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

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Apoderoides.pdf |Apoderoides.html
Apoderoides/json (API)
NEWS

# Install 'Apoderoides' in R:
install.packages('Apoderoides', repos = c('https://sa-to-shi-a-o-ki.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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:

On CRAN:

3.78 score 2 scripts 260 downloads 18 exports 6 dependencies

Last updated 4 months agofrom:d206449a55. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 08 2024
R-4.5-win-x86_64OKOct 08 2024
R-4.5-linux-x86_64OKOct 08 2024
R-4.4-win-x86_64OKOct 08 2024
R-4.4-mac-x86_64OKOct 08 2024
R-4.4-mac-aarch64OKOct 08 2024
R-4.3-win-x86_64OKOct 08 2024
R-4.3-mac-x86_64OKOct 08 2024
R-4.3-mac-aarch64OKOct 08 2024

Exports:autoDeletioncalc.ScorecalcIntScore_CcalcOutScore_CdeleteAnomalydeleteSubFuncextractOTUbyRankName_CfindSubTips_CfindUpperNodeget.upperRankgetAllCentroidsgetAllCentroids_CgetAllMRCAsgetAllRankNamesgetRankCentroid_CgetRankMRCAgetTipNo_Cis.monophyleticByRank

Dependencies:apedigestlatticenlmeRcppRcppProgress

Apoderoides Tutorial

Rendered fromvignette.Rmdusingknitr::rmarkdownon Oct 08 2024.

Last update: 2024-07-10
Started: 2024-06-14

Readme and manuals

Help Manual

Help pageTopics
Internal Apoderoides FunctionscalcIntScore_C calcOutScore_C deleteSubFunc extractOTUbyRankName_C findSubTips_C findUpperNode getAllCentroids_C getAllRankNames getRankCentroid_C getRankMRCA getTipNo_C is.monophyleticByRank
autoDeletionautoDeletion
calc.Scorecalc.Score
deleteAnomalydeleteAnomaly
get.upperRankget.upperRank
getAllCentroidsgetAllCentroids
getAllMRCAsgetAllMRCAs
testRankListtestRankList
testTreetestTree