Package: Apoderoides 3.0.0
Satoshi Aoki
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.tar.gz(r-4.5-noble)Apoderoides_3.0.0.tar.gz(r-4.4-noble)
Apoderoides_3.0.0.tgz(r-4.4-emscripten)Apoderoides_3.0.0.tgz(r-4.3-emscripten)
Apoderoides.pdf |Apoderoides.html✨
Apoderoides/json (API)
NEWS
| # Install 'Apoderoides' in R: |
| install.packages('Apoderoides', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sa-to-shi-a-o-ki/apoderoides/issues
- testRankList - TestRankList
- testTree - TestTree
Last updated 4 months agofrom:3ba50469b9. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 09 2024 |
| R-4.5-linux-x86_64 | OK | Oct 09 2024 |
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 |
