Ecosyste.ms: Issues

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

GitHub / emmanuelparadis/ape issues and pull requests

#120 - Add write.phyloXML() and corresponding tests

Pull Request - State: open - Opened by fmarotta 19 days ago - 1 comment

#119 - fix problems with x.lim and y.lim

Pull Request - State: closed - Opened by KlausVigo about 1 month ago - 1 comment

#118 - v5.8 drop.tip unexpected behavior

Issue - State: open - Opened by colejensen about 2 months ago - 3 comments

#117 - fix spelling mistake

Pull Request - State: closed - Opened by KlausVigo 2 months ago - 2 comments

#116 - axisPhylo() not extending all along the root edge

Issue - State: open - Opened by emmanuelparadis 3 months ago
Labels: enhancement

#115 - Warn if node labels mismatched

Pull Request - State: closed - Opened by ms609 3 months ago - 3 comments

#114 - read.tree() silently (but correctly) fails on malformed Newick file

Issue - State: closed - Opened by arcresu 3 months ago - 4 comments

#113 - write.tree() may export duplicate internal node labels without notification

Issue - State: closed - Opened by stitam 4 months ago - 3 comments

#111 - Some small improvements

Pull Request - State: closed - Opened by KlausVigo 5 months ago - 1 comment

#110 - source/func call assist

Pull Request - State: closed - Opened by peterdunson 5 months ago - 2 comments

#109 - help with source/func calls

Pull Request - State: closed - Opened by peterdunson 5 months ago - 1 comment

#108 - Update as.phylo.formula.R

Pull Request - State: closed - Opened by peterdunson 5 months ago

#107 - Confused about results of dist.nodes on BEAST output tree

Issue - State: closed - Opened by katherinermartin 5 months ago - 4 comments

#106 - Adds node labels to ace output if available

Pull Request - State: closed - Opened by TGuillerme 6 months ago - 1 comment

#105 - phymltest() producing the double amount of trees

Issue - State: open - Opened by mickvv 8 months ago - 6 comments
Labels: issue outside ape

#104 - Newick tree with a single tip and more than one node not read correctly

Issue - State: closed - Opened by emmanuelparadis 8 months ago - 1 comment
Labels: bug

#103 - tree with root node

Issue - State: closed - Opened by KlausVigo 8 months ago - 5 comments
Labels: bug, enhancement

#102 - Added a multiPhylo case to makeNodeLabel

Pull Request - State: closed - Opened by TGuillerme 8 months ago - 5 comments

#101 - write.tree not using tree.names

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

#100 - allow del.gaps, del.rowgapsonly, del.colgapsonly to work on AAbin obj…

Pull Request - State: closed - Opened by KlausVigo 9 months ago - 3 comments

#98 - Add color schemes to image.DNAbin and image.AAbin

Pull Request - State: closed - Opened by KlausVigo 10 months ago - 1 comment

#97 - Error in nj(x) : cannot allocate memory block of size 134217728 Tb

Issue - State: closed - Opened by migueldiascosta 10 months ago - 7 comments

#96 - Odd values in variance-covariance matrix

Issue - State: closed - Opened by kat3stewart 11 months ago - 2 comments

#95 - No tip label for one of the tips

Issue - State: closed - Opened by lpipes 12 months ago - 6 comments

#94 - wider support for zero-leaf trees

Issue - State: open - Opened by emmanuelparadis 12 months ago
Labels: enhancement

#93 - Handle zero-leaf trees

Pull Request - State: closed - Opened by ms609 12 months ago - 2 comments

#92 - Tree too large for cophenetic

Issue - State: closed - Opened by osidaksjdmw 12 months ago - 6 comments

#91 - @KlausVigo I checked your PR (#90) which sounds great to me.

Issue - State: closed - Opened by KlausVigo about 1 year ago - 1 comment

#90 - improve keep.tip and drop.tip

Pull Request - State: closed - Opened by KlausVigo about 1 year ago

#89 - Cannot install ape in RStudio

Issue - State: closed - Opened by strawberry098 about 1 year ago - 1 comment

#88 - Improvement

Issue - State: closed - Opened by KlausVigo about 1 year ago - 3 comments

#87 - new function: keep.as.tip

Pull Request - State: closed - Opened by HedvigS about 1 year ago - 9 comments

#86 - Cannot compute distance

Issue - State: closed - Opened by fullertonhe about 1 year ago - 2 comments

#85 - problem with nodelabels when frame="circle"

Issue - State: closed - Opened by Juanphg about 1 year ago - 2 comments
Labels: bug

#83 - is.binary function with 0 branch lengths

Issue - State: closed - Opened by Lars-B about 1 year ago - 3 comments
Labels: documentation

#82 - corPhylo error - Error in Rd %*% R : non-conformable arguments

Issue - State: closed - Opened by MalharAtre about 1 year ago - 5 comments
Labels: bug

#81 - model fit suspicious: gradients apparently non-finite

Issue - State: closed - Opened by xuechunxu about 1 year ago - 2 comments
Labels: question

#80 - `read.tree` seems to round branch lengths

Issue - State: closed - Opened by ajrominger about 1 year ago - 3 comments

#79 - Preserve Multiple Node Labels When Using drop.tip()

Issue - State: closed - Opened by simone-says about 1 year ago - 2 comments

#78 - Issue in tree assignment

Issue - State: closed - Opened by ms609 over 1 year ago

#77 - `1:length(x)` → `seq_along(x)`

Pull Request - State: closed - Opened by ms609 over 1 year ago

#76 - Specify class in .uncompressTipLabel

Pull Request - State: closed - Opened by ms609 over 1 year ago - 8 comments

#75 - fix errors in phangorn

Pull Request - State: closed - Opened by KlausVigo over 1 year ago - 1 comment

#74 - Add GitHub links to DESCRIPTION

Pull Request - State: closed - Opened by maelle over 1 year ago - 4 comments

#73 - rtt function no longer handles NAs in dates

Issue - State: closed - Opened by brj1 over 1 year ago - 5 comments

#72 - Parallelization in dist.topo

Issue - State: closed - Opened by V-Z over 1 year ago - 1 comment
Labels: enhancement

#71 - Parallelization for dist.topo()

Pull Request - State: closed - Opened by V-Z over 1 year ago

#70 - segfault when reading in tree

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

#69 - DESCRIPTION should list dependency R > 4.1

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

#68 - fix: Add dependency on R 4.1.0 because of native pipe usage

Pull Request - State: closed - Opened by maelle over 1 year ago - 14 comments

#67 - Unable to install

Issue - State: closed - Opened by sealavi over 1 year ago - 3 comments

#66 - make drop.tip and keep.tip generic

Pull Request - State: closed - Opened by KlausVigo over 1 year ago - 1 comment

#65 - consensus did not use postprocess.prop.part and might scramble nodela…

Pull Request - State: closed - Opened by KlausVigo almost 2 years ago - 1 comment

#64 - ape::cophenetic.phylo() - Tree too big - any workarounds?

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

#63 - possible bug in ace

Issue - State: open - Opened by RubyRedlich almost 2 years ago - 6 comments

#62 - Error: cannot use same sampling date for all the tips

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

#61 - speed up rtt function, allow multifurcations

Pull Request - State: closed - Opened by KlausVigo about 2 years ago - 1 comment

#60 - Bug fix in .write.tree2

Pull Request - State: closed - Opened by KlausVigo about 2 years ago - 1 comment

#59 - fix the edge.length or height when converting between the hclust and …

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

#58 - can't read in tree

Issue - State: closed - Opened by lpipes about 2 years ago - 3 comments

#57 - Bug fix for error introduced via #52

Pull Request - State: closed - Opened by KlausVigo about 2 years ago - 1 comment

#56 - Potential bug when reading Mesquite formatting from nexus files

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

#55 - remove recursions

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

#54 - Ladderize results C stack usage overflow

Issue - State: closed - Opened by teng-gao about 2 years ago - 6 comments

#53 - write.tree error

Issue - State: closed - Opened by lpipes about 2 years ago - 25 comments

#52 - Allow different "order" in unroot

Pull Request - State: closed - Opened by KlausVigo about 2 years ago - 3 comments

#51 - multi2di and di2multi might not work for compressed multiPhylo objects

Pull Request - State: closed - Opened by KlausVigo over 2 years ago

#49 - read.tree() struggling with certain tip and node labels

Issue - State: closed - Opened by HedvigS over 2 years ago - 17 comments

#48 - version of keep.tip which considers internal nodes as well?

Issue - State: closed - Opened by HedvigS over 2 years ago - 18 comments

#47 - Simplify workflows

Pull Request - State: closed - Opened by ms609 over 2 years ago - 1 comment

#46 - Don't build vignettes in R3.6.3

Pull Request - State: closed - Opened by ms609 over 2 years ago

#45 - Fix `[<-.multiPhylo`

Pull Request - State: closed - Opened by ms609 over 2 years ago - 11 comments

#44 - phangorn now requires R4.1

Pull Request - State: closed - Opened by ms609 over 2 years ago - 1 comment

#42 - Improve comparePhylo

Pull Request - State: closed - Opened by KlausVigo over 2 years ago - 2 comments

#41 - improve comparePhylo

Pull Request - State: closed - Opened by KlausVigo over 2 years ago - 1 comment

#40 - corBrownian error

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

#39 - can't write tree

Issue - State: closed - Opened by lpipes over 2 years ago - 9 comments

#38 - Support n < 2 in `unique.multiPhylo()`

Pull Request - State: closed - Opened by ms609 over 2 years ago - 1 comment

#37 - `c.multiPhylo` drops names

Issue - State: closed - Opened by ms609 over 2 years ago - 2 comments

#36 - `[<-.multiPhylo` does not support empty `[]`

Issue - State: closed - Opened by ms609 over 2 years ago - 1 comment

#35 - [<-.multiPhylo does not support empty []

Issue - State: closed - Opened by ms609 over 2 years ago - 1 comment

#34 - improve as.evonet.phylo

Pull Request - State: closed - Opened by KlausVigo over 2 years ago - 1 comment

#33 - fix the order of tip in as.hclust.phylo

Pull Request - State: closed - Opened by xiangpin almost 3 years ago - 1 comment

#32 - ape::drop.tip() unrooting tree

Issue - State: closed - Opened by HedvigS almost 3 years ago - 14 comments

#31 - Support lists of trees in `write.tree()`

Pull Request - State: closed - Opened by ms609 almost 3 years ago - 1 comment

#30 - Spelling: umatched → unmatched

Pull Request - State: closed - Opened by ms609 almost 3 years ago - 1 comment

#29 - fix issue of read.nexus to solve the labels of translation contains space

Pull Request - State: closed - Opened by xiangpin almost 3 years ago - 1 comment

#28 - where() function with aa sequences

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

#27 - Automate testing

Pull Request - State: closed - Opened by ms609 almost 3 years ago - 1 comment

#26 - function nj() is modifying distance matrix

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

#25 - Improve prop.part and consensus

Pull Request - State: closed - Opened by KlausVigo almost 3 years ago - 1 comment

#24 - Error when using ape::pcoa

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

#23 - Weird behaviour of parameter `random` in multi2di()

Issue - State: closed - Opened by fcampelo about 3 years ago - 6 comments

#22 - Glitch in dist.dna

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

#21 - Commit improve fan for trees without edge length

Pull Request - State: closed - Opened by KlausVigo about 3 years ago - 2 comments