This package is considered a duplicate. The official version of this package is found at:https://sa-to-shi-a-o-ki.r-universe.dev/Apoderoides

Package: Apoderoides 3.0.1

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:Satoshi Aoki [aut, cph, cre], Keita Fukasawa [ctb]

Apoderoides_3.0.1.tar.gz
Apoderoides_3.0.1.tar.gz(r-4.7-arm64)Apoderoides_3.0.1.tar.gz(r-4.7-x86_64)Apoderoides_3.0.1.tar.gz(r-4.6-arm64)Apoderoides_3.0.1.tar.gz(r-4.6-x86_64)
Apoderoides_3.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

testRankList - TestRankList
testTree - TestTree

On CRAN:

cpp openmp

2.00 score 2 scripts 248 downloads 18 exports 6 dependencies

Last updated from:63b07d223b. Checks:6 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	123
linux-devel-x86_64	OK	127
source / vignettes	OK	171
linux-release-arm64	OK	121
linux-release-x86_64	OK	162
wasm-release	OK	106

Exports:autoDeletion calc.Score calcIntScore_C calcOutScore_C deleteAnomaly deleteSubFunc extractOTUbyRankName_C findSubTips_C findUpperNode get.upperRank getAllCentroids getAllCentroids_C getAllMRCAs getAllRankNames getRankCentroid_C getRankMRCA getTipNo_C is.monophyleticByRank

Dependencies:ape digest lattice nlme Rcpp RcppProgress

Apoderoides Tutorial

Satoshi Aoki

Rendered fromvignette.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2024-07-11
Started: 2024-06-15

Citation

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