| amalgamate | Amalgamation contrast function |
| BalanceContrast | Project data matrix onto balance contrast (if data are... |
| bins | Outputs bins from a partition matrix, V, or from a list of... |
| clo | Closure function |
| crossVmap | maps groups from old to new communities for phylofactor... |
| 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 |
| getSignal | Replicate objective from phylofactor object |
| getStats | Grabs P value, F statistic and difference between null and... |
| gMean | Computes geometric mean using logarithms |
| gpf | Generalized phylofactorization |
| 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... |
| 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.crossValidateMap | Function for mapping phylogenetic factors in a phylofactor... |
| 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.heatmap | Heatmap for phylofactor data |
| 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.resume | Resume phylofactorization for a phylofactor object |
| 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... |
| predict.phylofactor | predict newdata with phylofactor object. Only works for... |
| print.phylofactor | Prints phylofactor class objects |
| print.phylofactor.summary | Prints phylofactor.summary objects |
| pvDeviance | obtains deviance for partitioning variables - default... |
| simHGT | Simulates brownian motion with HGT between random clades via... |
| summary.phylofactor | Summarize phylofactor objects |
| TaxaSplit | Describes the taxa split at a particular factor summarized by... |
| taxaTree | make tree from vector of standardized taxonomies |
| 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 |
