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readShapePoly <- function(fn, IDvar=NULL, proj4string=CRS(as.character(NA)),
verbose=FALSE, repair=FALSE, force_ring=FALSE, delete_null_obj=FALSE,
retrieve_ABS_null=FALSE) {
suppressWarnings(Map <- read.shape(filen=fn,
verbose=verbose, repair=repair))
if (!is.null(IDvar)) {
IDvar <- as.character(IDvar)
if (!IDvar %in% names(Map$att.data))
stop(paste("column not found:", IDvar))
IDvar <- as.character(Map$att.data[[IDvar]])
}
.Map2PolyDF(Map, IDs=IDvar, proj4string=proj4string,
force_ring=force_ring, delete_null_obj=delete_null_obj,
retrieve_ABS_null=retrieve_ABS_null)
}
writePolyShape <- function(x, fn, factor2char = TRUE, max_nchar=254) {
stopifnot(class(x) == "SpatialPolygonsDataFrame")
df <- as(x, "data.frame")
df <- data.frame(SP_ID=I(row.names(df)), df)
pls <- .SpP2polylist(as(x, "SpatialPolygons"))
suppressWarnings(write.polylistShape(pls, df, file=fn,
factor2char = factor2char, max_nchar=max_nchar))
}
.Map2PolyDF <- function(Map, IDs, proj4string=CRS(as.character(NA)),
force_ring=FALSE, delete_null_obj=FALSE, retrieve_ABS_null=FALSE) {
# ABS null part shapefiles Graham Williams 080403
# birds NULL part Allen H. Hurlbert 090610
nullParts <- sapply(Map$Shapes, function(x) x$nParts) == 0
if (delete_null_obj) {
nullParts <- which(nullParts)
if (length(nullParts) > 0) {
if (!retrieve_ABS_null) {
for (i in length(nullParts):1)
Map$Shapes[[nullParts[i]]] <- NULL
attr(Map$Shapes,'nshps') <- attr(Map$Shapes,'nshps') -
length(nullParts)
Map$att.data <- Map$att.data[-nullParts,]
warning(paste("Null objects with the following",
"indices deleted:", paste(nullParts, collapse=", ")))
} else {
res <- Map$att.data[nullParts,]
return(res)
}
}
} else {
# birds NULL part Allen H. Hurlbert 090610
if (any(nullParts))
stop(paste("NULL geometry found:", paste(which(nullParts), collapse=", "), "\n consider using delete_null_obj=TRUE"))
}
if (is.null(IDs))
IDs <- as.character(sapply(Map$Shapes, function(x) x$shpID))
SR <- .asSpatialPolygonsShapes(Map$Shapes, IDs,
proj4string=proj4string, force_ring=force_ring)
df <- Map$att.data
rownames(df) <- IDs
res <- SpatialPolygonsDataFrame(Sr=SR, data=df)
res
}
.asSpatialPolygonsShapes <- function(shapes, IDs,
proj4string=CRS(as.character(NA)), force_ring=FALSE) {
if (attr(shapes, "shp.type") != "poly")
stop("Not polygon shapes")
if (missing(IDs))
IDs <- as.character(sapply(shapes, function(x) x$shpID))
if (length(IDs) != attr(shapes,'nshps'))
stop("Number of shapes and IDs differ")
tab <- table(factor(IDs))
n <- length(tab)
IDss <- .mixedsort(names(tab))
# try to preserve sensible ordering
# IDss <- names(tab)
reg <- match(IDs, IDss)
belongs <- lapply(1:n, function(x) which(x == reg))
# assemble the list of Srings
Srl <- vector(mode="list", length=n)
for (i in 1:n) {
nParts <- length(belongs[[i]])
srl <- NULL
for (j in 1:nParts) {
jres <- .shp2srsI(shapes[[belongs[[i]][j]]],
.nParts.shpI(shapes[[belongs[[i]][j]]]),
force_ring=force_ring)
srl <- c(srl, jres)
}
Srl[[i]] <- Polygons(srl, ID=IDss[i])
}
res <- as.SpatialPolygons.PolygonsList(Srl, proj4string=proj4string)
res
}
# Function mixedorder copied from gtools 2.2.3 LGPL Gregory R. Warnes
.mixedsort <- function (x) {
x[.mixedorder(x)]
}
.mixedorder <- function (x) {
delim = "\\$\\@\\$"
numeric <- function(x) {
optwarn = options("warn")
on.exit(options(optwarn))
options(warn = -1)
as.numeric(x)
}
nonnumeric <- function(x) {
optwarn = options("warn")
on.exit(options(optwarn))
options(warn = -1)
ifelse(is.na(as.numeric(x)), toupper(x), NA)
}
x <- as.character(x)
which.nas <- which(is.na(x))
which.blanks <- which(x == "")
if (length(which.blanks) > 0)
x[which.blanks] <- -Inf
if (length(which.nas) > 0)
x[which.nas] <- Inf
delimited <- gsub("([+-]{0,1}[0-9.]+([eE][+-]{0,1}[0-9.]+){0,1})",
paste(delim, "\\1", delim, sep = ""), x)
step1 <- strsplit(delimited, delim)
step1 <- lapply(step1, function(x) x[x > ""])
step1.numeric <- lapply(step1, numeric)
step1.character <- lapply(step1, nonnumeric)
maxelem <- max(sapply(step1, length))
step1.numeric.t <- lapply(1:maxelem, function(i) sapply(step1.numeric,
function(x) x[i]))
step1.character.t <- lapply(1:maxelem, function(i) sapply(step1.character,
function(x) x[i]))
rank.numeric <- sapply(step1.numeric.t, rank)
rank.character <- sapply(step1.character.t,
function(x) as.numeric(factor(x)))
rank.numeric[!is.na(rank.character)] <- 0
rank.character <- t(t(rank.character) + apply(matrix(rank.numeric),
2, max, na.rm = TRUE))
rank.overall <- ifelse(is.na(rank.character), rank.numeric,
rank.character)
order.frame <- as.data.frame(rank.overall)
if (length(which.nas) > 0)
order.frame[which.nas, ] <- Inf
retval <- do.call("order", order.frame)
return(retval)
}
.shp2srsI <- function(shp, nParts, force_ring=FALSE) {
Pstart <- shp$Pstart
nVerts <- nrow(shp$verts)
from <- integer(nParts)
to <- integer(nParts)
from[1] <- 1
for (j in 1:nParts) {
if (j == nParts) to[j] <- nVerts
else {
to[j] <- Pstart[j+1]
from[j+1] <- to[j]+1
}
}
srl <- vector(mode="list", length=nParts)
for (j in 1:nParts) {
crds <- shp$verts[from[j]:to[j],,drop=FALSE]
if (force_ring) {
if (!isTRUE(identical(crds[1,], crds[nrow(crds),])))
crds <- rbind(crds, crds[1,])
}
srl[[j]] <- Polygon(coords=crds)
}
srl
}
.nParts.shpI <- function(shp) attr(shp, "nParts")
.xyList2NAmat <- function(xyList) {
nParts <- length(xyList)
res <- xyList[[1]]
if (nParts > 1) {
for(i in 2:nParts)
res <- rbind(res, c(NA,NA), xyList[[i]])
}
res
}
.SpP2polylist <- function(x) {
pls <- slot(x, "polygons")
n <- length(pls)
res <- vector(mode="list", length=n)
for (i in 1:n) {
xyL <- lapply(slot(pls[[i]], "Polygons"),
function(i) slot(i, "coords"))
nP <- length(xyL)
nVs <- sapply(xyL, nrow)
res[[i]] <- .xyList2NAmat(xyL)
attr(res[[i]], "nParts") <- as.integer(nP)
from <- integer(nP)
to <- integer(nP)
from[1] <- 1
to[1] <- nVs[1]
if (nP > 1) for (j in 2:nP) {
from[j] <- to[(j-1)] + 2
to[j] <- from[j] + nVs[j] - 1
}
attr(res[[i]], "pstart") <- list(from=as.integer(from),
to=as.integer(to))
attr(res[[i]], "bbox") <- c(bbox(pls[[i]]))
}
attr(res, "region.id") <- sapply(pls, function(i) slot(i, "ID"))
class(res) <- "polylist"
invisible(res)
}
.polylist2SpP <- function(pl) {
if (!inherits(pl, "polylist")) stop("not a polylist object")
n <- length(pl)
IDs <- attr(pl, "region.id")
pL <- vector(mode="list", length=n)
for (i in 1:n) {
nP <- attr(pl[[i]], "nParts")
Ps <- vector(mode="list", length=nP)
from <- attr(pl[[i]], "pstart")$from
to <- attr(pl[[i]], "pstart")$to
for (j in 1:nP) {
Ps[[j]] <- Polygon(pl[[i]][from[j]:to[j],])
}
pL[[i]] <- Polygons(Ps, IDs[i])
}
res <- SpatialPolygons(pL)
res
}
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