ms609/TreeTools issues and pull requests

#165 - Binary decomposition of additive characters

Pull Request - State: closed - Opened by ms609 about 1 month ago - 1 comment

#164 - Update to Bootstrap 5

Issue - State: open - Opened by ms609 about 1 month ago

#163 - v1.12.0

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

#162 - TopologyOnly()

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

#161 - Optimise `MatchNodes()`

Issue - State: open - Opened by ms609 2 months ago

#160 - Robust, Universal tree balance

Pull Request - State: closed - Opened by ms609 4 months ago

#159 - Use log factorials to allow TCI to be calculated for larger trees

Pull Request - State: closed - Opened by ms609 4 months ago

#158 - TCIContext(tree)$maximum overflow

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

#157 - Root tree on random edge

Pull Request - State: closed - Opened by ms609 6 months ago - 1 comment

#156 - Replace `.C` with `.Call`

Pull Request - State: closed - Opened by ms609 6 months ago - 1 comment

#155 - Remove `ape_node_depth`

Issue - State: closed - Opened by ms609 6 months ago

#154 - tree$node.label support

Pull Request - State: closed - Opened by ms609 6 months ago - 1 comment

#153 - DescendantEdges → C++

Pull Request - State: closed - Opened by ms609 6 months ago - 1 comment

#152 - Subtree() handles node labels

Pull Request - State: closed - Opened by ms609 6 months ago - 1 comment

#151 - Node numbers in `CollapseNode()`

Pull Request - State: closed - Opened by ms609 6 months ago

#150 - Handle node labels in `AddTip()`

Pull Request - State: closed - Opened by ms609 6 months ago

#149 - If tree has defined node.labels AddTips() will not change them

Issue - State: closed - Opened by stitam 7 months ago - 2 comments

#148 - str method for relevant classes

Issue - State: closed - Opened by ms609 7 months ago - 1 comment

#147 - Simulation of Birth-Death trees

Issue - State: open - Opened by ms609 7 months ago

#146 - YuleTree()

Pull Request - State: closed - Opened by ms609 7 months ago - 1 comment

#145 - Random Trees don't match balance

Issue - State: closed - Opened by ms609 7 months ago - 1 comment

#144 - DropTip will not remove tip on tree

Issue - State: closed - Opened by theo-allnutt-bioinformatics 11 months ago - 2 comments

#143 - Will not install on Rstudio

Issue - State: closed - Opened by theo-allnutt-bioinformatics 11 months ago - 2 comments

#142 - as.TreeNumber not identifying unique topologies

Issue - State: closed - Opened by jblandis 12 months ago - 4 comments

#141 - Error: This many leaves cannot be supported

Issue - State: open - Opened by noranekonobokkusu about 1 year ago - 13 comments
Labels: help wanted

#140 - Custom directory for caching

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

#139 - using WriteTNTcharacters() with continuous matrix

Issue - State: closed - Opened by jc17659 about 1 year ago - 5 comments

#138 - Read MrBayes trees

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

#137 - Tip timed tree

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

#136 - Replace `.C` with `.Call`

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

#135 - as.matrix

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

#134 - GH Actions templates

Issue - State: open - Opened by ms609 almost 2 years ago

#133 - Unsupported NEXUS file

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

#132 - check for na values

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

#131 - Support `ttags` in TNT trees

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

#130 - Consensus of many trees

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

#129 - demo()

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

#128 - Quality of a dataset

Issue - State: open - Opened by ms609 over 2 years ago

#127 - `ClusterTable` memory requirements

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

#126 - Multiline TNT

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

#125 - NexusTokens() shiny interaction

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

#124 - v1.7.2: Lapse Preorder

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

#123 - Tree balance index

Issue - State: open - Opened by ms609 over 2 years ago

#122 - R implementation of `ClusterTable` class

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

#121 - `as.MixedBase()` hangs (in `sort.multiPhylo()`)

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

#120 - Edge length issues

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

#119 - v1.7.0

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

#118 - C++ split manipulation

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

#117 - `MSTEdges()` fails gracefully on bad input

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

#116 - Rdpack nobrackets

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

#115 - Reference formatting, once Rdpack > 2.1.3

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

#114 - Fix `DropTip()`

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

#113 - `CollapseNode()` performance

Issue - State: open - Opened by ms609 over 2 years ago

#112 - Unrooted trees in `KeptVerts()`

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

#111 - `KeptPaths()`

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

#110 - Asan diagnostics

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

#109 - Use preorder to post-order

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

#108 - Diagnose ASAN failure

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

#107 - Weighted postorder

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

#106 - Sort weighted trees with SortTree()

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

#105 - Support edge lengths in `Preorder()`

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

#104 - MSTEdges() explodes if sent invalid input

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

#103 - SortTree by tip labels

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

#102 - Drop `drop_tip()`

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

#101 - Use Rcpp light

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

#100 - Deprecate `EnforceOutgroup()`

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

#99 - TNT multiline support

Issue - State: open - Opened by ms609 over 2 years ago

#98 - Convert between TreeNumber and MixedBase

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

#97 - Handle zero-split trees

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

#96 - Don't import `reorder.phylo()`

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

#95 - Make references inline

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

#94 - 1.6.0.9001

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

#93 - "Preorder" classification

Issue - State: open - Opened by ms609 over 2 years ago

#92 - Refactor DropTip()

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

#91 - DropTip(): retain (un)rootedness

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

#90 - Fix RootTree bug & use tabulate()

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

#89 - Support edge lengths in `UnrootTree()`

Issue - State: closed - Opened by marwa38 almost 3 years ago - 2 comments

#88 - Format of the tree?

Issue - State: closed - Opened by marwa38 almost 3 years ago - 2 comments

#87 - Remove phangorn dependency

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

#86 - v1.5.1

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

#85 - Implement `sort.multiPhylo()`

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

#84 - Sort trees by TreeNumber

Issue - State: closed - Opened by ms609 about 3 years ago

#83 - Switch order of equality & condition expectations

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

#82 - RoguePlot() width scales with `p` (i.e. consensus proportion)

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

#81 - v1.5.0

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

#80 - multiPhylo object with single `tip.label` not supported

Issue - State: closed - Opened by ms609 about 3 years ago

#79 - TestThat edition 3

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

#78 - `Consensus()`

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

#77 - Revert "`Consensus()`"

Pull Request - State: closed - Opened by ms609 about 3 years ago

#76 - ape memory allocation issues

Issue - State: closed - Opened by ms609 about 3 years ago

#75 - `Consensus()`

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

#74 - Plot position of rogue taxa

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

#73 - Remove Postorder tree size limit

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

#72 - artefacts

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

#71 - Optimize postorder

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

#70 - Upgrade to testthat edition 3

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

#69 - revdepcheck workflow

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

#68 - simplify quicksort_by_smallest()

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

#67 - Optimize postorder

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

#66 - preorder_edges_and_nodes

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

GitHub / ms609/TreeTools issues and pull requests