Package: phyext2 0.0.4

phyext2: An Extension (for Package 'SigTree') of Some of the Classes in Package 'phylobase'

Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.

Authors:J. Conrad Stack

phyext2_0.0.4.tar.gz
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phyext2.pdf |phyext2.html✨
phyext2/json (API)
NEWS

# Install 'phyext2' in R:
install.packages('phyext2', repos = c('https://johnrstevens.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.48 score 1 packages 8 scripts 158 downloads 58 exports 50 dependencies

Last updated 9 years agofrom:37038c4372. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winOKNov 14 2024
R-4.5-linuxOKNov 14 2024
R-4.4-winOKNov 14 2024
R-4.4-macOKNov 14 2024
R-4.3-winOKNov 14 2024
R-4.3-macOKNov 14 2024

Exports:.edge.index.get.nexus.block.inds.split.tokens.strip.tree.commentsaddSubNodecollapse.singletonscollapse.subnodescollapse.to.singlescontDatadeep.phy.copydiscDataexpand.singlesget.nexus.commentsget.nodenamesget.tree.weightsgetEmptyDataFramegetSubNodeDatagetSubNodeEdgeIndsgetSubNodePosishguess.datatypehas.blockhas.characters2has.weightshasDatahasDataColumnhasSubNodeshasWeightis.simmapmatch.ordernewlabels.v15newlabels.v1xnoneDatanSubNodesphyextphyextPlotread.characters2read.nexus.blockread.nexus.simmapread.simmapread.simmap.newrmdatashowSubNodessnbranchsndatasndata<-snidsnpositionstriptipdate.citreeHeightvalidPhylo4d_extweightweight<-write.characters2write.nexus.simmapwrite.simmapwrite.simmap.newwrite.simmap.old

Dependencies:ade4apeaskpassclicpp11crayoncurldigestdplyrfansigenericsgluehmshttrjsonlitelatticelifecyclemagrittrMASSmimenlmeopensslphylobasepillarpixmappkgconfigplyrprettyunitsprogresspurrrR6RcppRcppArmadilloreshape2rlangrnclRNeXMLspstringistringrsystibbletidyrtidyselectutf8uuidvctrswithrXMLxml2

Readme and manuals

Help Manual

Help pageTopics
Misc. functions from phyext packageaddSubNode collapse.singletons collapse.subnodes collapse.to.singles contData deep.phy.copy discData expand.singles get.nexus.comments get.nodenames get.tree.weights getEmptyDataFrame getSubNodeData getSubNodeEdgeInds getSubNodePosish guess.datatype has.block has.characters2 has.weights is.simmap match.order newlabels.v15 newlabels.v1x noneData nSubNodes phyextPlot read.characters2 read.nexus.block read.nexus.simmap read.simmap read.simmap.new showSubNodes strip tipdate.ci validPhylo4d_ext write.characters2 write.nexus.simmap write.simmap write.simmap.new write.simmap.old
Misc. functions from phyext package (class definitions)as as,phylo,phylo4d_ext-method as,phylo4,phylo4d_ext-method as,phylo4d,phylo4d_ext-method as-method coerce,phylo,phylo4d_ext-method coerce,phylo4,phylo4d_ext-method coerce,phylo4d,phylo4d_ext-method coerce-methods hasWeight hasWeight,list-method hasWeight,phylo4d_ext-method phylo4d_ext-class plot,phylo4d_ext,missing-method show,phylo4d_ext-method snbranch snbranch,list-method snbranch,phylo4d_ext-method sndata sndata,list-method sndata,phylo4d_ext-method sndata<- sndata<-,list-method sndata<-,phylo4d_ext-method snid snid,list-method snid,phylo4d_ext-method snposition snposition,list-method snposition,phylo4d_ext-method weight weight,list-method weight,phylo4d_ext-method weight<- weight<-,list-method weight<-,phylo4d_ext-method
Misc. functions from phyext package (methods definitions)hasData hasData,list-method hasData,phylo-method hasData,phylo4-method hasData,phylo4d-method hasData-methods hasDataColumn hasDataColumn,phylo,ANY-method hasDataColumn,phylo4,ANY-method hasDataColumn,phylo4d,character-method hasDataColumn,phylo4d,numeric-method hasDataColumn-methods hasSubNodes hasSubNodes,list-method hasSubNodes,phylo-method hasSubNodes,phylo4-method hasSubNodes,phylo4d_ext-method hasSubNodes-methods phyext phyext,character-method phyext,list-method phyext,phylo-method phyext,phylo4-method phyext,phylo4d-method phyext,phylo4d_ext-method phyext-methods rmdata rmdata,brownie,character,missing-method rmdata,brownie,numeric,ANY-method rmdata,brownie,numeric,missing-method rmdata,brownie,numeric,numeric-method rmdata,list,ANY,missing-method rmdata,phylo4d,character,missing-method rmdata,phylo4d,numeric,missing-method rmdata,phylo4d_ext,character,missing-method rmdata,phylo4d_ext,numeric,missing-method rmdata,phylo4d_ext,numeric,numeric-method rmdata-methods treeHeight treeHeight,phylo4-method treeHeight,phylo4d-method treeHeight,phylo4d_ext-method treeHeight-methods