1 Aim of this package, Apoderoides | 2 Installation | 3 How to use | 3.1 Import a phylogenetic tree | 3.2 Score calculation | 3.2.1. Score at genus level | 3.2.2. Score at the other rank | 3.3 Auto deletion of erroneous tree tips | 3.4 The other utilities to help analysis
Package: Apoderoides 3.0.0
Apoderoides: Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree
Finds, prioritizes and deletes erroneous taxa in a phylogenetic tree. This package calculates scores for taxa in a tree. Higher score means the taxon is more erroneous. If the score is zero for a taxon, the taxon is not erroneous. This package also can remove all erroneous taxa automatically by iterating score calculation and pruning taxa with the highest score.
Authors:
Apoderoides_3.0.0.tar.gz
Apoderoides_3.0.0.zip(r-4.7)Apoderoides_3.0.0.zip(r-4.6)Apoderoides_3.0.0.zip(r-4.5)
Apoderoides_3.0.0.tgz(r-4.6-x86_64)Apoderoides_3.0.0.tgz(r-4.6-arm64)Apoderoides_3.0.0.tgz(r-4.5-x86_64)Apoderoides_3.0.0.tgz(r-4.5-arm64)
Apoderoides_3.0.0.tar.gz(r-4.7-arm64)Apoderoides_3.0.0.tar.gz(r-4.7-x86_64)Apoderoides_3.0.0.tar.gz(r-4.6-arm64)Apoderoides_3.0.0.tar.gz(r-4.6-x86_64)
Apoderoides_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Apoderoides/json (API)
| # Install 'Apoderoides' in R: |
| install.packages('Apoderoides', repos = c('https://sa-to-shi-a-o-ki.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sa-to-shi-a-o-ki/apoderoides/issues
Datasets:
- testRankList - TestRankList
- testTree - TestTree
Last updated from:d206449a55. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 149 | ||
| linux-devel-x86_64 | OK | 127 | ||
| source / vignettes | OK | 160 | ||
| linux-release-arm64 | OK | 130 | ||
| linux-release-x86_64 | OK | 165 | ||
| macos-release-arm64 | OK | 127 | ||
| macos-release-x86_64 | OK | 238 | ||
| macos-oldrel-arm64 | OK | 134 | ||
| macos-oldrel-x86_64 | OK | 309 | ||
| windows-devel | OK | 113 | ||
| windows-release | OK | 111 | ||
| windows-oldrel | OK | 151 | ||
| wasm-release | OK | 135 |
Exports:autoDeletioncalc.ScorecalcIntScore_CcalcOutScore_CdeleteAnomalydeleteSubFuncextractOTUbyRankName_CfindSubTips_CfindUpperNodeget.upperRankgetAllCentroidsgetAllCentroids_CgetAllMRCAsgetAllRankNamesgetRankCentroid_CgetRankMRCAgetTipNo_Cis.monophyleticByRank
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Internal Apoderoides Functions | calcIntScore_C calcOutScore_C deleteSubFunc extractOTUbyRankName_C findSubTips_C findUpperNode getAllCentroids_C getAllRankNames getRankCentroid_C getRankMRCA getTipNo_C is.monophyleticByRank |
| autoDeletion | autoDeletion |
| calc.Score | calc.Score |
| deleteAnomaly | deleteAnomaly |
| get.upperRank | get.upperRank |
| getAllCentroids | getAllCentroids |
| getAllMRCAs | getAllMRCAs |
| testRankList | testRankList |
| testTree | testTree |
