getObjective: objective function for 'gpf'

In reptalex/phylofactor: phylofactor

objective function for gpf

Description

objective function for gpf

Usage

getObjective(grp, tree, Data, frmla, MetaData = NULL,
  PartitioningVariables = "", mStableAgg, expfamily = "gaussian",
  model.fcn = stats::glm, objective.fcn = pvDeviance,
  min.group.size = 1, ...)

Arguments

grp	list containing two disjoint lists of species, such as thouse output from getGroups
tree	phylo class object
Data	If mStableAgg==TRUE, a matrix whose rows are species and columns are samples. Otherwise, a data table whose columns include "Species" and "Sample" and whose key is "Species".
frmla	formula for model.fcn
MetaData	meta-data containing variables in formula and the column "Sample". If mStableAgg==F, this input is not used - all variables must be contained in Data
PartitioningVariables	character vector containing of interest for phylofactorization partitioning.
mStableAgg	logical. See gpf
expfamily	character string indicating manner of m-stable aggregation for mAggregation. Only "binomial" is meaningfully different.
model.fcn	model function, such as glm or gam.
objective.fcn	Objective function taking output from model.fcn as input. See gpf.
min.group.size	minimum size of group allowed for partitioning. Default is 1.
...	additional arguments for model.fcn

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