhuller, Ravneet
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Martin Dohrmann
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Thibaut Jombart
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Bhuller, Ravneet
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Klaus Schliep
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Liam Revell
  • Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Bhuller, Ravneet
• [R-sig-phylo] fitDiscrete question - super large likelihood and AIC values Lei Yang
  • Re: [R-sig-phylo] fitDiscrete question - super large likelihood and AIC values Liam J. Revell
  • Re: [R-sig-phylo] fitDiscrete question - super large likelihood and AIC values Lei Yang
  • Re: [R-sig-phylo] fitDiscrete question - super large likelihood and AIC values Liam J. Revell
• [R-sig-phylo] ape - nj, mvr questions Shai Tal
  • Re: [R-sig-phylo] ape - nj, mvr questions Emmanuel Paradis
• [R-sig-phylo] ape: chronos Daniel Lang
  • Re: [R-sig-phylo] ape: chronos Emmanuel Paradis
• [R-sig-phylo] suset DNAbin Kirston Barton
  • Re: [R-sig-phylo] subset DNAbin Andreas Kolter
  • Re: [R-sig-phylo] subset DNAbin Liam J. Revell
  • Re: [R-sig-phylo] suset DNAbin dga...@huskers.unl.edu
  • Re: [R-sig-phylo] suset DNAbin Emmanuel Paradis
• [R-sig-phylo] Query about Phylogenetics in R Bhuller, Ravneet
  • Re: [R-sig-phylo] Query about Phylogenetics in R Vojtěch Zeisek
  • Re: [R-sig-phylo] Query about Phylogenetics in R Brian O'Meara
  • Re: [R-sig-phylo] Query about Phylogenetics in R Liam J. Revell
  • Re: [R-sig-phylo] Query about Phylogenetics in R Bhuller, Ravneet
  • Re: [R-sig-phylo] Query about Phylogenetics in R Bhuller, Ravneet
  • Re: [R-sig-phylo] Query about Phylogenetics in R Vojtěch Zeisek
  • Re: [R-sig-phylo] Query about Phylogenetics in R Liam J. Revell
• [R-sig-phylo] Is there a way to “layer” multiple distance matrices onto a single PCoA plot? Shirley Lang
• [R-sig-phylo] Gathering richness information for Medusa Massana, Kathryn
• [R-sig-phylo] ggtree paper published Yu, Guangchuang
• [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie) Rafael S. Marcondes
  • Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie) Liam J. Revell
  • Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie) Rafael S. Marcondes
  • Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie) Rafael S. Marcondes
  • Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie) Liam J. Revell
  • Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie) Santiago Claramunt
  • Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie) Liam J. Revell
  • Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie) Brian O'Meara
• [R-sig-phylo] Ultrametric tree not recognized Martin Dohrmann
  • Re: [R-sig-phylo] Ultrametric tree not recognized Liam J. Revell
  • Re: [R-sig-phylo] Ultrametric tree not recognized Martin Dohrmann
  • Re: [R-sig-phylo] Ultrametric tree not recognized Joseph W. Brown
  • Re: [R-sig-phylo] Ultrametric tree not recognized Martin Dohrmann
  • Re: [R-sig-phylo] Ultrametric tree not recognized Klaus Schliep
  • Re: [R-sig-phylo] Ultrametric tree not recognized Joseph W. Brown
  • Re: [R-sig-phylo] Ultrametric tree not recognized Martin Dohrmann
  • Re: [R-sig-phylo] Ultrametric tree not recognized Klaus Schliep
  • Re: [R-sig-phylo] Ultrametric tree not recognized Joseph W. Brown
  • Re: [R-sig-phylo] Ultrametric tree not recognized Emmanuel Paradis
  • Re: [R-sig-phylo] Ultrametric tree not recognized Klaus Schliep
  • Re: [R-sig-phylo] Ultrametric tree not recognized Emmanuel Paradis
  • Re: [R-sig-phylo] Ultrametric tree not recognized Klaus Schliep
• [R-sig-phylo] How to contribute? Richel Bilderbeek
  • Re: [R-sig-phylo] How to contribute? Emmanuel Paradis
  • Re: [R-sig-phylo] How to contribute? Richel Bilderbeek
• [R-sig-phylo] BAMM / BAMMtools reliability Dan Rabosky
• [R-sig-phylo] Unable to reorder any phylo object with reorder.phylo Zach Culumber
  • Re: [R-sig-phylo] Unable to reorder any phylo object with reorder.phylo Liam Revell
  • Re: [R-sig-phylo] Unable to reorder any phylo object with reorder.phylo Zach Culumber
• [R-sig-phylo] Na/Nan/Inf error related to alpha value using corMartins in PGLS Church, Samuel
• [R-sig-phylo] 'Phylogenetic data analysis using R - STATS COURSE' Oliver Hooker
• [R-sig-phylo] model assumptions and optimizing lambda when running Pgls across a block of trees Jesse Delia
• [R-sig-phylo] statistical tests for phylogenetic independent contrasts Vivek
  • Re: [R-sig-phylo] statistical tests for phylogenetic independent contrasts Manabu Sakamoto
  • Re: [R-sig-phylo] statistical tests for phylogenetic independent contrasts Joe Felsenstein
• [R-sig-phylo] failure of mvrs (tree construction based on the minimum variance reduction) - workaround? Oliver Ratmann
• [R-sig-phylo] extracting from mrbayes John Denton
  • Re: [R-sig-phylo] extracting from mrbayes David Bapst
• [R-sig-phylo] When we say a trait is phylogenetically labile Chen, Ting-Wen
• [R-sig-phylo] data anlysis Rodrigo Gavira
  • Re: [R-sig-phylo] data anlysis Theodore Garland Jr
• [R-sig-phylo] suppress axes in phenogram() Jacob Berv
  • Re: [R-sig-phylo] suppress axes in phenogram() Liam J. Revell
  • Re: [R-sig-phylo] suppress axes in phenogram() Jacob Berv
  • Re: [R-sig-phylo] suppress axes in phenogram() Jacob Berv
  • Re: [R-sig-phylo] suppress axes in phenogram() GRAHAM JAMES SLATER
  • Re: [R-sig-phylo] suppress axes in phenogram() Jacob Berv
• [R-sig-phylo] Chronos function in ape Marco Fracassetti
  • Re: [R-sig-phylo] Chronos function in ape Brian O'Meara
  • Re: [R-sig-phylo] Chronos function in ape Emmanuel Paradis
• [R-sig-phylo] Bug report for CDF.birth.death.R Niko Yasui
  • Re: [R-sig-phylo] Bug report for CDF.birth.death.R Emmanuel Paradis
• [R-sig-phylo] get divergence date for all tips on a chronogram Chris Buddenhagen
  • Re: [R-sig-phylo] get divergence date for all tips on a chronogram Emmanuel Paradis
• [R-sig-phylo] Adjust position of tip labels in plot.phylo Kamila Naxerova
  • Re: [R-sig-phylo] Adjust position of tip labels in plot.phylo Liam J. Revell
  • Re: [R-sig-phylo] Adjust position of tip labels in plot.phylo Kamila Naxerova
  • Re: [R-sig-phylo] Adjust position of tip labels in plot.phylo Emmanuel Paradis
  • Re: [R-sig-phylo] Adjust position of tip labels in plot.phylo Emmanuel Paradis
  • [R-sig-phylo] Reconstruction of ancestral character state with no organ Wu, Cheng-Chiang
  • Re: [R-sig-phylo] Reconstruction of ancestral character state with no organ Liam J. Revell
  • Re: [R-sig-phylo] Reconstruction of ancestral character state with no organ Wu, Cheng-Chiang
  • Re: [R-sig-phylo] Adjust position of tip labels in plot.phylo Kamila Naxerova
• [R-sig-phylo] chronos ape package does it return confidence intervals too? Chris Buddenhagen
  • Re: [R-sig-phylo] chronos ape package does it return confidence intervals too? Emmanuel Paradis
• [R-sig-phylo] Nantucket phylogeny developeR bootcamp Klaus Schliep
  • [R-sig-phylo] Nantucket phylogeny developeR bootcamp Liam J. Revell
• [R-sig-phylo] Error in plotBS when number of taxa is small Kamila Naxerova
  • Re: [R-sig-phylo] Error in plotBS when number of taxa is small Klaus Schliep
• [R-sig-phylo] Pagel 94 Baysian Version 3 states? mailbox Franz
  • Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states? Manabu Sakamoto
  • Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states? mailbox Franz
  • Re: [R-sig-phylo] Pagel 94 Baysian Version 3 states? Manabu Sakamoto
• [R-sig-phylo] multi-regime OU models and PGLS saurabh
• [R-sig-phylo] genetic data analysis in R short course, Glasgow 16-20 Aug 2016 Thibaut Jombart
• [R-sig-phylo] identify duplicate topologies and add corresponding values John Denton
  • Re: [R-sig-phylo] identify duplicate topologies and add corresponding values Liam J. Revell
  • Re: [R-sig-phylo] identify duplicate topologies and add corresponding values Liam J. Revell
  • Re: [R-sig-phylo] identify duplicate topologies and add corresponding values Emmanuel Paradis
• [R-sig-phylo] Simulating datasets under models with very low rates Michael Foisy
• [R-sig-phylo] root tree in ape 3.4 vs 3.2 Tomas Fer
  • Re: [R-sig-phylo] root tree in ape 3.4 vs 3.2 Emmanuel Paradis
• [R-sig-phylo] Problem with drop.clade/drop.tip function? Gopal Murali
• [R-sig-phylo] Error in trees[[i]] : subscript out of bounds Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Error in trees[[i]] : subscript out of bounds Liam J. Revell
  • Re: [R-sig-phylo] Error in trees[[i]] : subscript out of bounds Emmanuel Paradis
  • Re: [R-sig-phylo] Error in trees[[i]] : subscript out of bounds Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Error in trees[[i]] : subscript out of bounds Emmanuel Paradis
• [R-sig-phylo] Using bind.tree on simmaps Christie Ziegler
  • Re: [R-sig-phylo] Using bind.tree on simmaps Liam J. Revell
• [R-sig-phylo] Unequal line widths for branches when sent to pdf in R Chris Buddenhagen
• [R-sig-phylo] Associated r created graphs or external images with specific nodes on a phylogeny Chris Buddenhagen
  • Re: [R-sig-phylo] Associated r created graphs or external images with specific nodes on a phylogeny Liam J. Revell
  • Re: [R-sig-phylo] Associated r created graphs or external images with specific nodes on a phylogeny Andreas Kolter
• [R-sig-phylo] Simulating data under precursor models Michael Foisy
  • Re: [R-sig-phylo] Simulating data under precursor models Michael Foisy
  • Re: [R-sig-phylo] Simulating data under precursor models Liam J. Revell
  • Re: [R-sig-phylo] Simulating data under precursor models Liam J. Revell
• [R-sig-phylo] simulating continuous data Bryan McLean
  • Re: [R-sig-phylo] simulating continuous data Joe Felsenstein
  • Re: [R-sig-phylo] simulating continuous data Theodore Garland Jr
  • Re: [R-sig-phylo] simulating continuous data Bryan McLean
  • Re: [R-sig-phylo] simulating continuous data Theodore Garland Jr
• [R-sig-phylo] [function like ratebystate, but for discrete characters?] Michael Foisy
  • Re: [R-sig-phylo] [function like ratebystate, but for discrete characters?] Liam J. Revell
  • Re: [R-sig-phylo] [function like ratebystate, but for discrete characters?] Michael Foisy
  • Re: [R-sig-phylo] [function like ratebystate, but for discrete characters?] Brian O'Meara

• Earlier messages
• Later messages