Ecosyste.ms: Issues

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

GitHub / KlausVigo/phangorn issues and pull requests

#173 - Consistency Index error

Issue - State: open - Opened by kr3118 29 days ago - 1 comment

#172 - Inquiry About Setting Character Weights in `optim.parsimony` Function

Issue - State: open - Opened by Xinru99 30 days ago - 1 comment

#171 - Duplicated sites are ignored when computing parsimony using "site" option

Issue - State: closed - Opened by cwbcm 2 months ago - 2 comments

#170 - iupac DNA seq

Issue - State: closed - Opened by nicolo-tellini 2 months ago - 1 comment

#169 - update man pages

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

#168 - sync Armadillo

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

#167 - Simulate coding nucleotide sequences

Issue - State: open - Opened by trilisser 4 months ago

#166 - fix labels land plot margins in plot.networx

Issue - State: open - Opened by KlausVigo 4 months ago

#164 - Please use `make_graph` instead of `graph`

Issue - State: closed - Opened by szhorvat 5 months ago - 1 comment

#162 - rotate labels

Issue - State: closed - Opened by locusclassicus 7 months ago - 5 comments

#161 - phangorn for webR / wasm

Issue - State: closed - Opened by isbool 7 months ago

#159 - OSX 14: Installation error

Issue - State: closed - Opened by akhst7 9 months ago - 2 comments

#158 - plm_bb gets into a endless Ratchet iteration loop ?

Issue - State: closed - Opened by akhst7 9 months ago - 2 comments

#157 - Error message 'R session aborted' when running modelTest(primates)

Issue - State: open - Opened by Zhangvvv 10 months ago - 2 comments

#156 - gamma shape completely change after optimisation

Issue - State: closed - Opened by trilisser 10 months ago - 4 comments

#155 - nnls.tree fails with some trees

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

#154 - R is crashed when loading a phangorn library

Issue - State: closed - Opened by trilisser 11 months ago - 5 comments

#153 - library(phangorn) error

Issue - State: open - Opened by wang0430 12 months ago - 3 comments

#152 - modelTest seems to require additional inputs

Issue - State: closed - Opened by Phylloxera 12 months ago - 5 comments

#151 - test

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

#150 - write.phyDat Problem

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

#149 - pml segfault: memory not mapped

Issue - State: open - Opened by lemmonquiche over 1 year ago - 3 comments

#148 - Data availability

Issue - State: open - Opened by Neclow over 1 year ago

#147 - optim.pml hangs infinitely

Issue - State: closed - Opened by hberger over 1 year ago - 4 comments

#146 - densiTree not working

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

#145 - Unable to load module "Fitch_mod": vector is too large

Issue - State: closed - Opened by mdhall272 over 1 year ago - 3 comments

#144 - `pml()` segfault: memory not mapped

Issue - State: open - Opened by iferres over 1 year ago - 2 comments

#143 - Replace rgl.texts with texts3d

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

#142 - add transfer bs and assigning bs

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

#141 - Different results from modelTest() with the same input file

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

#140 - RF distance inaccuracy

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

#139 - add bab and change figures

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

#138 - small improvements for vignettes

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

#137 - worked on vignettes and added mite files

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

#136 - rename for order

Pull Request - State: closed - Opened by iris-bk almost 2 years ago

#135 - implemented new features and improved structure

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

#134 - improvement

Pull Request - State: closed - Opened by iris-bk almost 2 years ago

#133 - move modelTest

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

#131 - Ancestral Sequence Reconstruction with ancestral.pml

Issue - State: open - Opened by MarStreicher about 2 years ago - 3 comments

#130 - error in networx

Issue - State: closed - Opened by basic99 about 2 years ago - 3 comments

#128 - treedist() no longer working for non-binary trees

Issue - State: closed - Opened by jc17659 about 2 years ago - 3 comments

#127 - Release phangorn 2.10.0

Issue - State: closed - Opened by KlausVigo over 2 years ago

#126 - NNI parallelization

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

#124 - install phangorn in R 3.6?

Issue - State: closed - Opened by marwa38 over 2 years ago - 2 comments

#123 - modelTest in batch mode

Issue - State: closed - Opened by LIEHUZUO123 almost 3 years ago - 1 comment

#122 - modelTest for tree with >100 tips

Issue - State: closed - Opened by dferran1 about 3 years ago - 3 comments

#121 - Update phylo.R

Pull Request - State: closed - Opened by thijsjanzen about 3 years ago - 1 comment

#120 - Pratchet duplicates tips

Issue - State: closed - Opened by kbhoehn over 3 years ago - 11 comments

#119 - open AA data in phyDat() from read.aa()

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

#118 - acctran overestimates branch lengths

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

#117 - pratchet function - Error in f$pscore_nni(INDEX[, 1L:4L]) : Not a matrix.

Issue - State: closed - Opened by fulviodan13 over 3 years ago - 8 comments

#116 - Segfault error when running pratchet

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

#115 - getRoot error?

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

#114 - CRAN issues

Issue - State: closed - Opened by ms609 over 3 years ago - 1 comment

#113 - Fixes to `ptree` code to fix Issue #112

Pull Request - State: closed - Opened by dwbapst over 3 years ago - 1 comment

#111 - Phangorn removal warning from CRAN

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

#110 - pratchet error with minimal example

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

#109 - `bootstrap.pml` very slow in version 2.6.2 compared to 2.5.5

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

#108 - Preserve internal node names in ancestral.pml

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

#105 - remove duplicated "with the" in bootstrap doc

Pull Request - State: closed - Opened by josephwb almost 4 years ago

#104 - attributes switched when producing trees using random.addition()

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

#103 - Should the RF.dist function emit a warning for non-binary tree if Normalize=FALSE?

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

#102 - acctrans sporadic demand for a binary tree

Issue - State: closed - Opened by axelwilhelm almost 4 years ago - 1 comment

#101 - Minor update in superTree documentation

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

#100 - Long vectors not supported when doing computation with dist.hamming

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

#99 - [conda] r-phangorn misses depenency openblas

Issue - State: open - Opened by lmuenter over 4 years ago - 2 comments

#97 - Inconsistent output from `SPR.dist()`

Issue - State: closed - Opened by ms609 over 4 years ago - 4 comments

#96 - How to output all the bootstrap trees

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

#95 - optim.pml error missing value where TRUE/FALSE neede

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

#94 - creating phyolgenetic tree using continuous data

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

#93 - Write ancestral reconstruction to file

Issue - State: closed - Opened by surh over 4 years ago - 6 comments

#92 - Memory leak in C_sprdist

Pull Request - State: closed - Opened by ms609 over 4 years ago - 2 comments

#91 - read.phydat error in snphylo

Issue - State: closed - Opened by birsandhu almost 5 years ago - 6 comments

#90 - densiTree does not show title

Issue - State: closed - Opened by richelbilderbeek almost 5 years ago - 1 comment

#89 - optim.pml()

Issue - State: open - Opened by JacobAFW almost 5 years ago

#88 - unexpected tiplabels behavior using network imported from splitstree

Issue - State: open - Opened by tim-oconnor almost 5 years ago - 1 comment

#87 - One tree has a different number of tips - bootstrap.pml() function runs

Issue - State: open - Opened by alptaciroglu almost 5 years ago - 2 comments

#85 - Adding co-authors broke build 2

Issue - State: open - Opened by richelbilderbeek almost 5 years ago

#84 - Fix quotes

Pull Request - State: closed - Opened by richelbilderbeek almost 5 years ago - 1 comment

#83 - Fix brackets

Pull Request - State: closed - Opened by richelbilderbeek almost 5 years ago - 2 comments

#82 - Adding co-authors broke build

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

#81 - Problems importing tree from Splitstree

Issue - State: closed - Opened by ywx1 about 5 years ago - 10 comments

#80 - Clarify simSeq documentation

Pull Request - State: closed - Opened by ms609 about 5 years ago - 2 comments

#79 - Minor fix on line 23

Pull Request - State: closed - Opened by kant about 5 years ago

#78 - Memory not mapped error when working on DECIPHER and phangorn packages

Issue - State: open - Opened by alptaciroglu over 5 years ago - 2 comments

#77 - Phangorn Midpoint root changing branch lengths

Issue - State: closed - Opened by lchall08 over 5 years ago - 1 comment

#76 - plotBS alternate or adaptation for 1000 node tree

Issue - State: closed - Opened by alptaciroglu over 5 years ago - 1 comment

#75 - How to extract the result of pratchet() ?

Issue - State: closed - Opened by Tina9 over 5 years ago - 5 comments

#74 - optim.pml not stopping iterating

Issue - State: open - Opened by nemartins over 5 years ago - 1 comment