Man pages for reptalex/phylofactor
phylofactor

amalg.ILRamalgamate two groups in a compositional data matrix to...
binPhyloPlotColor bins on a plot of a phylogeny
binsOutputs bins from a partition matrix, V, or from a list of...
binTaxareturns the taxonomic identity of taxa in bins
checkDatainternal 'PhyloFactor' quality-control function
cloClosure function
ColorTaxaColors tree edges based on taxanomic ID
compDatareplaces zeros and transforms data to relative abundances
crossVmapmaps groups from old to new communities for phylofactor...
decideMethoddecides Method automatically for phyca and twoSample data...
extractEdgesFunction by Dom J. Bennett from MoreTreeTools. Function...
findInterruptionsFinds interrupting edges along chain of edges
find.unsplit.GrpsFinds unsplit groups in a signed partition matrix, V
findWinnerInternal PhyloRegression function for finding the winning...
FTmicrobiomeFecal Tongue Microbiome Dataset
GAMinternal generalized additive model method for 'PhyloFactor'...
getAssignedGroupsinternal function for parallelized phylofactor
getFactoredEdgesReturns edges from a phylofactor
getFactoredEdgesPARParallelized version of getFactoredEdges
getLabelledGrpInternal phylofactor function - get labelled Group from...
getNewGroupsInternal phylofactor function - get new grouplist...
getObjectiveobjective function for 'gpf'
getPhyloGroupsGet list of groups defined by phylogeny
getStatsGrabs P value, F statistic and difference between null and...
gMeanComputes geometric mean using logarithms
gpfGeneralized phylofactorization - currently skeleton for...
HGTplotVisualize results form simHGT
ilrInvFunction to take inverse of ilr transform
ilrvecInternal function for computing an ilr balancing element...
listTaxaLists all unique taxonomic names in a Taxonomy at a given...
logDatareplaces zeros and log-transforms data
mAggregationmarginally stable aggregation of binomial data
objectiveFunctionobjective function for generalized phylofactorization
OTUtoTaxaInput OTUs and outputs their taxonomic detail, optinally...
pf.BINprojectionProjects phylofactored data onto bins defined by the factors...
pf.flowGenerates flow of phylofactor object
pf.getPhyloGroupsGets Groups considered at a given factor level
pf.ILRprojectionProjects Data onto basis defined by phylofactor object
pf.nullsimNull Simulation of phylofactor object
pf.plotLabel and visualize phylofactors
pf.predictPredicts based on phylofactorization
pf.summarySummary of pf object for a given node or factor number
pf.tidyConcise summarization of phylofactor summary
pf.treeggtree-based plotting of phylofactor bins or factors
pglmInternal wrapper for 'glm' for phylofactor
PhyCAPerforms Phylogenetic Principal Components Analysis
phyca.tidyclean description of phca object
phylobinget bin number for species
PhyloFactorRegression-based phylofactorization
phyloFclusterProduces cluster object with necessary libraries to perform...
phylo.frame.to.matrixconverts data frame in appropriate phylofactor format to...
PhyloRegressionPhyloFactor internal function to prep, find and summarize the...
replaceZerosreplace zeros in Data for compositional data.
simHGTSimulates brownian motion with HGT between random clades via...
TaxaSplitDescribes the taxa split at a particular factor summarized by...
trimTreetrims tree to tip-labels in dataset.
twoSampleFactorPhylofactorization of vector data using two-sample tests
uniqueTaxaFind shortest unique prefix in two taxonomic lists x and y
updateBinListUpdates Bin list given a split group
updateTreeListinternal Phylofactor function - splits the tree corresponding...
VARComputes variance for 'PhyloFactor' method='max.var'
whichBinSplitInternal function - id which bin in binList split
reptalex/phylofactor documentation built on Dec. 13, 2017, 9:16 p.m.