R/clmm.formula.R

In ordinal: Regression Models for Ordinal Data

#############################################################################
##    Copyright (c) 2010-2022 Rune Haubo Bojesen Christensen
##
##    This file is part of the ordinal package for R (*ordinal*)
##
##    *ordinal* is free software: you can redistribute it and/or modify
##    it under the terms of the GNU General Public License as published by
##    the Free Software Foundation, either version 2 of the License, or
##    (at your option) any later version.
##
##    *ordinal* is distributed in the hope that it will be useful,
##    but WITHOUT ANY WARRANTY; without even the implied warranty of
##    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
##    GNU General Public License for more details.
##
##    A copy of the GNU General Public License is available at
##    <https://www.r-project.org/Licenses/> and/or
##    <http://www.gnu.org/licenses/>.
#############################################################################
## This file contains:
## Functions to process lmer-style mixed-model formulae. These
## functions are borrowed from the lme4 package but have later been
## modified.

findbars <- function(term)
### Return the pairs of expressions that separated by vertical bars
{
    if (is.name(term) || !is.language(term)) return(NULL)
    if (term[[1]] == as.name("(")) return(findbars(term[[2]]))
    if (!is.call(term)) stop("term must be of class call")
    if (term[[1]] == as.name('|')) return(term)
    if (length(term) == 2) return(findbars(term[[2]]))
    c(findbars(term[[2]]), findbars(term[[3]]))
}

nobars <- function(term)
### term - usually the third element of a formula object: formula[[3]]
### returns a list of terms

### Return the formula omitting the pairs of expressions that are
### separated by vertical bars
{
    if (!('|' %in% all.names(term))) return(term)
    if (is.call(term) && term[[1]] == as.name('|')) return(NULL)
    if (length(term) == 2) {
	nb <- nobars(term[[2]])
	if (is.null(nb)) return(NULL)
	term[[2]] <- nb
	return(term)
    }
    nb2 <- nobars(term[[2]])
    nb3 <- nobars(term[[3]])
    if (is.null(nb2)) return(nb3)
    if (is.null(nb3)) return(nb2)
    term[[2]] <- nb2
    term[[3]] <- nb3
    term
}

subbars <- function(term)
### Substitute the '+' function for the '|' function
{
    if (is.name(term) || !is.language(term)) return(term)
    if (length(term) == 2) {
	term[[2]] <- subbars(term[[2]])
	return(term)
    }
    stopifnot(length(term) >= 3)
    if (is.call(term) && term[[1]] == as.name('|'))
	term[[1]] <- as.name('+')
    for (j in 2:length(term)) term[[j]] <- subbars(term[[j]])
    term
}

subnms <- function(term, nlist)
### Substitute any names from nlist in term with 1
{
    if (!is.language(term)) return(term)
    if (is.name(term)) {
        if (any(unlist(lapply(nlist, get("=="), term)))) return(1)
        return(term)
    }
    stopifnot(length(term) >= 2)
    for (j in 2:length(term)) term[[j]] <- subnms(term[[j]], nlist)
    term
}

slashTerms <- function(x)
### Return the list of '/'-separated terms in an expression that
### contains slashes
{
    if (!("/" %in% all.names(x))) return(x)
    if (x[[1]] != as.name("/"))
        stop("unparseable formula for grouping factor")
    list(slashTerms(x[[2]]), slashTerms(x[[3]]))
}

makeInteraction <- function(x)
### from a list of length 2 return recursive interaction terms
{
    if (length(x) < 2) return(x)
    trm1 <- makeInteraction(x[[1]])
    trm11 <- if(is.list(trm1)) trm1[[1]] else trm1
    list(substitute(foo:bar, list(foo=x[[2]], bar = trm11)), trm1)
}

expandSlash <- function(bb)
### expand any slashes in the grouping factors returned by findbars
{
    if (!is.list(bb)) return(expandSlash(list(bb)))
    ## I really do mean lapply(unlist(... - unlist returns a
    ## flattened list in this case
    unlist(lapply(bb, function(x) {
        if (length(x) > 2 && is.list(trms <- slashTerms(x[[3]])))
            return(lapply(unlist(makeInteraction(trms)),
                          function(trm) substitute(foo|bar,
                                                   list(foo = x[[2]],
                                                        bar = trm))))
        x
    }))
}