https://github.com/cran/MuMIn
Tip revision: 1f8ac64cc410215ef2e55e5e297eaa5bd15a0b84 authored by Kamil BartoĊ on 25 January 2012, 13:25:36 UTC
version 1.7.0
version 1.7.0
Tip revision: 1f8ac64
getAllTerms.R
`getAllTerms.default` <-
function(x, ...) getAllTerms.formula(as.formula(formula(x)), ...)
`getAllTerms.lm` <-
function(x, ...)
if(inherits(x, "gam"))
getAllTerms.terms(terms(formula(x)), ...) else
getAllTerms.terms(terms(x), ...)
`getAllTerms.terms` <-
function(x, offset = TRUE, intercept = FALSE, ...) {
interceptLabel <- "(Intercept)"
variables <- attr(x, "variables")[-1L]
if (!is.null(attr(x, "offset"))){
offs <- sapply(variables[attr(x, "offset")], deparse)
} else offs <- NULL
ret <- attr(x, "term.labels")
# Get term names, with higher order term components arranged alphabetically
if (length(ret) > 0) {
factors <- attr(x, "factors")
factors <- factors[order(rownames(factors)), , drop = FALSE]
v <- rownames(factors)
ret <- apply(factors != 0L, 2L, function(x) paste(v[x], collapse = ":"))
}
# Leave out random terms (lmer type)
#ran <- attr(x, "variables")[-1][-c(attr(x, "offset"), attr(x, "response"))]
ran <- variables
ran <- as.character(ran[sapply(ran,
function(x) length(x) == 3L && x[[1L]] == "|")])
ifx <- !(ret %in% ran)
ret <- ret[ifx] # ifx - indexes of fixed terms
#retUnsorted <- ret
# finally, sort by order and then alphabetically
#ret <- unname(ret[order(attr(x, "order")[ifx], ret)])
ord <- order(attr(x, "order")[ifx], gsub("I\\((.*)\\)", "\\1", ret))
ret <- unname(ret[ord])
if(intercept && attr(x, "intercept")) {
ret <- c(interceptLabel, ret)
ord <- c(1, ord + 1L)
}
if (!is.null(offs[1L])) {
if (offset) {
ret <- c(ret, offs)
ord <- c(ord, length(ord) + 1L)
}
attr(ret, "offset") <- offs
}
attr(ret, "intercept") <- attr(x, "intercept")
attr(ret, "interceptLabel") <- interceptLabel
if (length(ran) > 0L) {
attr(ret, "random.terms") <- ran
attr(ret, "random") <- reformulate(c(".", paste("(", ran, ")",
sep = "")), response = ".")
}
response <- attr(x, "response")
response <- if(response == 0L) NULL else variables[[response]]
attr(ret, "response") <- response
attr(ret, "order") <- order(ord)
return(ret)
}
`getAllTerms.formula` <-
function(x, ...) getAllTerms.terms(terms(x), ...)
`getAllTerms.lme` <-
function(x, ...) {
ret <- getAllTerms.terms(terms(x), ...)
attr(ret, "random") <- . ~ .
# Code from nlme:::print.reStruct, modified slightly
reStruct <- x$modelStruct$reStruct
nobj <- length(reStruct)
if (is.null(namx <- names(reStruct)))
names(reStruct) <- nobj:1L
aux <- t(array(rep(names(reStruct), nobj), c(nobj, nobj)))
aux[lower.tri(aux)] <- ""
reStruct[] <- rev(reStruct)
aux <- t(array(rep(names(reStruct), nobj), c(nobj, nobj)))
aux[lower.tri(aux)] <- ""
attr(ret, "random.terms") <- paste(lapply(lapply(reStruct, attr, "formula"),
"[[", 2L), "|",
rev(apply(aux, 1L, function(z) paste(z[z != ""], collapse = " %in% "))))
return(ret)
}
# `getAllTerms.glmer` <- # For backwards compatibility
# `getAllTerms.lmer` <- # with older versions of lme4
`getAllTerms.mer` <-
function(x, ...) getAllTerms(lme4::formula(x), ...)
# Apparently there is no (explicit) intercept in coxph, but 'terms' gives
# attr(,"intercept") == 1.
`getAllTerms.coxph` <- function (x, ...) {
ret <- getAllTerms.default(x, ...)
attr(ret, "intercept") <- 0L
attr(ret, "interceptLabel") <- NULL
return(ret)
}
`getAllTerms.glmmML` <- function (x, ...) {
ret <- getAllTerms.terms(terms(x), ...)
#attr(ret, "random.terms") <- deparse(call("|", 1, x$call$cluster))
attr(ret, "random.terms") <- paste("1 |", x$call$cluster)
ret
}
`getAllTerms` <-
function(x, ...) UseMethod("getAllTerms")