Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / liamrevell/phytools issues and pull requests

#162 - contMap crashes if ancestral states are named with node names

Issue - State: open - Opened by bredelings about 1 month ago - 1 comment

#160 - Error in ace function (ape)

Issue - State: closed - Opened by qahenoch 2 months ago

#159 - Plot a map area cross Longitude 180

Issue - State: open - Opened by Ruiqi-CUB 5 months ago

#158 - Upside down Phylogeny when plotting with a map

Issue - State: open - Opened by Ruiqi-CUB 5 months ago

#157 - fitThresh with tip priors matrix

Issue - State: closed - Opened by evo-palaeo 6 months ago - 4 comments

#155 - missing value color argument?

Issue - State: open - Opened by HedvigS 9 months ago

#154 - mcmMk should set likelihood to "fitMk" when data input is matrix

Issue - State: closed - Opened by rdiaz02 9 months ago - 2 comments

#153 - cophylo not plotting the second tree

Issue - State: open - Opened by bshahid5 10 months ago

#151 - Feature request: branch coloring in phylo.to.map

Issue - State: open - Opened by alexweisberg 10 months ago

#150 - cophylo with polytomies error

Issue - State: open - Opened by cmt2 11 months ago

#148 - subscript out of bounds

Issue - State: open - Opened by ZestingJin about 1 year ago

#146 - install error

Issue - State: closed - Opened by wang0430 over 1 year ago - 1 comment

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

Issue - State: closed - Opened by ilcneto over 1 year ago - 1 comment

#144 - phylo.heatmap remove elements and smush

Issue - State: closed - Opened by HedvigS over 1 year ago - 1 comment

#143 - add.species.to.genus could not match your species to a genus

Issue - State: closed - Opened by alrichardbollans over 1 year ago - 1 comment

#141 - recent maps for phylo.to.map

Issue - State: open - Opened by ChloBeaul over 1 year ago - 1 comment

#140 - Problem when setting priors on stem edges with make.simmap

Issue - State: closed - Opened by Lwoots over 1 year ago - 1 comment

#139 - Error in optimizing with phylosig lambda

Issue - State: closed - Opened by lilyb3 over 1 year ago - 2 comments

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

Issue - State: closed - Opened by Zoey-Aminah over 1 year ago - 2 comments

#137 - Custom linking line colors in cophylogeny using association file?

Issue - State: closed - Opened by myco-bradshaw over 1 year ago - 1 comment

#136 - outline color argument to dotTree

Issue - State: closed - Opened by HedvigS over 1 year ago - 8 comments

#135 - as.princomp on phy.pca using mode="cor"

Issue - State: closed - Opened by aleungplants over 1 year ago - 1 comment

#134 - nodelabels mixes up existing node labels

Issue - State: closed - Opened by theo-allnutt-bioinformatics over 1 year ago - 2 comments

#133 - Tip numbers / labels

Issue - State: closed - Opened by theo-allnutt-bioinformatics over 1 year ago - 2 comments

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

Issue - State: closed - Opened by xuechunxu almost 2 years ago - 5 comments

#131 - Betacoronaviruses tree has wrong case

Issue - State: closed - Opened by hlapp almost 2 years ago - 1 comment

#130 - `paintBranches` error when sapply within function returns ii as list

Issue - State: open - Opened by rubysaltbush almost 2 years ago - 1 comment

#129 - fixed bug in option mean.edge about length of edge.length

Pull Request - State: open - Opened by fpavone almost 2 years ago

#127 - wrong scale bar size in plot.cophylo

Issue - State: closed - Opened by dvs almost 2 years ago - 2 comments

#126 - Create github page

Issue - State: closed - Opened by brunomioto almost 2 years ago - 2 comments

#125 - ratebytree not converging - what should I do?

Issue - State: closed - Opened by soungalo almost 2 years ago - 4 comments

#124 - Add rooted argument to consensus.edges.R

Pull Request - State: closed - Opened by AEgit about 2 years ago - 2 comments

#123 - consensus.edges() produces only (!) unrooted trees (with solution)

Issue - State: closed - Opened by AEgit about 2 years ago - 2 comments

#122 - R4.2.2 for windows and Rstudio crash every time I library phytools

Issue - State: closed - Opened by syuu2021 about 2 years ago - 5 comments

#121 - Error when using "ContMap"

Issue - State: closed - Opened by loaizarachnid4 about 2 years ago - 1 comment

#120 - Error when using "as.multiPhylo"

Issue - State: closed - Opened by OttoHenning over 2 years ago - 1 comment

#118 - read.newick() occasionally crushes R

Issue - State: closed - Opened by kfuku52 over 2 years ago - 4 comments

#117 - dotTree with missing data

Issue - State: open - Opened by HedvigS over 2 years ago - 1 comment

#116 - Using make.simmap with previously inferred transition rates

Issue - State: closed - Opened by Belinda333 over 2 years ago - 7 comments

#115 - Bug: brownie.lite doesn't rearrange standard errors

Issue - State: closed - Opened by blasiusz over 2 years ago - 1 comment

#114 - make.simmap

Issue - State: open - Opened by navilo over 2 years ago - 2 comments

#113 - Strange discrepancy in duration of processing for make.simmap

Issue - State: closed - Opened by flashton2003 over 2 years ago - 2 comments

#112 - Clarification on the ace output of simmap summary

Issue - State: closed - Opened by flashton2003 over 2 years ago - 2 comments

#111 - source of phylogram() in phylo.heatmap

Issue - State: closed - Opened by ThomWorm over 2 years ago - 1 comment

#110 - collapse.to.star not working as before

Issue - State: closed - Opened by dominicev almost 3 years ago - 2 comments

#109 - phylANOVA

Issue - State: closed - Opened by Edison2021 almost 3 years ago

#108 - Ancestral state reconstructions are incorrect when pis are not equal

Issue - State: closed - Opened by arklumpus almost 3 years ago - 3 comments

#107 - midpoint.root stealing/moving edge labels

Issue - State: closed - Opened by joshrest almost 3 years ago - 1 comment

#106 - specify that getDescendants takes one node

Pull Request - State: closed - Opened by HedvigS almost 3 years ago

#105 - getDescendants not fetching all descendants?

Issue - State: closed - Opened by HedvigS almost 3 years ago - 7 comments

#104 - How can I get coords from a ltt95 plot?

Issue - State: open - Opened by pelow22 almost 3 years ago

#103 - Error in installing package

Issue - State: closed - Opened by losblancos3 about 3 years ago - 1 comment

#101 - ContMap throws error for some trees

Issue - State: closed - Opened by voidikova about 3 years ago - 1 comment

#100 - How to do an analyses for two categorical variables in Phytools?

Issue - State: closed - Opened by emxly86 about 3 years ago - 1 comment

#99 - Feature Request: FitzJohn et al. (2009) root prior in make.simmap

Issue - State: closed - Opened by mpnelsen over 3 years ago - 2 comments

#98 - What happens if make.simmap() gets an unrooted tree?

Issue - State: closed - Opened by HedvigS over 3 years ago - 3 comments

#97 - Unable to load library(phytools)

Issue - State: closed - Opened by layhiang1995 over 3 years ago - 2 comments

#96 - getting uncertainty/distributions of ancestral states from simmap

Issue - State: closed - Opened by HedvigS over 3 years ago - 1 comment

#95 - "subscript out of bounds" in ancestral state estimation using phytools

Issue - State: closed - Opened by avvypaks over 3 years ago - 1 comment

#94 - SCM extracting values at internal nodes (or an approximation of it)

Issue - State: closed - Opened by HedvigS over 3 years ago - 5 comments

#93 - Changing type to cladogram within cophylo

Issue - State: closed - Opened by JonathonMifsud over 3 years ago - 1 comment

#92 - Error in describe.simmap

Issue - State: closed - Opened by takaW496 over 3 years ago - 2 comments

#91 - nodeHeights produces non identical but identical node heights

Issue - State: closed - Opened by jacobmaugoust over 3 years ago - 1 comment

#90 - Formatting phylo.to.map plot - subregion of map and point shape

Issue - State: closed - Opened by EveTC over 3 years ago - 1 comment

#88 - allow adding a tip whose origin is older than the root

Pull Request - State: open - Opened by josephwb almost 4 years ago - 2 comments

#87 - Feature request: cophylo of more than 2 trees

Issue - State: open - Opened by alexweisberg almost 4 years ago

#86 - phylo.heatmap error

Issue - State: open - Opened by SolayMane almost 4 years ago

#85 - phyl.pca outputs all imaginary coordinates

Issue - State: closed - Opened by amsesk almost 4 years ago - 7 comments

#82 - plotTree.boxplot()cuts off top and bottom of boxplot

Issue - State: closed - Opened by schmitt8 about 4 years ago - 1 comment

#81 - Error in seq.int(from, to, length.out = n) : 'to' must be a finite number

Issue - State: closed - Opened by ReemH91 over 4 years ago - 1 comment

#80 - pbtree behaviour: taxa-stop criterion not working as expected

Issue - State: closed - Opened by josephwb over 4 years ago - 4 comments

#79 - object 'last_plot.phylo' not found & Error in seq.default(0, length = n)

Issue - State: open - Opened by Cactusolo over 4 years ago - 3 comments

#78 - data format for phytools

Issue - State: closed - Opened by rthapa1 over 4 years ago - 1 comment

#77 - Error in `[<-`(`*tmp*`, x == seq[i], i, value = 1) : subscript out of bounds

Issue - State: closed - Opened by ymilesz over 4 years ago - 3 comments

#76 - adjust position of scale bar in cophylo

Issue - State: open - Opened by alexweisberg over 4 years ago

#75 - Issue/bug with rotateNodes and colouring of tip bars

Issue - State: open - Opened by Thijmen18 over 4 years ago

#74 - Installing phytools (version 0.7-47) on Mac OS 10.15.6 under R version 4.0.2

Issue - State: closed - Opened by eliamson over 4 years ago - 2 comments

#73 - plotSimmap does not respect show.tip.label = FALSE

Issue - State: closed - Opened by SimonGreenhill over 4 years ago - 1 comment

#72 - plotTree.wBars and type="fan" now thows a 'rep' error

Issue - State: closed - Opened by maxfarrell over 4 years ago - 1 comment

#71 - Can't add optional arguments to sim.multiCtt/sim.ctt

Issue - State: closed - Opened by stfriedman over 4 years ago - 1 comment

#70 - Bug: consensus tree

Issue - State: open - Opened by abraao-crypto over 4 years ago

#69 - Map state/providence divitions

Issue - State: open - Opened by AgustinPardo over 4 years ago

#68 - Tree branches colors

Issue - State: closed - Opened by AgustinPardo over 4 years ago - 14 comments

#67 - Line up tree node labeles

Issue - State: closed - Opened by AgustinPardo over 4 years ago - 2 comments

#66 - Imperfectly drawn tree-map (unrooted problem?)

Issue - State: open - Opened by AgustinPardo over 4 years ago

#65 - Tree data sets

Issue - State: closed - Opened by AgustinPardo over 4 years ago - 1 comment

#64 - How to custom change colours on the map?

Issue - State: closed - Opened by tahamimo over 4 years ago - 5 comments

#63 - Problems installing in R version 3.3.2 (CentOS 7)

Issue - State: closed - Opened by agroppi over 4 years ago - 2 comments