phylofactor

amalg.ILR | amalgamate two groups in a compositional data matrix to... |

binPhyloPlot | Color bins on a plot of a phylogeny |

bins | Outputs bins from a partition matrix, V, or from a list of... |

binTaxa | returns the taxonomic identity of taxa in bins |

checkData | internal 'PhyloFactor' quality-control function |

clo | Closure function |

ColorTaxa | Colors tree edges based on taxanomic ID |

compData | replaces zeros and transforms data to relative abundances |

crossVmap | maps groups from old to new communities for phylofactor... |

decideMethod | decides Method automatically for phyca and twoSample data... |

extractEdges | Function by Dom J. Bennett from MoreTreeTools. Function... |

findInterruptions | Finds interrupting edges along chain of edges |

find.unsplit.Grps | Finds unsplit groups in a signed partition matrix, V |

findWinner | Internal PhyloRegression function for finding the winning... |

FTmicrobiome | Fecal Tongue Microbiome Dataset |

GAM | internal generalized additive model method for 'PhyloFactor'... |

getAssignedGroups | internal function for parallelized phylofactor |

getFactoredEdges | Returns edges from a phylofactor |

getFactoredEdgesPAR | Parallelized version of getFactoredEdges |

getLabelledGrp | Internal phylofactor function - get labelled Group from... |

getNewGroups | Internal phylofactor function - get new grouplist... |

getObjective | objective function for 'gpf' |

getPhyloGroups | Get list of groups defined by phylogeny |

getStats | Grabs P value, F statistic and difference between null and... |

gMean | Computes geometric mean using logarithms |

gpf | Generalized phylofactorization - currently skeleton for... |

HGTplot | Visualize results form simHGT |

ilrInv | Function to take inverse of ilr transform |

ilrvec | Internal function for computing an ilr balancing element... |

listTaxa | Lists all unique taxonomic names in a Taxonomy at a given... |

logData | replaces zeros and log-transforms data |

mAggregation | marginally stable aggregation of binomial data |

matrix.to.phyloframe | Converts matrix to phyloframe |

OTUtoTaxa | Input OTUs and outputs their taxonomic detail, optinally... |

pf.BINprojection | Projects phylofactored data onto bins defined by the factors... |

pf.flow | Generates flow of phylofactor object |

pf.getPhyloGroups | Gets Groups considered at a given factor level |

pf.groupsTospecies | Converts integer-indexed groups to species-labelled groups in... |

pf.ILRprojection | Projects Data onto basis defined by phylofactor object |

pf.nullsim | Null Simulation of phylofactor object |

pf.plot | Label and visualize phylofactors |

pf.predict | Predicts based on phylofactorization |

pf.summary | Summary of pf object for a given node or factor number |

pf.taxa | summarizes taxonomic composition at given factor |

pf.tidy | Concise summarization of phylofactor summary |

pf.tree | ggtree-based plotting of phylofactor bins or factors |

pglm | Internal wrapper for 'glm' for phylofactor |

PhyCA | Performs Phylogenetic Principal Components Analysis |

phyca.tidy | clean description of phca object |

phylobin | get bin number for species |

PhyloFactor | Regression-based phylofactorization |

phyloFcluster | Produces cluster object with necessary libraries to perform... |

phyloFrame | Tacks "phylo" variable onto data frame for 'gpf' |

phyloframe.to.matrix | Converts input data frame for gpf to matrix for faster... |

PhyloRegression | PhyloFactor internal function to prep, find and summarize the... |

pvDeviance | obtains deviance for partitioning variables - default... |

replaceZeros | replace zeros in Data for compositional data. |

simHGT | Simulates brownian motion with HGT between random clades via... |

TaxaSplit | Describes the taxa split at a particular factor summarized by... |

trimTree | trims tree to tip-labels in dataset. |

twoSampleFactor | Phylofactorization of vector data using two-sample tests |

uniqueTaxa | Find shortest unique prefix in two taxonomic lists x and y |

updateBinList | Updates Bin list given a split group |

updateTreeList | internal Phylofactor function - splits the tree corresponding... |

VAR | Computes variance for 'PhyloFactor' method='max.var' |

whichBinSplit | Internal function - id which bin in binList split |

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