Introduction | The Phylogenetic eigenvector maps (PEM) expression | Preparing the data | Calculating PEM | Edge weighting function | Phylogenetic graph | Building the eigenvector map | Heterogeneous evolutionary process | Estimate weighting parameters empirically | Prediction scores | Phylogenetic modelling | Making predictions | Cross-validation of PEM predictions | Other utility functions | Influence matrix | Update and a PEM with new parameters | References
Package: MPSEM 0.6-1
Guillaume Guénard
MPSEM: Modelling Phylogenetic Signals using Eigenvector Maps
Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Authors:
MPSEM_0.6-1.tar.gz
MPSEM_0.6-1.zip(r-4.7-x86_64)MPSEM_0.6-1.zip(r-4.7-arm64)MPSEM_0.6-1.zip(r-4.6-x86_64)MPSEM_0.6-1.zip(r-4.6-arm64)MPSEM_0.6-1.zip(r-4.5-x86_64)
MPSEM_0.6-1.tgz(r-4.6-x86_64)MPSEM_0.6-1.tgz(r-4.6-arm64)MPSEM_0.6-1.tgz(r-4.5-x86_64)MPSEM_0.6-1.tgz(r-4.5-arm64)
MPSEM_0.6-1.tar.gz(r-4.7-arm64)MPSEM_0.6-1.tar.gz(r-4.7-x86_64)MPSEM_0.6-1.tar.gz(r-4.6-arm64)MPSEM_0.6-1.tar.gz(r-4.6-x86_64)
MPSEM_0.6-1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MPSEM/json (API)
| # Install 'MPSEM' in R: |
| install.packages('MPSEM', repos = c('https://guenardg.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/guenardg/mpsem/issues
Last updated from:6c44d72d81. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 130 | ||
| linux-devel-x86_64 | OK | 162 | ||
| source / vignettes | OK | 190 | ||
| linux-release-arm64 | OK | 128 | ||
| linux-release-x86_64 | OK | 167 | ||
| macos-release-arm64 | OK | 172 | ||
| macos-release-x86_64 | OK | 227 | ||
| macos-oldrel-arm64 | OK | 193 | ||
| macos-oldrel-x86_64 | OK | 429 | ||
| windows-devel-arm64 | OK | 354 | ||
| windows-devel-x86_64 | OK | 171 | ||
| windows-release-arm64 | OK | 364 | ||
| windows-release-x86_64 | OK | 110 | ||
| windows-oldrel-x86_64 | OK | 102 | ||
| wasm-release | OK | 147 |
Exports:add.edgeadd.vertexaggregateOnVertexas.graphconcatenateDNAratedrawDNASequencedrawEvolRatedstGraphedgeedge<-edgenamesedgenames<-evolution.modelgeometrygeometry<-getConnectedgetMediangetNonConnectedgetOrigingetTerminalgraphgraphDistgraphModplothmeanInflMatinvDistWeightingisDivergentisLinearisTreeisUnderEdgeisUnderVertexlabels<-locatemodel.datamolEvolSimnedgePEMpemlmPEMweightsPsquarepurge.medianpurge.terminalrandomGraphreorderGraphrm.edgerm.vertexshow.sequencesimulateSequencesimulateTraittraitEvolSimweighted.hmeanwrite.fasta
Dependencies:apeclassclassIntDBIdigeste1071expmKernSmoothlatticemagrittrMASSMatrixnlmeproxyRcpps2sfunitswk
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Modelling Phylogenetic Signals using Eigenvector Maps | MPSEM-package |
| Sequence Concatenation | concatenate |
| Distance-Based Directed Graph | dstGraph |
| Class and Method for Directed Graphs | $<-.graph as.graph.phylo as.phylo.graph geometry.graph geometry<-.graph graph-class locate.graph nedge.graph plot.graph print.graph |
| MPSEM Graph Manipulation Functions | add.edge add.vertex graph graph-functions rm.edge rm.vertex |
| MPSEM Graph Purging Functions | graph-purge purge.median purge.terminal |
| Graph Utility Functions | getConnected getMedian getNonConnected getOrigin getTerminal graph-utils graphDist isDivergent isLinear isTree reorderGraph |
| Graph Plot Editor | graphModplot |
| Harmonic Mean | harmonicMean hmean weighted.hmean |
| Influence Matrix | edge.InflMat edge<-.InflMat edgenames.InflMat edgenames<-.InflMat InflMat inflMat InflMat-class nedge.InflMat print.InflMat |
| Inverse Distance Weighting | invDistWeighting |
| Linear Modelling Utility Functions | lm-utils model.data Psquare utils |
| Molecular Evolution Simulator | DNArate drawDNASequence drawEvolRate molEvolSim simulateSequence |
| Generic Function (Methods) | as.graph edge edge.graph edge<- edge<-.graph edgenames edgenames.graph edgenames<- edgenames<-.graph evolution.model geometry geometry<- labels<- locate MPSEM-generics nedge |
| Class and Methods for Phylogenetic Eigenvector Maps (PEM) | as.data.frame.PEM as.matrix.PEM evolution.model.PEM PEM PEM-class predict.PEM print.PEM update.PEM |
| Phylogenetic Eigenvector Maps | PEM-functions PEMweights |
| Utility Function for Phylogenetic Eigenvector Maps | aggregateOnVertex isUnderEdge isUnderVertex PEM-utils |
| PEM Linear Model Interface | anova.pemlm pemlm pemlm-class predict.pemlm print.pemlm summary.pemlm |
| Random Graph Generator | randomGraph |
| Show DNA Sequences | show.sequence |
| Trait Evolution Simulator | print.QTEM simulateTrait traitEvolSim |
| Write Sequences to a FASTA Text File | write.fasta |