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
#112 - chronos() problems with convergence -- sometimes getting stuck entirely
Issue -
State: closed - Opened by amizeranschi 5 months ago
- 5 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
#99 - biplot.pcoa() function produces different projections for the same variable when it is scaled.
Issue -
State: closed - Opened by daroari 10 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
#84 - njs, bionj, and bionjs sometimes cause RStudio to abort when run on only 2 sequences
Issue -
State: closed - Opened by FreekManders about 1 year ago
- 2 comments
#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
#50 - wrong behaviour of is.monophyletic() with duplicated labels
Issue -
State: closed - Opened by emmanuelparadis 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
#43 - boot.phylo(): 'Error in 'bitsplits(phy)': INTEGER() can only be applied to a 'integer', not a 'double'
Issue -
State: closed - Opened by pawelqs over 2 years ago
- 5 comments
#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