Ecosyste.ms: Issues

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

GitHub / crsl4/PhyloNetworks.jl issues and pull requests

#212 - documentation: workflow, badges, workshop link, ftest warnings

Pull Request - State: closed - Opened by cecileane about 1 month ago - 5 comments

#211 - fix 2-cycle (parallel edges) bug in snaq

Pull Request - State: closed - Opened by cecileane 2 months ago

#210 - 2-cycle (parallel edges) proposed in SNaQ

Issue - State: closed - Opened by cecileane 3 months ago - 1 comment

#209 - Fix for the slow but constant increase in memory usage

Pull Request - State: closed - Opened by NathanKolbow 5 months ago - 3 comments

#208 - MrBayer error

Issue - State: closed - Opened by tsm-tsm 6 months ago - 3 comments

#206 - fix #201 and #205

Pull Request - State: closed - Opened by cecileane 8 months ago - 1 comment

#205 - fitdiscrete error with new String7 from CSV

Issue - State: closed - Opened by crsl4 8 months ago - 1 comment

#204 - The confusion of starting topology

Issue - State: closed - Opened by zhangwenda0518 9 months ago - 1 comment

#203 - Feedback on Detected EXCEPTION-HANDLING

Issue - State: closed - Opened by zyue110026 10 months ago

#202 - CompatHelper: bump compat for NLopt to 1, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 1 comment

#201 - infinite loop in `readTopologyLevel1`

Issue - State: closed - Opened by NathanKolbow 12 months ago - 8 comments

#200 - for v0.16.2

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

#199 - CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 1 comment

#198 - Inheritance Probability Confidence Interval?

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

#197 - read nexus tree blocks: with translate tables and networks

Pull Request - State: closed - Opened by cecileane about 1 year ago - 2 comments

#196 - near v0.16.0

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

#195 - CompatHelper: bump compat for StatsModels to 0.7, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment

#194 - Get rid of `Tableregressionmodel`

Pull Request - State: closed - Opened by pbastide over 1 year ago - 6 comments

#193 - Support extended Newick?

Issue - State: closed - Opened by cossio over 1 year ago - 7 comments

#192 - Ghost introgression

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

#191 - bootsnaq parallelization error

Issue - State: open - Opened by crsl4 over 1 year ago
Labels: bug

#190 - standardize and export getter names

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

#189 - CompatHelper: bump compat for Functors to 0.4, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment

#188 - bug fix to read table of qCFs

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

#187 - parametric EdgeT with vector of concrete node type

Pull Request - State: closed - Opened by cecileane almost 2 years ago - 9 comments

#186 - better handling of 2-cycle at the root

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

#185 - Get rid of `TableRegressionModel`

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

#184 - v0.15.2: redirect edges if re-rooting failed. new: shrinkedge!

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

#183 - CompatHelper: bump compat for FASTX to 2, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment

#182 - bug fix for biconnected components

Pull Request - State: closed - Opened by cecileane almost 2 years ago - 6 comments

#181 - removedegree2nodes! : option to keep the root

Pull Request - State: closed - Opened by cecileane almost 2 years ago - 4 comments

#180 - Error when the network has negative or missing branches for phylolm

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

#179 - Network with undefined branches makes phylolm fail

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

#178 - CompatHelper: bump compat for Functors to 0.3, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago - 1 comment

#177 - newick parsing: handle negative edge lengths, comments

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

#176 - readTopology with negative edge lengths

Issue - State: closed - Opened by fogg-uw about 2 years ago

#175 - Update nulldeviance for models with no intercept

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

#174 - CompatHelper: bump compat for StatsFuns to 1, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago - 2 comments

#173 - Fast read multi topology

Pull Request - State: closed - Opened by gaballench over 2 years ago - 6 comments

#172 - Project.toml, not REQUIRE

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

#171 - added contributing file

Pull Request - State: closed - Opened by crsl4 over 2 years ago - 3 comments

#168 - PhyloNetworks prevents BioSequences package upgrade

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

#167 - CompatHelper: bump compat for BioSequences to 3, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] over 2 years ago - 1 comment

#166 - Minor doc typo

Issue - State: closed - Opened by crsl4 over 2 years ago - 1 comment

#165 - bug fix, for v0.14.2

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

#164 - CompatHelper: bump compat for CSV to 0.9, (keep existing compat)

Pull Request - State: closed - Opened by github-actions[bot] almost 3 years ago - 1 comment

#163 - CompatHelper: bump compat for "BioSymbols" to "5"

Pull Request - State: closed - Opened by github-actions[bot] about 3 years ago - 1 comment

#162 - Lambda models with individual variation

Issue - State: open - Opened by claireh93 about 3 years ago - 1 comment

#161 - CompatHelper: bump compat for "Distributions" to "0.25"

Pull Request - State: closed - Opened by github-actions[bot] about 3 years ago - 3 comments

#160 - migrate tests+doc from travis-ci to github actions

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

#159 - CompatHelper: bump compat for "DataFrames" to "1.0"

Pull Request - State: closed - Opened by github-actions[bot] about 3 years ago - 2 comments

#157 - TagBot trigger issue

Issue - State: closed - Opened by JuliaTagBot over 3 years ago - 14 comments

#156 - prep for v0.13.0; travis-ci.com migration; rm test broken by GLM v1.4

Pull Request - State: closed - Opened by cecileane over 3 years ago - 2 comments

#155 - performance suggestion make trees more type stable

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

#154 - hybridBootstrapSupport error

Issue - State: closed - Opened by smallfishcui over 3 years ago - 13 comments

#153 - deleteleaf method bug

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

#152 - PhyLiNC manual

Pull Request - State: open - Opened by coraallensavietta over 3 years ago

#151 - CompatHelper: bump compat for "StaticArrays" to "1.0"

Pull Request - State: closed - Opened by github-actions[bot] over 3 years ago - 1 comment

#150 - CompatHelper: bump compat for "DataFrames" to "0.22"

Pull Request - State: closed - Opened by github-actions[bot] over 3 years ago - 2 comments

#149 - CompatHelper: bump compat for "CSV" to "0.8"

Pull Request - State: closed - Opened by github-actions[bot] over 3 years ago - 2 comments

#148 - fliphybrid root fix, nnidistance functions, PhyLiNC fixed network optimization

Pull Request - State: open - Opened by coraallensavietta over 3 years ago - 2 comments

#147 - equal rates model fitdiscrete bug

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

#146 - CompatHelper: bump compat for "Distributions" to "0.24"

Pull Request - State: closed - Opened by github-actions[bot] over 3 years ago - 3 comments

#145 - Tree component functions

Pull Request - State: closed - Opened by jingchengx over 3 years ago - 2 comments

#144 - Add tree_edge_components and updateroot! functions

Pull Request - State: closed - Opened by jingchengx over 3 years ago - 3 comments

#143 - multiple alleles: bug in mapAllelesCFtable?

Issue - State: closed - Opened by cecileane almost 4 years ago - 3 comments

#142 - Fix bug in backward likelihood calculation

Pull Request - State: closed - Opened by coraallensavietta almost 4 years ago - 3 comments

#141 - Cannot precompile PhyloPlots

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

#140 - Extend phyloNetworklm to fit measurement-error models

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

#139 - Flip Hybrid Edge Move

Pull Request - State: closed - Opened by coraallensavietta almost 4 years ago - 8 comments

#138 - writeTopologyLevel1 changes the network when printID=true

Issue - State: open - Opened by crsl4 almost 4 years ago - 2 comments
Labels: to do

#137 - CompatHelper: bump compat for "DataStructures" to "0.18"

Pull Request - State: closed - Opened by github-actions[bot] almost 4 years ago - 7 comments

#136 - major re-write on snaq check root

Issue - State: open - Opened by crsl4 almost 4 years ago - 2 comments
Labels: to do

#135 - Minor fixes: added 2 spaces and QuartetNetwork docstring

Pull Request - State: closed - Opened by crsl4 almost 4 years ago - 16 comments

#134 - Additional Data Info in PhyLiNC prints

Pull Request - State: closed - Opened by coraallensavietta almost 4 years ago - 2 comments

#133 - prep for v0.12.0

Pull Request - State: closed - Opened by cecileane almost 4 years ago - 1 comment

#132 - update to BioSymbols 4.0, BioSequences 2.0, add FASTX

Pull Request - State: closed - Opened by cecileane almost 4 years ago - 2 comments

#131 - update to DataFrames v0.21, CSV v0.7

Pull Request - State: closed - Opened by cecileane almost 4 years ago - 3 comments

#130 - How to use snp to do phylogenetic networks analysis using PhyloNetworks.jl?

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

#129 - write/plot bug when root at leaf

Issue - State: closed - Opened by crsl4 about 4 years ago - 6 comments
Labels: bug

#128 - models for rate variation across sites: +I and +G+I

Pull Request - State: closed - Opened by cecileane about 4 years ago - 6 comments

#127 - hardwiredClusterDistance fix

Pull Request - State: closed - Opened by coraallensavietta about 4 years ago - 4 comments

#126 - multiple alleles: within-species alleles not monophyletic

Issue - State: open - Opened by crsl4 about 4 years ago - 3 comments
Labels: to do

#125 - minor typo in documentation

Issue - State: closed - Opened by crsl4 about 4 years ago - 2 comments

#124 - implementing multivariate BM process

Pull Request - State: closed - Opened by gabehassler about 4 years ago - 11 comments

#123 - bug fixes: root and gamma NaN

Pull Request - State: closed - Opened by coraallensavietta about 4 years ago - 11 comments

#122 - Simulating trait data under multivariate Brownian diffusion

Pull Request - State: closed - Opened by gabehassler about 4 years ago - 5 comments

#121 - AddHybridEdgeLiNC Bug Fix

Pull Request - State: closed - Opened by coraallensavietta about 4 years ago - 5 comments

#120 - wrong warning readTableCF

Issue - State: closed - Opened by crsl4 about 4 years ago - 3 comments

#119 - gradient-based optimization of branch lengths

Pull Request - State: closed - Opened by cecileane about 4 years ago - 8 comments

#118 - readTrees2CF does not work

Issue - State: closed - Opened by migerschw about 4 years ago - 2 comments

#117 - phyLiNC Bug Fixes

Pull Request - State: closed - Opened by coraallensavietta about 4 years ago - 3 comments

#116 - bootstrap step is too slow

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

#115 - Install TagBot as a GitHub Action

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

#114 - Optimize Network Wrappers

Pull Request - State: closed - Opened by coraallensavietta over 4 years ago - 9 comments

#113 - error in hybridlambdaformat

Issue - State: closed - Opened by crsl4 over 4 years ago - 8 comments