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:Klaus Schliep [aut, cre], Thibaut Jombart [aut], Zhian Namir Kamvar [aut], Eric Archer [aut], Rebecca Harris [aut]

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apex.pdf |apex.html✨
apex/json (API)
NEWS

# Install 'apex' in R:

install.packages('apex', repos = c('https://thibautjombart.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/thibautjombart/apex/issues

On CRAN:

6.65 score 5 stars 54 scripts 1.1k downloads 3 mentions 24 exports 75 dependencies

Last updated 10 months agofrom:7d6898226e. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 02 2024
R-4.5-win	NOTE	Nov 02 2024
R-4.5-linux	NOTE	Nov 02 2024
R-4.4-win	OK	Nov 02 2024
R-4.4-mac	OK	Nov 02 2024
R-4.3-win	OK	Nov 02 2024
R-4.3-mac	OK	Nov 02 2024

Exports:add.gaps concatenate dist.multidna getLocusNames getNumInd getNumLoci getNumSequences getSequenceNames getSequences getTree initialize multidna2alignment multidna2genind multidna2multiphyDat multiphyDat2alignment multiphyDat2genind multiphyDat2multidna plot read.multidna read.multiFASTA read.multiphyDat rm.gaps setLocusNames<-show

Dependencies:ade4 adegenet ape base64enc boot bslib cachem cli cluster colorspace commonmark cpp11 crayon digest dplyr fansi farver fastmap fastmatch fontawesome fs generics ggplot2 glue gtable htmltools httpuv igraph isoband jquerylib jsonlite labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme permute phangorn pillar pixmap pkgconfig plyr promises quadprog R6 rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rlang sass scales segmented seqinr shiny sourcetools sp stringi stringr tibble tidyselect utf8 vctrs vegan viridisLite withr xtable

Phylogenetic Methods for Multiple Gene Data

Thibaut Jombart

Rendered fromapex.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2024-01-29
Started: 2015-03-26

Citation

Development and contributors

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