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

In reptalex/phylofactor: phylofactor

PhyloFactor internal function to prep, find and summarize the best ILR coordinate

Description

PhyloFactor internal function to prep, find and summarize the best ILR coordinate

Usage

PhyloRegression(TransformedData, X, frmla, Grps = NULL,
  contrast.fcn = NULL, choice, treeList = NULL, cl, totalvar = NULL,
  ix_cl, treetips = NULL, grpsizes = NULL, tree_map = NULL,
  nms = NULL, choice.fcn, method = "glm", ...)

Arguments

TransformedData	Transformed data matrix whose rows are species and columns are samples.
X	independent variables for input into glm.
frmla	Formula for input into glm by lapply(Y,FUN = pglm,x=xx,frmla=frmla,choice,...).
Grps	Groups - a list whose elements are two-element lists containing the groups and their compliments for amalgamation into ILR coordinates
contrast.fcn	Function taking as input contrast.fcn(Grps,TransformedData) and returning a matrix with rows corresponding to Grps and columns corresponding to columns in TransformedData. Must work for both list of Grps and a single element, e.g. Grps[[1]]. For advanced phylofactorization with customized choice.fcn, the output from contrast.fcn is input directly into choice.fcn.
choice	Choice function for determining the group maximizing the objective function. Currently the only allowable inputs are 'var' - minimize residual varaince - and 'F' - minimize test-statistic from anova.
treeList	List of trees formed by phylofactorization and cutting trees along factored edges.
cl	phyloFcluster for built-in parallelization of phylofactorization calculations.
totalvar	Total variance of dataset.
ix_cl	Cluster split of nodes in treeList
treetips	Number of tips in treeList for quickly identifying whether nodes correspond to a root
grpsizes	Number of nodes in each tree of treeList
tree_map	Cumulative number of nodes in trees of treeList - allows rapid mapping of nodes in ix_cl to appropriate tree in treeList.
nms	rownames of TransformedData, allowing reliable mapping of rows of data to tree.
choice.fcn	optional customized choice function to choose 'best' edge; see PhyloFactor
method	See PhyloFactor
...	optional input arguments for glm

reptalex/phylofactor documentation built on Feb. 28, 2024, 3:19 p.m.