liamrevell/phytools

Issues

• mcmMk should set likelihood to "fitMk" when data input is matrix

  #154 opened 7 months ago by rdiaz02
  2

• Plot a map area cross Longitude 180

  #159 opened 4 months ago by Ruiqi-CUB
  0

• Upside down Phylogeny when plotting with a map

  #158 opened 4 months ago by Ruiqi-CUB
  0

• fitThresh with tip priors matrix

  #157 opened 5 months ago by evo-palaeo
  4

• how to remove labels from `cophylo(tree1, tree2, rotate = TRUE)`?

  #156 opened 5 months ago by liamxg
  0

• Bug: phytools::plotTree.boxplot -- argument "x" is missing, with no default

  #152 opened 7 months ago by stiatragul
  1

• missing value color argument?

  #155 opened 9 months ago by HedvigS
  0

• dotTree with missing data

  #117 opened 2 years ago by HedvigS
  1

• cophylo not plotting the second tree

  #153 opened 9 months ago by bshahid5
  0

• Feature request: branch coloring in phylo.to.map

  #151 opened 10 months ago by alexweisberg
  0

• cophylo with polytomies error

  #150 opened 10 months ago by cmt2
  0

• Error in apply(X, 1, sum/rstate) : dim(X) must have a positive length

  #149 opened a year ago by alrichardbollans
  0

• subscript out of bounds

  #148 opened a year ago by ZestingJin
  0

• recent maps for phylo.to.map

  #141 opened a year ago by ChloBeaul
  1

• Cannot change scale font size or control horizontal position in barplot

  #147 opened a year ago by theo-allnutt-bioinformatics
  11

• Error in plot.window(xlim, ylim, log = log, ...) : need finite 'xlim' values

  #138 opened a year ago by Zoey-Aminah
  2

• Error in optimizing with phylosig lambda

  #139 opened a year ago by lilyb3
  2

• Problem when setting priors on stem edges with make.simmap

  #140 opened a year ago by Lwoots
  1

• Dumb question: Why are the PCA scores different from the positions of the points in a plot of the PCA?

  #142 opened a year ago by aleungplants
  1

• phylo.heatmap remove elements and smush

  #144 opened a year ago by HedvigS
  1

• "Error in tree$maps[[jj[i]]] : invalid subscript type 'list'"

  #145 opened a year ago by ilcneto
  1

• install error

  #146 opened a year ago by wang0430
  1

• consensus.edges() produces only (!) unrooted trees (with solution)

  #123 opened 2 years ago by AEgit
  2

• add.species.to.genus could not match your species to a genus

  #143 opened a year ago by alrichardbollans
  1

• `paintBranches` error when sapply within function returns ii as list

  #130 opened 2 years ago by rubysaltbush
  1

• Tip numbers / labels

  #133 opened a year ago by theo-allnutt-bioinformatics
  2

• Disagreement between phylosig(, method="lambda") and plot.phylosig() - possible bug?

  #128 opened a year ago by cameron-weadick
  3

• as.princomp on phy.pca using mode="cor"

  #135 opened 2 years ago by aleungplants
  1

• Custom linking line colors in cophylogeny using association file?

  #137 opened 2 years ago by myco-bradshaw
  1

• outline color argument to dotTree

  #136 opened 2 years ago by HedvigS
  8

• nodelabels mixes up existing node labels

  #134 opened 2 years ago by theo-allnutt-bioinformatics
  2

• Error in matexpo(Q * EL[i]) : NA/NaN/Inf in foreign function call (arg 1)

  #132 opened 2 years ago by xuechunxu
  5

• Betacoronaviruses tree has wrong case

  #131 opened 2 years ago by hlapp
  1

• make.simmap

  #114 opened 3 years ago by navilo
  2

• wrong scale bar size in plot.cophylo

  #127 opened 2 years ago by dvs
  2

• Create github page

  #126 opened 2 years ago by brunomioto
  2

• Error when using "ContMap"

  #121 opened 2 years ago by loaizarachnid4
  1

• ratebytree not converging - what should I do?

  #125 opened 2 years ago by soungalo
  4

• R4.2.2 for windows and Rstudio crash every time I library phytools

  #122 opened 2 years ago by syuu2021
  5

• Strange discrepancy in duration of processing for make.simmap

  #113 opened 2 years ago by flashton2003
  2

• plotTree/plotSimmap converting underscores to spaces without option to keep underscores

  #119 opened 2 years ago by AlesBucek
  1

• Error when using "as.multiPhylo"

  #120 opened 2 years ago by OttoHenning
  1

• read.newick() occasionally crushes R

  #118 opened 2 years ago by kfuku52
  4

• Using make.simmap with previously inferred transition rates

  #116 opened 2 years ago by Belinda333
  7

• Bug: brownie.lite doesn't rearrange standard errors

  #115 opened 2 years ago by blasiusz
  1

• Clarification on the ace output of simmap summary

  #112 opened 3 years ago by flashton2003
  2

• source of phylogram() in phylo.heatmap

  #111 opened 3 years ago by ThomWorm
  1

• collapse.to.star not working as before

  #110 opened 3 years ago by dominicev
  2

• phylANOVA

  #109 opened 3 years ago by Edison2021
  0

• Ancestral state reconstructions are incorrect when pis are not equal

  #108 opened 3 years ago by arklumpus
  3