r-sig-phylo  

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• • Re: [R-sig-phylo] Question on pCCA (phyl.cca) Julien Clavel
  • Re: [R-sig-phylo] Question on pCCA (phyl.cca) Julien Clavel
  • Re: [R-sig-phylo] Question on pCCA (phyl.cca) sandra goutte
  • Re: [R-sig-phylo] Question on pCCA (phyl.cca) Julien Clavel
  • Re: [R-sig-phylo] Question on pCCA (phyl.cca) krzysztofbartoszek
  • Re: [R-sig-phylo] Question on pCCA (phyl.cca) Julien Clavel
  • Re: [R-sig-phylo] Question on pCCA (phyl.cca) krzysztofbartoszek
• [R-sig-phylo] get mean support and sd for 100s of gene trees - also node match counting gene trees vs reference Chris Buddenhagen
  • Re: [R-sig-phylo] get mean support and sd for 100s of gene trees - also node match counting gene trees vs reference Liam J. Revell
• [R-sig-phylo] adding scale bar to plots produced using cophyloplot Julie Lee-Yaw
  • Re: [R-sig-phylo] adding scale bar to plots produced using cophyloplot Liam J. Revell
  • Re: [R-sig-phylo] adding scale bar to plots produced using cophyloplot Julie Lee-Yaw
• [R-sig-phylo] output of phangorn::midpoint is not compatible with ape::ladderize? Yu, Guangchuang
  • Re: [R-sig-phylo] output of phangorn::midpoint is not compatible with ape::ladderize? Klaus Schliep
  • Re: [R-sig-phylo] output of phangorn::midpoint is not compatible with ape::ladderize? Yu, Guangchuang
  • Re: [R-sig-phylo] output of phangorn::midpoint is not compatible with ape::ladderize? Emmanuel Paradis
• [R-sig-phylo] issue in ape's rphylo (and workaround) Nick Matzke
  • Re: [R-sig-phylo] issue in ape's rphylo (and workaround) Klaus Schliep
  • Re: [R-sig-phylo] issue in ape's rphylo (and workaround) Emmanuel Paradis
• [R-sig-phylo] plotting a tree from large matrix Rufaida Al Breiki
• [R-sig-phylo] Zero eigenvalues in corHMM Teofil Nakov
• [R-sig-phylo] Distance between two species from a Jonathan Greenberg
  • Re: [R-sig-phylo] Distance between two species from a Liam Revell
  • Re: [R-sig-phylo] Distance between two species from a Liam Revell
  • Re: [R-sig-phylo] Distance between two species from a Joseph W. Brown
  • Re: [R-sig-phylo] Distance between two species from a Jonathan Greenberg
  • Re: [R-sig-phylo] Distance between two species from a Liam J. Revell
• [R-sig-phylo] Hillis & Huelsenbeck 1992 g1 test? Simon Greenhill
• [R-sig-phylo] Important update to geomorph Adams, Dean [EEOBS]
• [R-sig-phylo] next release of ape Emmanuel Paradis
  • Re: [R-sig-phylo] next release of ape Emmanuel Paradis
• [R-sig-phylo] New package: Linarius Gilles Benjamin Leduc
• [R-sig-phylo] different p-values for K using phylosignal vs. phylosig Nicole Rafferty
• [R-sig-phylo] using chronos() from the ape package for large bacterial phylogeny Fabian Roger
  • Re: [R-sig-phylo] using chronos() from the ape package for large bacterial phylogeny Franz Krah
  • Re: [R-sig-phylo] using chronos() from the ape package for large bacterial phylogeny Brian O'Meara
  • Re: [R-sig-phylo] using chronos() from the ape package for large bacterial phylogeny Emmanuel Paradis
• [R-sig-phylo] new phylogenetic comparative method for shape data John Denton
• [R-sig-phylo] Dollo character using ace/make.simmap Graeme Lloyd
  • Re: [R-sig-phylo] Dollo character using ace/make.simmap Nicholas Crouch
  • Re: [R-sig-phylo] Dollo character using ace/make.simmap Matt Pennell
  • Re: [R-sig-phylo] Dollo character using ace/make.simmap Liam J. Revell
  • Re: [R-sig-phylo] Dollo character using ace/make.simmap Graeme Lloyd
  • Re: [R-sig-phylo] Dollo character using ace/make.simmap David Bapst
  • Re: [R-sig-phylo] Dollo character using ace/make.simmap Brian O'Meara
• Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument' Uwe Menzel
  • Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument' Emmanuel Paradis
• [R-sig-phylo] phylo.ANOVA.intra Bruno Frédérich
  • Re: [R-sig-phylo] phylo.ANOVA.intra Julien Clavel
• [R-sig-phylo] Plotting rooted tree with bootstrap values (ape/phangorn) Kamila Naxerova
  • Re: [R-sig-phylo] Plotting rooted tree with bootstrap values (ape/phangorn) Klaus Schliep
  • Re: [R-sig-phylo] Plotting rooted tree with bootstrap values (ape/phangorn) Emmanuel Paradis
• [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Felipe Rossetto
  • Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Vojtěch Zeisek
  • Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Vojtěch Zeisek
  • Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Felipe Rossetto
  • Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Felipe Rossetto
  • Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Christie Ziegler
  • Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Upham, Nathan
  • Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Felipe Rossetto
  • Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus Felipe Rossetto
• [R-sig-phylo] R Sig Phylo Question Large Phylogenies Karen Gordon
  • Re: [R-sig-phylo] R Sig Phylo Question Large Phylogenies Liam J. Revell
  • Re: [R-sig-phylo] R Sig Phylo Question Large Phylogenies Christie Ziegler
  • Re: [R-sig-phylo] R Sig Phylo Question Large Phylogenies Karen Gordon
• [R-sig-phylo] Cannot plot above 500 superimposed trees with densiTree (Phangorn) Marina Strelin
  • Re: [R-sig-phylo] Cannot plot above 500 superimposed trees with densiTree (Phangorn) Klaus Schliep
• [R-sig-phylo] Difficulties with Rooting Rodrigo Aluizio
  • Re: [R-sig-phylo] Difficulties with Rooting Liam J. Revell
  • Re: [R-sig-phylo] Difficulties with Rooting Rodrigo Aluizio
• [R-sig-phylo] root edge issue in picante::evol.distinct() Giulio V. Dalla Riva
• [R-sig-phylo] PGLS multiple regression with dummy variables and interaction terms Patrick Gemmell
  • Re: [R-sig-phylo] PGLS multiple regression with dummy variables and interaction terms Chris Organ
  • Re: [R-sig-phylo] PGLS multiple regression with dummy variables and interaction terms Theodore Garland Jr
• [R-sig-phylo] Plotting error edgelabels in phylogeny type="fan" Julia Dupin
  • Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type="fan" Klaus Schliep
  • Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type="fan" Liam J. Revell
  • Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type="fan" Julia Dupin
  • Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type="fan" Emmanuel Paradis
• [R-sig-phylo] simulating rate shifts Eric Lewitus
  • Re: [R-sig-phylo] simulating rate shifts Emmanuel Paradis
  • Re: [R-sig-phylo] simulating rate shifts Liam J. Revell
  • Re: [R-sig-phylo] simulating rate shifts Eric
  • Re: [R-sig-phylo] simulating rate shifts Theodore Garland Jr
  • Re: [R-sig-phylo] simulating rate shifts Liam J. Revell
  • Re: [R-sig-phylo] simulating rate shifts eric
• [R-sig-phylo] MEDUSA error question Benjamin Blanchard
• [R-sig-phylo] Obtaining a scaled tree out of GEIGER rjmcmc.bm() A Chira
• [R-sig-phylo] Weird abline Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Weird abline Sergio Ferreira Cardoso
• [R-sig-phylo] ANOVA type II with gls() Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] ANOVA type II with gls() Emmanuel Paradis
• [R-sig-phylo] R-squared alternative for gls Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] R-squared alternative for gls Theodore Garland Jr
  • Re: [R-sig-phylo] R-squared alternative for gls Sergio Ferreira Cardoso
• [R-sig-phylo] Problem with runSurface {surface} Diego Salazar
  • Re: [R-sig-phylo] Problem with runSurface {surface} Arley Camargo
• [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels David Bapst
  • Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels Emmanuel Paradis
  • Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels David Bapst
  • Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels Emmanuel Paradis
  • Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels Emmanuel Paradis
  • Re: [R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels David Bapst
• Re: [R-sig-phylo] testing for variation in rates of evolution among traits Adams, Dean [EEOBS]
• [R-sig-phylo] testing for variation in rates of evolution among traits Karla Shikev
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Theodore Garland Jr
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Giulio V. Dalla Riva
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Giulio V. Dalla Riva
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Karla Shikev
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Chad Eliason
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits [email protected]
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Joe Felsenstein
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Adams, Dean [EEOBS]
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Julien Clavel
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Julien Clavel
  • Re: [R-sig-phylo] testing for variation in rates of evolution among traits Julien Clavel
• [R-sig-phylo] Different Lambda estimations Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Different Lambda estimations Emmanuel Paradis
  • Re: [R-sig-phylo] Different Lambda estimations Sergio Ferreira Cardoso
• [R-sig-phylo] PGLS with non-ultrametric tree Solomon Chak
  • Re: [R-sig-phylo] PGLS with non-ultrametric tree Theodore Garland Jr
  • Re: [R-sig-phylo] PGLS with non-ultrametric tree Solomon Chak
  • Re: [R-sig-phylo] PGLS with non-ultrametric tree Paolo Piras
  • Re: [R-sig-phylo] PGLS with non-ultrametric tree Theodore Garland Jr
  • Re: [R-sig-phylo] PGLS with non-ultrametric tree David Bapst
• [R-sig-phylo] Prune very large tree Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Prune very large tree Matt Pennell
  • Re: [R-sig-phylo] Prune very large tree Florian Boucher
  • Re: [R-sig-phylo] Prune very large tree Klaus Schliep
  • Re: [R-sig-phylo] Prune very large tree Sergio Ferreira Cardoso
• [R-sig-phylo] sorry for the wrong link in the previous email Re: boxplots next to phylogeny Martin Bulla
  • Re: [R-sig-phylo] sorry for the wrong link in the previous email Re: boxplots next to phylogeny Emmanuel Paradis
• [R-sig-phylo] Build consensus trees Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Build consensus trees Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Build consensus trees Sergio Ferreira Cardoso
• [R-sig-phylo] Different estimate of Bloomberg's k in ape and caper in R Solomon Chak
  • Re: [R-sig-phylo] Different estimate of Bloomberg's k in ape and caper in R Slater, Graham
• [R-sig-phylo] Diversification shift, LTT plot comparison Adama FAYE
• [R-sig-phylo] boxplots next to phylogeny Martin Bulla
  • Re: [R-sig-phylo] boxplots next to phylogeny Liam J. Revell
  • Re: [R-sig-phylo] boxplots next to phylogeny Martin Bulla
  • Re: [R-sig-phylo] boxplots next to phylogeny Liam J. Revell
  • Re: [R-sig-phylo] boxplots next to phylogeny Martin Bulla
  • Re: [R-sig-phylo] boxplots next to phylogeny Martin Bulla
  • Re: [R-sig-phylo] boxplots next to phylogeny Emmanuel Paradis
  • Re: [R-sig-phylo] boxplots next to phylogeny Martin Bulla
• Re: [R-sig-phylo] Constraining node values in an OUCH analysis (Aaron King)Re: Constraining node values in an OUCH analysis (Krzysztof Bartoszek) krzysztofbartoszek
• [R-sig-phylo] simulating a labile trait Glenn Seeholzer
  • Re: [R-sig-phylo] simulating a labile trait Theodore Garland Jr
  • Re: [R-sig-phylo] simulating a labile trait Emmanuel Paradis
  • Re: [R-sig-phylo] simulating a labile trait Liam J. Revell
• [R-sig-phylo] Handling polytomies in PGLS Brian A. Gill
  • Re: [R-sig-phylo] Handling polytomies in PGLS Liam J. Revell
• [R-sig-phylo] adegenet 2.0.0 on CRAN! Jombart, Thibaut
• [R-sig-phylo] Export Ancestral Mapping From Mesquite into Figtree Jackson, Laura Marie
  • Re: [R-sig-phylo] Export Ancestral Mapping From Mesquite into Figtree Liam J. Revell
• [R-sig-phylo] Ancestral Reconstruction with Polymorphic States Jackson, Laura Marie
  • Re: [R-sig-phylo] Ancestral Reconstruction with Polymorphic States Brian O'Meara
• [R-sig-phylo] convergence problem using phyloglm and IG10 [email protected]
  • Re: [R-sig-phylo] convergence problem using phyloglm and IG10 Cécile Ané
  • Re: [R-sig-phylo] convergence problem using phyloglm and IG10 Lam Ho
  • Re: [R-sig-phylo] convergence problem using phyloglm and IG10 ANTHONY R IVES
• [R-sig-phylo] doubt Lilian Sayuri Ouchi de Melo
  • Re: [R-sig-phylo] doubt Liam J. Revell
  • Re: [R-sig-phylo] doubt Lilian Sayuri Ouchi de Melo
  • Re: [R-sig-phylo] doubt David Bapst
  • Re: [R-sig-phylo] doubt Lilian Sayuri Ouchi de Melo
• [R-sig-phylo] an error running make.simmap Rubén Torices Blanco
  • Re: [R-sig-phylo] an error running make.simmap Liam J. Revell
• [R-sig-phylo] Get SNP information lavanya c
• [R-sig-phylo] corDISC binary coding problems [email protected]
  • Re: [R-sig-phylo] corDISC binary coding problems Brian O'Meara
  • Re: [R-sig-phylo] corDISC binary coding problems Franz Krah
• [R-sig-phylo] phyres function R package caper Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] phyres function R package caper Theodore Garland Jr
  • Re: [R-sig-phylo] phyres function R package caper Liam J. Revell
  • Re: [R-sig-phylo] phyres function R package caper Theodore Garland Jr
  • Re: [R-sig-phylo] phyres function R package caper Sergio Ferreira Cardoso
• [R-sig-phylo] NNI/SPR Distance Karla Shikev
• [R-sig-phylo] Margin Artifact in plot.phylo with Very Long Tip Labels, despite show.tip.label=FALSE David Bapst
  • Re: [R-sig-phylo] Margin Artifact in plot.phylo with Very Long Tip Labels, despite show.tip.label=FALSE Liam J. Revell
  • Re: [R-sig-phylo] Margin Artifact in plot.phylo with Very Long Tip Labels, despite show.tip.label=FALSE Emmanuel Paradis
• [R-sig-phylo] Looking for beta users for rotl (an R package to access the Open Tree of Life) François Michonneau
  • Re: [R-sig-phylo] Looking for beta users for rotl (an R package to access the Open Tree of Life) François Michonneau
• [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) David Bapst
  • Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) Liam J. Revell
  • Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) David Bapst
  • Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) Brian O'Meara
  • Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) Eduardo Ascarrunz
  • Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) Liam J. Revell
  • Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) David Bapst
  • Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) Liam J. Revell
  • Re: [R-sig-phylo] Missing States in ML Reconstruction of Discrete Ancestral States (phytools, ape) Emmanuel Paradis
• [R-sig-phylo] Non Parametric PGLS Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Non Parametric PGLS Daniel Fulop
  • Re: [R-sig-phylo] Non Parametric PGLS Liam J. Revell
  • Re: [R-sig-phylo] Non Parametric PGLS Simon Blomberg
  • Re: [R-sig-phylo] Non Parametric PGLS Sergio Ferreira Cardoso
  • Re: [R-sig-phylo] Non Parametric PGLS Liam J. Revell
  • Re: [R-sig-phylo] Non Parametric PGLS Sergio Ferreira Cardoso

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