R: Create list of structures needed for models with random...

mkReTrms {reformulas}

R Documentation

Create list of structures needed for models with random effects

Description

From the result of findbars applied to a model formula and and the evaluation frame, create the model matrix, etc. associated with random-effects terms. See the description of the returned value for a detailed list.

Usage

mkReTrms(
  bars,
  fr,
  drop.unused.levels = TRUE,
  reorder.terms = TRUE,
  reorder.vars = FALSE,
  calc.lambdat = TRUE
)

Arguments

`bars`	a list of parsed random-effects terms
`fr`	a model frame in which to evaluate these terms
`drop.unused.levels`	(logical) drop unused factor levels?
`reorder.terms`	arrange random effects terms in decreasing order of number of groups (factor levels)?
`reorder.vars`	arrange columns of individual random effects terms in alphabetical order?
`calc.lambdat`	(logical) compute `Lambdat` and `Lind` components? (At present these components are needed for `lme4` machinery but not for `glmmTMB`, and may be large in some cases; see Bates et al. 2015

Value

a list with components

`Zt`	transpose of the sparse model matrix for the random effects
`Ztlist`	list of components of the transpose of the random-effects model matrix, separated by random-effects term
`Lambdat`	transpose of the sparse relative covariance factor
`Lind`	an integer vector of indices determining the mapping of the elements of the `theta` to the `"x"` slot of `Lambdat`
`theta`	initial values of the covariance parameters
`lower`	lower bounds on the covariance parameters
`flist`	list of grouping factors used in the random-effects terms
`cnms`	a list of column names of the random effects according to the grouping factors
`Gp`	a vector indexing the association of elements of the conditional mode vector with random-effect terms; if `nb` is the vector of numbers of conditional modes per term (i.e. number of groups times number of effects per group), `Gp` is `c(0,cumsum(nb))` (and conversely `nb` is `diff(Gp)`)
`nl`	names of the terms (in the same order as `Zt`, i.e. reflecting the `reorder.terms` argument)

References