Package: apex 1.0.6
Klaus Schliep
apex: Phylogenetic Methods for Multiple Gene Data
Toolkit for the analysis of multiple gene data (Jombart et al. 2017) <doi:10.1111/1755-0998.12567>. 'apex' implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.
Authors:
apex_1.0.6.tar.gz
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apex_1.0.6.tgz(r-4.4-any)apex_1.0.6.tgz(r-4.3-any)
apex_1.0.6.tar.gz(r-4.5-noble)apex_1.0.6.tar.gz(r-4.4-noble)
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apex.pdf |apex.html✨
apex/json (API)
NEWS
| # Install 'apex' in R: |
| install.packages('apex', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thibautjombart/apex/issues
Last updated 10 months agofrom:7d6898226e. Checks:ERROR: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Nov 25 2024 |
| R-4.5-win | ERROR | Nov 25 2024 |
| R-4.5-linux | ERROR | Nov 25 2024 |
| R-4.4-win | ERROR | Nov 25 2024 |
| R-4.4-mac | ERROR | Nov 25 2024 |
| R-4.3-win | ERROR | Nov 25 2024 |
| R-4.3-mac | ERROR | Nov 25 2024 |
Exports:add.gapsconcatenatedist.multidnagetLocusNamesgetNumIndgetNumLocigetNumSequencesgetSequenceNamesgetSequencesgetTreeinitializemultidna2alignmentmultidna2genindmultidna2multiphyDatmultiphyDat2alignmentmultiphyDat2genindmultiphyDat2multidnaplotread.multidnaread.multiFASTAread.multiphyDatrm.gapssetLocusNames<-show
Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2gluegtablehtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepermutephangornpillarpixmappkgconfigplyrpromisesquadprogR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangsassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vctrsveganviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Subset multidna objects | [,multidna,ANY,ANY,ANY-method [,multidna-method [,multiphyDat,ANY,ANY,ANY-method [,multiphyDat-method [.multidna [.multiphyDat |
| multidna Accessors | accessors getLocusNames getLocusNames,multidna getLocusNames,multidna-method getLocusNames,multiphyDat getLocusNames,multiphyDat-method getNumInd getNumInd,multidna getNumInd,multidna-method getNumInd,multiphyDat getNumInd,multiphyDat-method getNumLoci getNumLoci,multidna getNumLoci,multidna-method getNumLoci,multiphyDat getNumLoci,multiphyDat-method getNumSequences getNumSequences,multidna getNumSequences,multidna-method getNumSequences,multiphyDat getNumSequences,multiphyDat-method getSequenceNames getSequenceNames,multidna getSequenceNames,multidna-method getSequenceNames,multiphyDat getSequenceNames,multiphyDat-method getSequences getSequences,multidna getSequences,multidna-method getSequences,multiphyDat getSequences,multiphyDat-method setLocusNames<- setLocusNames<-,multidna setLocusNames<-,multidna-method setLocusNames<-,multiphyDat setLocusNames<-,multiphyDat-method |
| Add gap-only sequences for missing data | add.gaps add.gaps,multidna-method add.gaps,multiphyDat-method add.gaps.generic add.gaps.multidna add.gaps.multiphyDat |
| Concatenate genes into a single matrix | concatenate concatenate,multidna-method concatenate,multiphyDat-method concatenate.generic concatenate.multidna concatenate.multiphyDat |
| Pairwise distances for multiple gene data | dist.multidna |
| Build phylogenies from multiple gene data | getTree |
| multidna constructor | initialize,multidna-method initialize,multidna-methods new.multidna |
| multiphyDat constructor | initialize,multiphyDat-method initialize,multiphyDat-methods new.multiphyDat |
| multidna: class for multiple gene data | data.frameOrNULL listOrNULL multidna multidna-class |
| Convert from multidna into alignment (seqinr) | multidna2alignment multiphyDat2alignment |
| Convert multidna into genind | multidna2genind multiphyDat2genind |
| Conversions between multidna and multiphyDat | multidna2multiphyDat multiphyDat2multidna |
| multiphyDat: class for multiple gene data | multiphyDat multiphyDat-class |
| Display multidna objects | plot,multidna-method plot.multidna |
| Read multiple DNA alignments | read.multidna read.multiFASTA read.multiphyDat |
| Remove gap-only sequences for missing data | rm.gaps rm.gaps,multidna-method rm.gaps,multiphyDat-method rm.gaps.generic rm.gaps.multidna rm.gaps.multiphyDat |
| Display multidna objects | show,multidna-method show.multidna |
| Display multiphyDat objects | show,multiphyDat-method show.multiphyDat |
