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### =========================================================================
### The combine() generic
### -------------------------------------------------------------------------
###
### A "combine" default method + methods for some standard types are
### also provided.
###
setGeneric("combine",
function(x, y, ...)
{
if (length(list(...)) > 0L) {
combine(x, do.call(combine, list(y, ...)))
} else {
standardGeneric("combine")
}
}
)
setMethod("combine", c("ANY", "missing"), function(x, y, ...) x)
setMethod("combine", c("data.frame", "data.frame"),
function(x, y, ...)
{
if (all(dim(x) == 0L) && all(dim(y) == 0L))
return(x)
else if (all(dim(x) == 0L)) return(y)
else if (all(dim(y) == 0L)) return(x)
uniqueRows <- unique(c(row.names(x), row.names(y)))
uniqueCols <- unique(c(names(x), names(y)))
sharedCols <- intersect(names(x), names(y))
## check possible to combine
alleq <- function(x, y) {
res <- all.equal(x, y, check.attributes=FALSE)
if (!is.logical(res)) {
warning(res)
FALSE
} else TRUE
}
sharedRows <- intersect(row.names(x), row.names(y))
ok <- sapply(sharedCols,
function(nm) {
if (!all(class(x[[nm]]) == class(y[[nm]])))
return(FALSE)
switch(class(x[[nm]])[[1L]],
factor={
if (!alleq(levels(x[[nm]]), levels(y[[nm]]))) {
warning("data frame column '", nm,
"' levels not all.equal",
call.=FALSE)
TRUE
} else if (!alleq(x[sharedRows, nm, drop=FALSE],
y[sharedRows, nm, drop=FALSE])) {
warning("data frame column '", nm,
"' shared rows not all equal",
call.=FALSE)
FALSE
} else TRUE
},
## ordered and non-factor columns need to
## satisfy the following identity; it seems
## possible that ordered could be treated
## differently, but these have not been
## encountered.
ordered=,
if (!alleq(x[sharedRows, nm, drop=FALSE],
y[sharedRows, nm, drop=FALSE])) {
warning("data frame column '", nm,
"' shared rows not all equal")
FALSE
} else TRUE)
})
if (!all(ok))
stop("data.frames contain conflicting data:",
"\n\tnon-conforming colname(s): ",
paste(sharedCols[!ok], collapse=", "))
## x or y with zero rows -- make palatable to merge, but drop
## before return
if (length(uniqueRows) == 0L) {
x <- x["tmp",,drop=FALSE]
y <- y["tmp",,drop=FALSE]
} else if (nrow(x) == 0L) {
x <- x[row.names(y),,drop=FALSE]
row.names(x) <- row.names(y)
} else if (nrow(y) == 0L) {
y <- y[row.names(x),,drop=FALSE]
row.names(y) <- row.names(x)
}
## make colnames of merged data robust
if (length(uniqueCols) > 0L)
extLength <- max(nchar(sub(".*\\.", "", uniqueCols))) + 1L
else extLength <- 1L
extX <- paste(c(".", rep("x", extLength)), collapse="")
extY <- paste(c(".", rep("y", extLength)), collapse="")
z <- merge(x, y, by="row.names", all=TRUE, suffixes=c(extX, extY))
## shared cols
for (nm in sharedCols) {
nmx <- paste(nm, extX, sep="")
nmy <- paste(nm, extY, sep="")
z[[nm]] <-
switch(class(z[[nmx]])[[1]],
AsIs=I(ifelse(is.na(z[[nmx]]), z[[nmy]], z[[nmx]])),
factor={
col <- ifelse(is.na(z[[nmx]]),
as.character(z[[nmy]]),
as.character(z[[nmx]]))
if (!identical(levels(z[[nmx]]), levels(z[[nmy]])))
factor(col)
else
factor(col, levels=levels(z[[nmx]]))
},
{
col <- ifelse(is.na(z[[nmx]]), z[[nmy]], z[[nmx]])
class(col) <- class(z[[nmx]])
col
})
}
## tidy
row.names(z) <- if (is.integer(attr(x, "row.names")) &&
is.integer(attr(y, "row.names")))
as.integer(z$Row.names)
else
z$Row.names
z$Row.names <- NULL
z[uniqueRows, uniqueCols, drop=FALSE]
}
)
setMethod("combine", c("matrix", "matrix"),
function(x, y, ...)
{
if (length(y) == 0L)
return(x)
else if (length(x) == 0L)
return(y)
if (mode(x) != mode(y))
stop("matrix modes ", mode(x), ", ", mode(y), " differ")
if (typeof(x) != typeof(y))
warning("matrix typeof ", typeof(x), ", ", typeof(y), " differ")
xdim <- dimnames(x)
ydim <- dimnames(y)
if (is.null(xdim) || is.null(ydim) ||
any(sapply(xdim, is.null)) ||
any(sapply(ydim, is.null)))
stop("matricies must have dimnames for 'combine'")
sharedRows <- intersect(xdim[[1L]], ydim[[1L]])
sharedCols <- intersect(xdim[[2L]], ydim[[2L]])
ok <- all.equal(x[sharedRows, sharedCols], y[sharedRows, sharedCols])
if (!isTRUE(ok))
stop("matrix shared row and column elements differ: ", ok)
unionRows <- union(xdim[[1L]], ydim[[1L]])
unionCols <- union(xdim[[2L]], ydim[[2L]])
m <- matrix(new(class(as.vector(x))),
nrow=length(unionRows), ncol=length(unionCols),
dimnames=list(unionRows, unionCols))
m[rownames(x), colnames(x)] <- x
m[rownames(y), colnames(y)] <- y
m
}
)
|
