https://github.com/cran/RandomFields
Tip revision: 091cb3f90520d153e1ed6ee6a0ea4c61694500df authored by Martin Schlather on 27 January 2015, 00:00:00 UTC
version 3.0.59
version 3.0.59
Tip revision: 091cb3f
convert.R
PrepareModel2 <- function(model, ...) {
if (missing(model) || is.null(model)) stop("'model' must be given.")
m <- parseModel(model, ...)
#if (!is.list(model))
# if (class(try(all.equal(parseModel(list2RMmodel(m)), m, check.attr=FALSE)))=="try-error"){
# print("AlexWarning in PrepareModel2: ruecktrafo via list2RMmodel waere falsch oder nich dasselbe ... bitte model mir zuschicken")
# print("doppelt hin und zurueck:")
# print(try(all.equal(parseModel(list2RMmodel(parseModel(list2RMmodel(m)))), parseModel(list2RMmodel(m)), check.attr=FALSE)))
# }
if (notplus <- !(m[[1]] %in% ZF_PLUS)) m <- list(ZF_SYMBOLS_PLUS, m)
for (i in 2:length(m)) {
if ((m[[i]][[1]] %in% ZF_MIXED) && length(m[[i]]$X)==1 &&
is.numeric(m[[i]]$X) && m[[i]]$X==1 && !is.null(m[[i]]$b)) {
m[[i]] <- list(ZF_TREND[2], mean=m[[i]]$b)
if (RFoptions()$general$printlevel > PL_IMPORTANT)
message(paste("The '1' in the mixed model definition has been replaced by '", ZF_TREND[1], "(mean=", m[[i]]$mean, ")'.", sep=""))
}
}
if (notplus) m <- m[[2]]
class(m) <- "RM_model"
return(m)
# if (class(model) != "formula") {
# if (is.list(model)) return(model)
# else stop("model of unknown form -- maybe you have used an obsolete definition. See ?RMmodel for the model definition")
# }
# return(listmodel)
}
PrepareModel <- function(model, param, trend=NULL,
nugget.remove=TRUE, method=NULL) {
## any of the users model definition (standard, nested, list) for the
## covariance function is transformed into a standard format, used
## especially in the c programs
##
## overwrites in some situation the simulation method for nugget.
## allows trend to be NA (or any other non finite value -- is not checked!)
## trend has not been implemented yet!
if (is(model, ZF_MODEL))
stop("models of class ZF_MODEL cannot be combined with obsolete RandomFields functions")
if (!is.null(method)) stop("to give method in PrepareModel is obsolete")
if (!is.null(trend))
if (!is.numeric(trend) || length(trend)!=1)
stop("in the obsolete setting, only constant mean can used")
if (is.list(model) && is.character(model[[1]]) &&
(is.null(names(model)) || names(model)[[1]]=="")) {
if (!missing(param) && !is.null(param))
stop("param cannot be given in the extended definition")
if (is.null(trend)) return(model)
trend <- list(ZF_TREND[2], mean=trend)
if (model[[1]] %in% ZF_PLUS) return(c(model, list(trend)))
else return(list(ZF_SYMBOLS_PLUS, model, trend))
}
printlevel <- RFoptions()$general$printlevel
STOP <- function(txt) {
if (printlevel>=PL_ERRORS) {
cat("model: ")
if (!missing.model) Print(model) else cat(" missing.\n") #
cat("param: ")
if (!missing.param) Print(param) else cat(" missing.\n") #
cat("trend: ")
Print(trend) #
}
stop("(in PrepareModel) ", txt, call.=FALSE)
}
transform <- function(model) {
if (!is.list(model)) {
STOP("some elements of the model definition are not lists")
}
m <- list(DOLLAR[1], var=model$v)
lm <- length(model) - 3 # var, scale/aniso, name
if (!is.null(model$a)) m$aniso <- model$a else m$scale <- model$scale
## model <- c(model, if (!is.null(model$a))
## list(aniso=model$a) else list(scale=model$s)) ## ???
if (!is.na(p <- pmatch("meth", names(model), duplicates.ok=TRUE))) {
if (printlevel>=PL_ERRORS) Print(p, model) #
stop("method cannot be given with the model anymore. It must be given as a parameter to the function. See 'RFoptions' and 'RFsimulate'")
}
if (!is.null(model$me))
stop("'mean' seems to be given within the inner model definitions");
if (!is.character(model$m)) {
stop("'model' was not given extacly once each odd number of list entries or additional unused list elements are given.")
}
m1 <- list(model$m)
if (!is.null(model$k)) {
lm <- lm - 1
if (length(model$k) != 0)
for (i in 1:length(model$k)) {
eval(parse(text=paste("m1$k", i, " <- model$k[", i, "]", sep="")))
}
}
if (lm != 0) {
if (printlevel>=PL_ERRORS) Print(lm, model) #
stop("some parameters do not fit")
}
m <- c(m, list(m1))
return(m)
} # end transform
op.list <- c(ZF_SYMBOLS_PLUS, ZF_SYMBOLS_MULT) ## if others use complex list definition !
missing.model <- missing(model)
missing.param <- missing(param) || is.null(param)
if (full.model <- missing.param && is.null(model$param)) { ## full model
if (RFoptions()$internal$warn_oldstyle)
warning("the sequential list format is depreciated.")
if (missing.model || (length(model)==0)) model <- list()
else if (!is.list(model))
STOP("if param is missing, model must be a list of lists (or a list in the extended notation)")
if (is.null(trend) + is.null(model$mean) + is.null(model$trend)<2)
STOP("trend/mean is given twice")
if (!is.null(model$mean)) trend <- model$mean else
if (!is.null(model$trend)) trend <- model$trend else trend <- NULL
model$trend <- model$mean <- NULL
## the definition might be given at a deeper level as element
## $model of the list:
if (is.list(model$model)) {
if (!is.list(model$model[[1]]))
STOP("if param is missing, the model$model must be a list of lists")
model <- model$model
}
if (length(model)==0) { ## deterministic
return(if (is.null(trend)) NULL else list(ZF_TREND[2], mean=trend))
}
if (length(model) %% 2 !=1) STOP("list for model definition should be odd")
if (length(model)==1)
return(if (is.null(trend) ||
is.numeric(trend) && length(trend)==1 && !is.na(trend)&&trend==0)
transform(model[[1]])
else list(ZF_SYMBOLS_PLUS, transform(model[[1]]),
list(ZF_TREND[2], mean=trend)));
op <- pmatch(c(model[seq(2, length(model), 2)], recursive=TRUE),
op.list, duplicates.ok=TRUE) - 1
if (!all(is.finite(op))) STOP("operators are not all allowed; see the extended list definition for extensions")
model <- model[seq(1, length(model), 2)]
plus <- which(op==0)
if (length(plus) == 0) {
m <- list("*", lapply(model, transform))
} else {
plus <- c(0, plus, length(op)+1)
m <- list(ZF_SYMBOLS_PLUS)
for (i in 1:(length(plus) - 1)) {
m[[i+1]] <-
if (plus[i] + 1 == plus[i+1]) transform(model[[plus[i] + 1]])
else list(ZF_SYMBOLS_MULT,
lapply(model[(plus[i] + 1) : plus[i+1]], transform))
}
}
model <- m
} else { ## standard definition or nested model
if (missing.param) { ## a simple list of the model and the
## parameters is also possible
if (is.null(param <- model$p)) STOP("is.null(model$param)")
stopifnot(is.null(trend) || is.null(model$trend))
if (is.null(trend)) trend <- model$trend
if (!is.null(model$mean)) {
if (!is.null(trend)) STOP("mean and trend given twice")
trend <- model$mean
}
model <- model$model
}
stopifnot(is.character(model), length(model)==1)
if (is.matrix(param)) { ## nested
if (nrow(param) == 1)
return(PrepareModel(model=model, param=c(param[1], 0, param[-1]),
trend=trend))
name <- model
model <- list(ZF_SYMBOLS_PLUS)#, method=method)
for (i in 1:nrow(param)) {
model <- c(model,
if (is.na(param[i, 2]) || param[i, 2] != 0)
list(list(DOLLAR[1], var=param[i, 1], scale=param[i, 2],
if (ncol(param) >2) list(name, k=param[i,-1:-2])
else list(name)))
else list(list(DOLLAR[1], var=param[i,1],
list(ZF_NUGGET[2]))))
}
} else if (is.vector(param)) { ## standard, simple way
## falls trend gegeben, dann ist param um 1 Komponente gekuerzt
if (is.null(trend)) {
trend <- param[1]
param <- param[-1]
} else message("It is assumed that no mean is given so that the first component of param is the variance")
if (model == ZF_NUGGET[2]) {
model <- transform(list(model=model, var=sum(param[1:2]), scale=1))
} else {
if (length(param) > 3)
model <- transform(list(model=model, var=param[1], scale=param[3],
k=param[-1:-3]))
else
model <- transform(list(model=model, var=param[1], scale=param[3]))
if (is.na(param[2]) || param[2] != 0 || !nugget.remove) {# nugget
model <- list(ZF_SYMBOLS_PLUS,
model,
transform(list(model=ZF_NUGGET[2], var=param[2], scale=1)))
}
## if (!is.null(method)) model <- c(model, method=method) ## doppelt
}
} else stop("unknown format") # end nested/standard definition
}
return(if (is.null(trend) ||
is.numeric(trend) && length(trend)==1 && !is.na(trend) &&trend==0)
return(model)
else if (model[[1]] %in% ZF_PLUS)
c(model, list(list(ZF_TREND[2], mean=trend)))
else list(ZF_SYMBOLS_PLUS, model, list(ZF_TREND[2], mean=trend)))
}
seq2grid <- function(x, name, grid, warn_ambiguous, gridtolerance) {
xx <- matrix(nrow=3, ncol=length(x))
step0 <- rep(FALSE, length(x))
gridnotgiven <- missing(grid) || length(grid) == 0
for (i in 1:length(x)) {
if (length(x[[i]]) == 1) {
xx[,i] <- c(x[[i]], 0, 1)
next
}
step <- diff(x[[i]])
if (step[1] == 0.0) {
ok <- step0[i] <- all(step == 0.0)
} else {
ok <- max(abs(step / step[1] - 1.0)) <= gridtolerance
}
if (!ok) {
if (gridnotgiven) return(FALSE)
if (!TRUE)
Print(i, x[[i]][1:min(100, length(x[[i]]))], #
step[1:min(100,length(step))],
range(diff(step[1:min(100,length(step))])))
stop("Different grid distances detected, but the grid must ",
"have equal distances in each direction -- if sure that ",
"it is a grid, increase the value of 'gridtolerance' which equals ",
gridtolerance,".\n")
}
xx[,i] <- c(x[[i]][1], step[1], if (step0[i]) 1 else length(x[[i]]))
}
if (FALSE && gridnotgiven && warn_ambiguous && length(x) > 1) {
RFoptions(internal.warn_ambiguous = FALSE)
message("Ambiguous interpretation of coordinates. Better give 'grid=TRUE' explicitly. (This message appears only once per session.)")
}
if (any(step0)) {
if (all(step0)) {
if (gridnotgiven) return(FALSE)
else stop("Within a grid, the coordinates must be distinguishable")
} else {
if (gridnotgiven && warn_ambiguous) {
RFoptions(internal.warn_ambiguous = FALSE)
warning("Interpretation as degenerated grid. Better give 'grid' explicitely. (This warning appears only once per session.)")
}
}
}
return(xx)
}
CheckXT <- function(x, y=NULL, z=NULL, T=NULL, grid, distances=NULL,
dim=NULL, # == spdim!
length.data,
y.ok = FALSE,
printlevel = RFoptions()$general$printlevel){
## converts the given coordinates into standard formats
## (one for arbitrarily given locations and one for grid points)
RFopt <- RFoptions()
curunits <- RFopt$coords$coordunits
newunits <- RFopt$coords$new_coordunits
coord_system <- RFopt$coords$coord_system
new_coord_system <- RFopt$coords$new_coord_system
if (!missing(distances) && length(distances) > 0) {
stopifnot(is.matrix(distances) || (!missing(dim) && !is.null(dim)),
(missing(grid) || length(grid) == 0),
missing(x) || is.null(x),
is.null(y),
is.null(z),
is.null(T))
if (coord_system != new_coord_system && new_coord_system != "keep")
stop("coordinate systems differ")
if (class(distances) == "dist") {
x <- as.vector(distances)
l <- length(x)
} else if (is.matrix(distances) || is.vector(distances)) {
if (is.matrix(distances)) {
len <- nrow(distances)
if (is.null(dim)) dim = ncol(distances)
else if (dim != ncol(distances))
stop("matrix of distances does not fit the given dimension")
} else {
len <- length(distances)
if (is.null(dim))
stop("dim is not given although 'distances' are used")
}
x <- distances
l <- as.integer(1e-9 + 0.5 * (1 + sqrt(1 + 8 * len)))
if (l * (l-1) / 2 != len) l <- NaN
} else {
stop("'distances' not of required format.")
}
return(list(x=as.matrix(x),
T=NULL,
Zeit=FALSE,
restotal = l,
l = l,
spatialdim=dim,
grid = FALSE,
distances = TRUE,
coordunits = curunits,
new_coordunits = newunits
)
)
}
stopifnot(!missing(x))
if (is(x, "RFsp") || isSpObj(x)) {
return(CheckXT(x=coordinates(x), y=y, z=z, T=T, grid=grid,
distances=distances, dim=dim, length.data=length.data,
y.ok=y.ok, printlevel=printlevel))
}
if (is.raster(x)) x <- as(x, 'GridTopology')
if ((missing(grid) || length(grid) == 0) && !missing(length.data)) {
new <- try(CheckXT(x=x, y=y, z=z, T=T, grid=TRUE, distances=distances,
dim=if (!missing(dim)) dim,
length.data = length.data, y.ok =y.ok,
printlevel = printlevel
), silent=TRUE)
if (grid <- (class(new) != "try-error")) {
ratio <- length.data / new$restotal
if (grid <- ratio == as.integer(ratio)) {
if (printlevel>=PL_IMPORTANT && new$spatialdim > 1)
message("Grid detected. If it is not a grid, set grid=FALSE.\n")
}
}
return(if (grid) new else {
CheckXT(x, y, z, T, grid=FALSE, distances,
if (!missing(distances) && length(distances) > 0) dim=1,
length.data = length.data,
printlevel = printlevel) }
)
} # if (missing(grid) && !missing(length.data))
gridtriple <- FALSE
if (is.GridTopology <- is(x, "GridTopology")){
x <- rbind(x@cellcentre.offset,
x@cellsize,
x@cells.dim)
if ((missing(grid) || length(grid) == 0)) grid <- TRUE else stopifnot(grid)
gridtriple <- TRUE
}
##else {
## is.GridTopology <- FALSE
##}
if (is.data.frame(x)) {
if (ncol(x)==1) x <- as.vector(x) else x <- as.matrix(x)
}
stopifnot(length(x) != 0)
# stopifnot(all(unlist(lapply(as.list(x), FUN=function(li) is.numeric(li))))) ## wann benoetigt???
stopifnot(is.numeric(x))# um RFsimulte(model, data) statt data=data abzufangen
# stopifnot(all(is.finite(x)), all(is.finite(y)), all(is.finite(z))) ; s.u. unlist
if (is.matrix(x)) {
if (!is.numeric(x)) stop("x is not numeric.")
if (!is.null(z)) stop("If x is a matrix, then z may not be given")
if (!is.null(y)) {
if (!y.ok) stop("If x is a matrix, then y may not be given")
if (!is.null(T))
stop("If x is a matrix and y is given, then T may not be given")
if (!is.matrix(y) || ncol(y) != ncol(x) ||
nrow(x)==3 && nrow(y)!=3 && ((missing(grid) || length(grid) == 0) ||
grid))
stop("y does not match x (it must be a matrix)")
}
if (coord_system == COORD_SYS_NAMES[coord_auto + 1] && ncol(x) >= 2
&& ncol(x) <= 3 && !is.null(n <- dimnames(x)[[2]])) {
if (any(idx <- earth_coordinate_names(n))) {
if (length(idx) == 2 && !all(idx == 1:2))
stop("earth coordinates not in order longitude/latitude")
cur <- curunits[1]
newunits <- RFopt$coords$new_coordunits
curunits <- RFopt$coords$coordunits
curunits[1:2] <- c("longitude", "latitude")
if (newunits[1] == "") newunits[1] <- UNITS_NAMES[units_km + 1]
newunits[2:3] <- newunits[1]
if (RFopt$internal$warn_coordinates)
message("\n\nNOTE: current units are ",
if (cur=="") "not given and" else paste("'", cur, "', but"),
" earth coordinates detected:\n",
"earth coordinates will be transformed into units of '",
newunits[1],
"'.\nIn particular, the values of all scale parameters of ",
"any model defined\nin R^3 (currently all models!) are ",
"understood in units of '", newunits[1],
"'.\nChange options 'coord_system' and/or 'units' if ",
"necessary.\n(This message appears only once per session.)\n")
coord_system <- COORD_SYS_NAMES[earth + 1]
RFoptions(coords.coord_system = coord_system,
coords.coordunits = curunits,
coords.new_coordunits = newunits,
internal.warn_coordinates=FALSE)
} else {
RFoptions(coords.coord_system = COORD_SYS_NAMES[cartesian + 1])
}
}
spatialdim <- ncol(x)
len <- nrow(x)
if (spatialdim==1 && len != 3 && (missing(grid) || length(grid) == 0)) {
if (length(x) <= 2) grid <- TRUE
else {
dx <- diff(x)
grid <- max(abs(diff(dx))) < dx[1] * RFopt$general$gridtolerance
}
} # else {
if ((missing(grid) || length(grid) == 0) &&
any(apply(x, 2, function(z) (length(z) <= 2) || max(abs(diff(diff(z))))
> RFopt$general$gridtolerance))) {
grid <- FALSE
}
if ((missing(grid) || length(grid) == 0) || !is.logical(grid)) {
grid <- TRUE
if (spatialdim > 1 && RFopt$internal$warn_ambiguous) {
RFoptions(internal.warn_ambiguous = FALSE)
warning("Ambiguous interpretation of the coordinates. Better give the logical parameter 'grid=TRUE' explicitely. (This warning appears only once per session.)")
}
}
if (grid && !is.GridTopology) {
if (gridtriple <- len==3) {
if (printlevel >= PL_SUBIMPORTANT && RFopt$internal$warn_oldstyle) {
message("x was interpreted as a gridtriple; the new gridtriple notation is:\n 1st row of x is interpreted as starting values of sequences,\n 2nd row as step,\n 3rd row as number of points (i.e. length),\n in each of the ", ncol(x), " directions.")
}
} else len <- rep(len, times=spatialdim) # Alex 8.10.2011
}
if (grid && !gridtriple) {
## list with columns as list elements -- easier way to
## do it??
x <- lapply(apply(x, 2, list), function(r) r[[1]])
if (!is.null(y)) y <- lapply(apply(y, 2, list), function(r) r[[1]])
}
} else { ## x, y, z given separately
if (is.null(y) && !is.null(z)) stop("y is not given, but z")
xyzT <- list(x=if (!missing(x)) x, y=y, z=z, T=T)
for (i in 1:4) {
if (!is.null(xyzT[[i]]) && !is.numeric(xyzT[[i]])) {
if (printlevel>PL_IMPORTANT)
message(names(xyzT)[i],
" not being numeric it is converted to numeric")
assign(names(xyzT)[i], as.numeric(xyzT[[i]]))
}
}
remove(xyzT)
spatialdim <- 1 + (!is.null(y)) + (!is.null(z))
if (spatialdim==1 && ((missing(grid) || length(grid) == 0) || !grid)) {
## ueberschreibt Einstellung des Nutzers im Falle d=1
if (length(x) <= 2) newgrid <- TRUE
else {
dx <- diff(x)
newgrid <- max(abs(diff(dx))) < dx[1] * RFopt$general$gridtolerance
}
if ((missing(grid) || length(grid) == 0)) grid <- newgrid
else if (xor(newgrid, grid) && RFopt$internal$warn_on_grid) {
RFoptions(internal.warn_on_grid = FALSE)
message("coordinates", if (grid) " do not",
" seem to be on a grid, but grid = ", grid)
}
}
len <- c(length(x), length(y), length(z))[1:spatialdim]
if (!(missing(grid) || length(grid) == 0) && !grid) { ## sicher nicht grid, ansonsten ausprobieren
if (any(diff(len) != 0)) stop("some of x, y, z differ in length")
x <- cbind(x, y, z)
## make a matrix out of the list
len <- len[1]
} else {
if ((missing(grid) || length(grid) == 0) && any(len != len[1]))
grid <- TRUE
x <- list(x, y, z)[1:spatialdim]
}
y <- z <- NULL ## wichtig dass y = NULL ist, da unten die Abfrage
} ## end of x, y, z given separately
if (!all(is.finite(unlist(x)))) stop("coordinates are not all finite")
if ((missing(grid) || length(grid) == 0) || grid) {
if (gridtriple) {
if (len != 3)
stop("In case of simulating a grid with option gridtriple, exactly 3 numbers are needed for each direction")
lr <- x[3,] # apply(x, 2, function(r) length(seq(r[1], r[2], r[3])))
##x[2,] <- x[1,] + (lr - 0.999) * x[3,] ## since own algorithm recalculates
## the sequence, this makes sure that
## I will certainly get the result of seq
## altough numerical errors may occurs
restotal <- prod(x[3, ])
if (!is.null(y) && !all(y[3,] == x[3,]))
stop("the grids of x and y do not match ")
} else {
xx <- seq2grid(x, "x", grid,
RFopt$internal$warn_ambiguous, RFopt$general$gridtolerance)
if (!is.null(y)) {
yy <- seq2grid(y, "y", grid,
RFopt$internal$warn_ambiguous,
RFopt$general$gridtolerance)
if (xor(is.logical(xx), is.logical(yy)) ||
(!is.logical(xx) && !all(yy[3,] == xx[3,])))
stop("the grids for x and y do not match")
}
if (missing(grid) || length(grid) == 0) grid <- !is.logical(xx)
if (grid) {
x <- xx
if (!is.null(y)) y <- yy
restotal <- prod(len)
len <- 3
} else {
x <- sapply(x, function(z) z)
if (!is.null(y)) y <- sapply(y, function(z) z)
}
}
if (grid && any(x[3, ] <= 0))
stop(paste("step must be postive. Got as steps",
paste(x[3,], collapse=",")))
##if (len == 1) stop("Use grid=FALSE if only a single point is simulated")
}
if (!grid) { ## not grid
restotal <- nrow(x)
if (is.null(y)) {
if (restotal < 200 && any(as.double(dist(x)) == 0)) {## 2000
d <- as.matrix(dist(x))
diag(d) <- 1
idx <- which(as.matrix(d) ==0)
if (printlevel>PL_ERRORS)
Print(x, dim(d), idx , cbind( 1 + ((idx-1)%% nrow(d)), #
1 + as.integer((idx - 1) / nrow(d))) )
warning("locations are not distinguishable")
}
## fuer hoehere Werte con total ist ueberpruefung nicht mehr praktikabel
}
}
if (coord_system == "earth") {
# if (ncol(x) > 4) stop("earth coordinates have maximal 3 components")
global.units <- RFoptions()$coords$new_coordunits[1]
if (global.units[1] == "") global.units <- "km"
Raumdim <- if (grid) ncol(x) else nrow(x)
new_is_cartesian <- new_coord_system %in% CARTESIAN_SYSTEMS
if (new_is_cartesian) {
if (!is.null(y))
stop("cannot take 'y' as an argument if 'x' is a (internal) matrix")
code <- switch(new_coord_system,
"cartesian" = CARTESIAN_COORD,
"gnomonic" = GNOMONIC_PROJ,
"orthographic" = ORTHOGRAPHIC_PROJ,
stop("unknown projection method")
)
x <- RFfctn(RMtrafo(new=code), x, grid=grid,
coords.new_coordunits=global.units,
coords.new_coord_system = "keep")
if (new_coord_system == "cartesian") {
Raumdim <- max(3, Raumdim)
spatialdim <- Raumdim
}
dim(x) <- c(length(x) /Raumdim, Raumdim)
#x <- t(x)
## never try to set the following lines outside the 'if (new_coord_system'
## as in case of ..="keep" none of the following lines should be set
RFoptions(coords.coord_system =
if (new_is_cartesian) "cartesian" else new_coord_system)
grid <- FALSE
} else if (!(new_coord_system %in% c("keep", "sphere", "earth"))) {
warning("unknown new coordinate system")
}
}
if (Zeit <- !is.null(T)) {
Ttriple <- length(T) == 3;
if (length(T) <= 2) Tgrid <- TRUE
else {
dT <- diff(T)
Tgrid <- max(abs(diff(dT))) < dT[1] * RFopt$general$gridtolerance
}
if (is.na(RFopt$general$Ttriple)) {
if (Ttriple && Tgrid)
stop("ambiguous definition of 'T'. Set RFoptions(Ttriple=TRUE) or ",
"RFoptions(Ttriple=FALSE)")
if (!Ttriple && !Tgrid) stop("'T' does not have a valid format")
} else if (RFopt$general$Ttriple) {
if (!Ttriple)
stop("'T' is not given in triple format 'c(start, step, length)'")
Tgrid <- FALSE
} else {
if (!Tgrid) stop("'T' does not define a grid")
Ttriple <- FALSE
}
if (Tgrid)
T <- as.vector(seq2grid(list(T), "T", Tgrid,
RFopt$internal$warn_ambiguous,
RFopt$general$gridtolerance))
restotal <- restotal * T[3]
}
if (!missing(dim) && !is.null(dim) && spatialdim != dim) {
stop("'dim' should be given only when 'distances' are given. Here, 'dim' contradicts the given coordinates.")
}
storage.mode(x) <- "double"
if (is.null(y)) {
return(list(x=x, T=T, Zeit=Zeit, restotal=restotal, l=len,
spatialdim=spatialdim, grid=grid, distances=FALSE,
coordunits = curunits, new_coordunits = newunits))
} else {
storage.mode(y) <- "double"
return(list(x=x, y=y, T=T, Zeit=Zeit, restotal=restotal, l=len,
spatialdim=spatialdim, grid=grid, distances=FALSE,
coordunits = curunits, new_coordunits = newunits))
}
}
RFearth2cartesian <- function(coord, units=NULL, system = "cartesian",
grid=FALSE) {
if (is.character(system)) system <- pmatch(system, ISONAMES) - 1
stopifnot(system %in%
c(CARTESIAN_COORD, GNOMONIC_PROJ, ORTHOGRAPHIC_PROJ))
if (is.null(units)) {
global.units <- RFoptions()$coords$new_coordunits[1]
units <- if (global.units[1] == "") "km" else global.units
}
if (!is.matrix(coord)) coord <- t(coord)
res <- RFfctn(RMtrafo(new=system), coord, grid=grid,
coords.new_coord_system = "keep",
coords.new_coordunits=units,
coords.coord_system="earth")
return(res)
}
RFearth2dist <- function(coord, units=NULL, system="cartesian",
grid=FALSE, ...) {
if (is.character(system)) system <- pmatch(system, ISONAMES) - 1
stopifnot(system %in%
c(CARTESIAN_COORD, GNOMONIC_PROJ, ORTHOGRAPHIC_PROJ))
if (is.null(units)) {
global.units <- RFoptions()$coords$new_coordunits[1]
units <- if (global.units[1] == "") "km" else global.units
}
if (!is.matrix(coord)) coord <- t(coord)
z <- RFfctn(RMtrafo(new=system), coord, grid=grid,
coords.new_coord_system = "keep",
coords.new_coordunits=units,
coords.coord_system="earth")
return(dist(z, ...))
}
CheckData <- function(model, x, y, z, T, distances, grid, data,
given=NULL, allowFirstCols=TRUE, vdim, repet,
dim, ...) {
if (!missing(distances) && length(distances)>0)
stop("option distances not programmed yet.")
if (missing(data)) stop("missing data")
if (missing(model)) model <- list("null")
else model <- PrepareModel2(model, ...)
missing.given <- length(given) == 0
missing.x <- missing(x) && missing.given
if (isSpObj(data)) data <- sp2RF(data)
if (isRFsp <- is(data, "RFsp")) {
if (length(given) != 0) {
stop("the coordinates for the measured data are given ambigiously (by 'given' and within 'data')")
}
data <- selectDataAccordingFormula(data, model=model)
if (!is.null(data@.RFparams)) {
vdim <- data@.RFparams$vdim
repet <- data@.RFparams$n
} else {
vdim <- repet <- NULL
}
variab.names <- colnames(data@data)
if (grid.fulldata <- isGridded(data)) {
data <- rfspDataFrame2conventional(data) ## zeitkritisch ! to do
given <- list(x=data$x, T=data$T, grid=TRUE)
data <- as.matrix(data$data)
} else {
given <- list(x=coordinates(data), grid=FALSE) ## stehend; darf nicht gaendert werden
data <- as.matrix(data@data)
}
} else {
if (!hasArg("vdim")) vdim <- NULL
if (!hasArg("repet")) repet <- NULL
# Print(allowFirstCols)
if (missing.x) {
if (allowFirstCols)
data.col <- data.columns(data, dim, force=TRUE, halt=FALSE)
else data.col <- data.columns(data)
given <- list(x=data[, data.col$x, drop=FALSE], grid=FALSE)
data <- data[ , data.col$data, drop=FALSE]
}
}
if (!missing.given) {
if (!missing(x))
stop("x coordinates of the data given in two different ways")
stopifnot(missing(y) || is.null(y), missing(z) || is.null(z),
missing(T) || is.null(T))
if (!is.list(given)) given <- list(x=given)
}
if (length(given) == 0)
given <- CheckXT(x = x, y = y, z = z, T = T, grid = grid,
distances=distances,
if (!missing(distances) && length(distances) > 0)
dim = if (hasArg("dim")) dim else 1
##, length.data=length(data)
)
else
given <- do.call(CheckXT, given)
if (missing(dim) || length(dim) == 0)
dim <- as.integer(given$spatialdim + given$Zeit)
else stopifnot(dim == given$spatialdim + given$Zeit)
if (is.vector(data)) {
dimdata <- c(length(data), 1)
} else {
if (!is.array(data)) {
data <- as.matrix(data)
}
dimdata <- base::dim(data)
}
if (length(dim(data)) != 2) {
## Achtung! data verliert die Row-/col-Namen mit der
## naechsten Anweisung!!
datanames <- dimnames(data)
base::dim(data) <- c(dimdata[1], prod(dimdata[-1]))
}
vdimrepet <- as.integer(length(data) / given$restotal)
if (vdimrepet * given$restotal != length(data))
stop("dimension of data does not match coordinates")
variab.names <- colnames(data)
names <- GetDataNames(model=model, coords=given$x, locinfo=given)#ohne data!
if (is.null(names$variab.names))
names$variab.names <-
if (class(variab.names) == "try-error") NULL else variab.names
return(c(ts.xdim = dim,
vdim =vdim,
repet = repet,
list(## xgr = if (given$grid) cbind(given$x, given$T) else NULL,
fullgiven = given,
coord.names=names$coord.names,
variab.names=names$variab.names,
model = model, #userdefined = userdefined,
data.col = if (missing.x && !isRFsp) data.col else NULL,
fulldata = data),
missing.x=missing.x
))
}