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STS = function(sp, time, index, endTime = delta(time)) {
new("STS", ST(sp, time, endTime), index = index)
}
STSDF = function(sp, time, data, index, endTime = delta(time)) {
new("STSDF", STS(sp, time, index, endTime), data = data)
}
setMethod("coordinates", "STS", function(obj) {
myCoordinates(obj@sp)[obj@index[,1],,drop=FALSE] # BG: added drop=FALSE to be consistent for single locations in space and time
}
)
index.STS = function(x, ...) {
index(x@time)[x@index[,2]]
}
index.STSDF = index.STS
as.data.frame.STS = function(x, row.names = NULL, ...) {
if (is.null(row.names(x@sp)))
row.names(x@sp) = 1:nrow(x@sp)
timedata = as.data.frame(x@time)[x@index[,2], , drop = FALSE]
ret = data.frame(as.data.frame(coordinates(x)),
sp.ID = row.names(x@sp)[x@index[,1]],
time = index(x),
endTime = x@endTime[x@index[,2]],
timedata, row.names = row.names, ...)
if ("data" %in% slotNames(x@sp))
data.frame(ret, x@sp@data[x@index[,1], , drop = FALSE])
else
ret
}
setAs("STS", "data.frame", function(from) as.data.frame.STS(from))
as.data.frame.STSDF = function(x, row.names = NULL, ...) {
f = as.data.frame(as(x, "STS"))
data.frame(f, x@data, row.names = row.names, ...)
}
setAs("STSDF", "data.frame", function(from) as.data.frame.STSDF(from))
setAs("STSDF", "xts", function(from) as(as(from, "STFDF"), "xts")) # a good idea?
subs.STSDF <- function(x, i, j, ... , drop = is(x, "STSDF")) {
n.args = nargs()
dots = list(...)
missing.i = missing(i)
missing.j = missing(j)
# check wheter variables get selected
missing.k = TRUE
if (length(dots) > 0) {
missing.k <- FALSE
k <- dots[[1]]
}
if (!missing.i & !missing.j) {
if (is.matrix(i)) {
missing.k <- FALSE
k <- j
}
}
if (missing.i && missing.j && missing.k)
return(x)
if (missing.k)
k = TRUE
else {
if (missing.j && n.args == 2) {
x@data = x@data[ , k, drop = FALSE]
return(x)
}
}
if (!missing.i && is(i, "STS")) { # highjack i and j:
j = which(!is.na(timeMatch(x,i)))
i = which(!is.na(over(x@sp, geometry(i@sp))))
missing.j = FALSE
}
matrix.i <- FALSE
# space
#######
# keep track of original spatial indicies - if not yet
if (!is.character(row.names(x@sp)))
row.names(x@sp) <- as.character(row.names(x@sp))
if (missing.i)
s = 1:length(x@sp)
else {
if (is.matrix(i)) { # BG
stopifnot(ncol(i)==2)
i <- i[order(i[,2]),,drop=FALSE]
s <- i[,1]
missing.j <- FALSE
matrix.i <- TRUE
} else {
if (is(i, "Spatial"))
s = which(!is.na(over(x@sp, geometry(i))))
else if (is.logical(i)) {
i = rep(i, length.out = length(x@sp))
s = which(i)
} else if (is.character(i)) # suggested by BG:
s = match(i, row.names(x@sp), nomatch = FALSE)
else
s = i
}
}
# time
if (missing.j)
t = 1:nrow(x@time)
else {
if (matrix.i)
t <- i[,2]
else {
if (is.logical(j))
j = which(j)
nct = ncol(x@time)
.time = cbind(x@time, 1:nrow(x@time))
# uses [.xts, deals with character/iso8601;
# takes care of negative indices:
.time = .time[j]
# get back the corresponding index vector t, to use for @data:
t = as.vector(.time[, nct+1])
}
}
si = x@index[,1]
ti = x@index[,2]
if (matrix.i) # BG
sel <- unlist(sapply(1:nrow(i), function(x) which((si %in% s[x]) & (ti %in% t[x]))))
else {
if (length(unique(s)) < length(s) | length(unique(t)) < length(t)) {
sel <- numeric(0)
for (ts in t)
for (ss in s)
sel <- c(sel, which((si %in% ss) & (ti %in% ts)))
} else
sel = (si %in% s) & (ti %in% t)
}
if (is(x, "STSDF"))
x@data = x@data[sel, k, drop = FALSE]
# TG: Tom Gottfried reported at
# https://stat.ethz.ch/pipermail/r-sig-geo/2011-March/011231.html
x@index = x@index[sel,, drop=FALSE]
# inserted drop=FALSE to handle (length(i)==1 && length(j)==1) # TG
# now simplify everything, and drop any S/T not refered to, but keep the ordering of "s":
u1 = unique(s[s %in% x@index[,1]]) # was: unique(x@index[,1]))
u2 = unique(x@index[,2])
x@sp = x@sp[u1,]
x@time = x@time[u2,]
x@endTime = x@endTime[u2]
x@index[,1] <- match(x@index[,1], u1)
x@index[,2] <- match(x@index[,2], u2)
reOrder <- numeric(nrow(x@index))
for (ts in unique(x@index[,2])) { # reordering data and index slot accoring to s
selRow <- which(x@index[,2] == ts)
reOrder[selRow] <- selRow[order(x@index[selRow,1])]
}
x@index[,1] <- x@index[reOrder,1]
if (is(x, "STSDF"))
x@data = x@data[reOrder, ,drop=FALSE]
if (drop) {
if (length(s) == 1) { # space index has only 1 item:
if (length(t) == 1)
x = x@data[1, , drop = (ncol(x@data) == 1)] # TRUE would return a list if ncol > 1
else {
ix = index(x@time[x@index[,2]])
xs = cbind(x@data, as.data.frame(x@time)) # JS
if (is(ix, "Date"))
x = xts(xs, ix)
else
x = xts(xs, ix, tzone = tzone(x@time))
# added index to achieve
# (nrow(x)==length(order.by)) in index() # TG
}
} else {
if (length(t) == 1) { # only one time item
if (is(x, "STSDF")) {
sp = x@sp[x@index[,1],]
if ("data" %in% slotNames(sp))
x@data = cbind(x@data, sp@data) # otherwise they'd get lost
x = addAttrToGeom(sp, x@data, match.ID = FALSE)
# added index to achieve matching SpatialPoints and data.frame # TG
} else
x = x@sp[x@index[,1],]
}
}
}
x
}
setMethod("[", "STSDF", subs.STSDF)
setMethod("[", "STS", subs.STSDF)
setMethod("addAttrToGeom", signature(x = "STS", y = "data.frame"),
function(x, y, match.ID, ...)
new("STSDF", x, data = y)
)
length.STS = function(x) { nrow(x@index) }
length.STSDF = function(x) { nrow(x@index) }
setMethod("geometry", "STSDF", function(obj) as(obj, "STS"))
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