https://github.com/cran/MuMIn
Tip revision: b4fae7a102a8a67407ddf3b3ef825ed34735704b authored by Kamil BartoĊ on 18 December 2019, 19:20:02 UTC
version 1.43.14
version 1.43.14
Tip revision: b4fae7a
model.selection.R
`coefTable.model.selection` <-
function (model, ...) {
rval <- attr(model, "coefTables")
names(rval) <- rownames(model)
rval
}
`coef.model.selection` <-
function (object, ...) {
ct <- attr(object, "coefTables")
n <- length(ct)
allcf <- unique(unlist(lapply(ct, rownames)))
rval <- matrix(NA_real_, nrow = n, ncol = length(allcf),
dimnames = list(rownames(object), allcf))
for(i in seq_len(n))
rval[i, match(rownames(ct[[i]]), allcf)] <- ct[[i]][, 1L]
rval
}
`coeffs.model.selection` <-
function (model) coef.model.selection(model)
`coefArray` <- function(object) {
coefNames <- fixCoefNames(unique(unlist(lapply(object, rownames),
use.names = FALSE)))
nCoef <- length(coefNames)
nModels <- length(object)
rval <- array(NA_real_, dim = c(nModels, 3L, nCoef),
dimnames = list(names(object), c("Estimate", "Std. Error", "df"), coefNames))
for(i in seq_along(object)) {
z <- object[[i]]
rval[i, seq_len(ncol(z)), ] <- t(z[match(coefNames, fixCoefNames(rownames(z))), ])
}
rval
}
`getCall.model.selection` <-
function (x, i = NULL, ...) {
if(is.null(i)) return(attr(x, "call", exact = TRUE))
if(length(i) == 1L) return(attr(x, "model.calls", exact = TRUE)[[i]])
return(attr(x, "model.calls", exact = TRUE)[i])
}
getModelClass <-
function(x) {
if(inherits(x, "model.selection")) {
if(!is.null(attr(x, "global"))) return(class(attr(x, "global"))[1L])
if("class" %in% colnames(x)) return(as.character(x[, "class"]))
if(!is.null(attr(x, "model.class"))) return(attr(x, "model.class"))
}
return(NULL)
}
`print.model.selection` <-
function(x, abbrev.names = TRUE, warnings = getOption("warn") != -1L, ...) {
origx <- x
class(x) <- "data.frame"
xterms <- attr(origx, "terms")
if(is.null(xterms) || !all(xterms %in% colnames(x)[seq_along(xterms)])) {
print.data.frame(x, ...)
} else {
if(abbrev.names) xterms <- abbreviateTerms(xterms, 6L, 3L, deflate = TRUE)
colnames(x)[seq_along(xterms)] <- xterms
globcl <- attr(origx, "global.call")
if(!is.null(globcl)) {
cat("Global model call: ")
print(globcl)
cat("---\n")
random.terms <- attr(getAllTerms(attr(origx, "global")), "random.terms")
if(!is.null(random.terms)) random.terms <- list(random.terms)
} else random.terms <- attr(origx, "random.terms")
cat("Model selection table \n")
dig <- c(terms = NA, varying = NA, extra = NA, df = 0L, loglik = 3L, ic = 1L, delta = 2L,
weight = 3L)
column.types <- attr(origx, "column.types")
#stopifnot(names(dig) == levels(column.types)) ## DEBUG
decprint <- dig[column.types[colnames(x)]]
i <- vapply(x, is.numeric, FALSE) & is.na(decprint)
x[, i] <- signif(x[, i], 4L)
k <- which(!is.na(decprint))
for(i in k) x[, i] <- round(x[, i], digits = decprint[i])
vLegend <- NULL
if(abbrev.names) {
vCols <- type2colname(column.types, "varying")
vCols <- vCols[(vCols %in% colnames(x)) & !(vCols %in% c("class"))]
vlen <- nchar(vCols)
vLegend <- vector(length(vCols), mode = "list")
names(vLegend) <- vCols
if(!is.null(vCols)) {
for(i in vCols) {
if(!is.factor(x[, i])) next
lev <- levels(x[, i])
lev <- lev[!(lev %in% c("", "NULL"))]
shlev <- abbreviateTerms(lev, nchar(i), deflate = TRUE)
x[, i] <- factor(x[, i], levels = lev, labels = shlev)
if(any(j <- shlev != lev)) vLegend[[i]] <-
paste(shlev[j], "=", sQuote(lev[j]))
}
vLegend <- vLegend[!vapply(vLegend, is.null, TRUE)]
}
}
uqran <- unique(unlist(random.terms, use.names = FALSE))
abbran <- abbreviateTerms(gsub("1 | ", "", uqran, fixed = TRUE), 1L,
deflate = TRUE)
colran <- vapply(random.terms, function(s) paste(abbran[match(s, uqran)],
collapse = "+"), "")
if(addrandcol <- length(unique(colran)) > 1L) {
k <- which(colnames(x) == "df")[1L]
x <- cbind(x[, 1L:(k - 1L), drop = FALSE], random = colran, x[, k:ncol(x), drop = FALSE], deparse.level = 0L)
}
if(nrow(x) == 0L) {
print.default(colnames(x), quote = FALSE)
cat("<0 rows>", "\n")
} else
print.default(as.matrix(x)[, !vapply(x, function(y) all(is.na(y)), FALSE),
drop = FALSE], na.print = "", quote = FALSE, right = TRUE)
if(abbrev.names && length(vLegend)) {
cat("Abbreviations:", sep = "\n")
for(i in names(vLegend)) {
cat(vLegend[[i]], sep = ", ", fill = TRUE, labels =
c(paste0(i, ":"), rep(paste(rep(" ", nchar(i) + 1L),
collapse = ""), length(vLegend[[i]]) - 1L)))
}
}
cat("Models ranked by", asChar(attr(attr(origx, 'rank'), "call")), "\n")
if(!is.null(random.terms)) {
if(addrandcol) {
cat("Random terms: \n")
cat(paste(abbran, "=", sQuote(uqran)), sep = "\n")
} else {
cat("Random terms (all models): \n")
cat(paste(sQuote(uqran)), sep = ", ")
cat("\n")
}
}
if (warnings && !is.null(attr(origx, "warnings"))) {
cat("\n"); print.warnings(attr(origx, "warnings"))
}
}
invisible(origx)
}
`update.model.selection` <- function (object, global.model, ..., evaluate = TRUE) {
cl <- attr(object, "call")
if (is.null(cl)) stop("need an object with call component")
extras <- match.call(expand.dots = FALSE)$...
if(!missing(global.model))
extras <- c(list(global.model = substitute(global.model)), extras)
if (length(extras)) {
existing <- !is.na(match(names(extras), names(cl)))
for (a in names(extras)[existing]) cl[a] <- extras[a]
if (any(!existing)) {
cl <- c(as.list(cl), extras[!existing])
cl <- as.call(cl)
}
}
if (evaluate) eval.parent(cl) else cl
}
`logLik.model.selection` <- function (object, ...) {
nobs <- attr(object, "nobs")
n <- nrow(object)
rval <- vector(n, mode = "list")
for(i in 1L:n) rval[[i]] <-
structure(object[i, "logLik"], df = object[i, "df"], nobs = nobs,
class = "logLik")
rval
}
`family.model.selection` <-
function (object, ...) {
if(!is.null(attr(object, "global"))) {
model.calls <- attr(object, "model.calls")
if(!is.null(model.calls[[1L]][["family"]])) {
fam <- lapply(model.calls, "[[", "family")
#fam1 <- unique(fam)
rval <- lapply(unique(fam), eval)[
as.integer(as.factor(vapply(fam, asChar, "")))
]
names(rval) <- rownames(object)
## WTF?
#index <- split(seq_along(fam), vapply(fam, asChar, ""))
#for(i in seq_along(fam1)) fam1[[i]] <- list(family = eval(fam1[[i]]), index = index[[i]])
#fam <- family(dd1)
#index <- lapply(fam, "[[", "index")
#rval <- rep(lapply(fam, "[[", "family"), vapply(index, length, 1L))[order(unlist(index))]
return(rval)
} else return(family(attr(object, "global")))
} else {
attr(object, "model.family")
}
}
`nobs.model.selection` <-
function (object, ...)
attr(object, "nobs")
## internal: translate column type to column indices
type2col <-
function (x, type) {
if (inherits(x, "model.selection"))
x <- attr(x, "column.types")
k <- match(x, type, nomatch = 0L)
i <- k != 0
which(i)[order(k[i])]
}
## internal: translate column type to column names
type2colname <-
function(x, type)
names(x)[type2col(x, type)]
`item<-` <- function(x, name, i, value)
`[<-.data.frame`(x, i, name, value)
`item` <- function(x, name, i, ...)
`[.data.frame`(x, i, name, ...)
`itemByType` <- function(x, type, i, ...)
`[.data.frame`(x, i, type2col(x, type), ...)
`itemByType<-` <- function(x, type, i, value)
`[<-.data.frame`(x, i, type2col(x, type), value)