packedModel-class: Class packedModel

In ndukler/phyloGLM: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

Description

Class packedModel holds all the data necessary to construct a rate model

Slots

alleleData

an allele data object in a locked environment

edgeGroups

a data.table with four columns: parent, child, edgeGroup. All parent-child combos must be valid for alleleData object.

rateFormula

A formula that uses the variables in the allele data object to compute turnover rate

piFormula

A formula that uses the variables in the allele data object to compute pi

rateDM

the design matrix for the rate

piDM

the design matrix for pi

phylogeny

parameter object holding all the parameters for phylogenetic computations

fixed

a logical vector indicating which variables are fixed

ndukler/phyloGLM documentation built on Sept. 25, 2019, 9:17 p.m.