https://github.com/cran/RandomFields
Tip revision: 9298a5792ec3101f8d2a98edeb37d86b7263e34e authored by Martin Schlather on 24 July 2015, 00:00:00 UTC
version 3.1.0
version 3.1.0
Tip revision: 9298a57
convert.R
## Authors
## Martin Schlather, schlather@math.uni-mannheim.de
##
##
## Copyright (C) 2015 Martin Schlather
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License
## as published by the Free Software Foundation; either version 3
## of the License, or (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program; if not, write to the Free Software
## Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
PrepareModel2 <- function(model, ..., x=NULL) {
if (missing(model) || is.null(model)) stop("'model' must be given.")
method <- "ml"
if (class(model) == "RF_fit") model <- model[[method]]$model
else if (class(model) == "RFfit") model <- model[method]
m <- parseModel(model, ..., x=x)
if (notplus <- !(m[[1]] %in% ZF_PLUS)) m <- list(ZF_SYMBOLS_PLUS, m)
for (i in 2:length(m)) {
if ((m[[i]][[1]] %in% ZF_MIXED) && length(m[[i]]$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message(paste("The '1' in the mixed model definition has been replaced by '", ZF_TREND[1], "(mean=", m[[i]]$mean, ")'.", sep=""))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 (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, # == spatialdim!
length.data,
y.ok = FALSE,
printlevel = RFoptions()$general$printlevel){
## do not pass anything on "..." ! --- only used for internal calls
## when lists are re-passed
## converts the given coordinates into standard formats
## (one for arbitrarily given locations and one for grid points)
#print("CheckXT in convert.R")#Berreth
if (!missing(x)) {
if (is(x, "CheckXT")) return(x)
if (is.list(x)) {
if (!is.list(x[[1]])) return(do.call("CheckXT", x))
L <- list()
for (i in 1:length(x)) {
L[[i]] <-
if (is(x[[i]], "CheckXT")) x[[i]] else do.call("CheckXT", x[[i]])
}
if (length(x) > 1) {
if (!all(diff(sapply(L, function(x) x$Zeit)) == 0) ||
!all(diff(sapply(L, function(x) x$spatialdim)) == 0))
stop("all sets must have the same dimension")
if (!all(diff(sapply(L, function(x) x$dist.given)) == 0))
stop("either all the sets must be based on distances or none")
}
class(L) <- "CheckXT"
return(L)
}
}
RFopt <- RFoptions()
curunits <- RFopt$coords$coordunits
newunits <- RFopt$coords$new_coordunits
coord_system <- RFopt$coords$coord_system
new_coord_system <- RFopt$coords$new_coord_system
ex.red <- RFopt$internal$examples_reduced
if (!missing(distances) && !is.null(distances)) { ## length==0 OK!
stopifnot(is.matrix(distances) || (!missing(dim) && !is.null(dim)),
(missing(grid) || length(grid) == 0),
missing(x) || is.null(x),
length(y)==0,
length(z)==0,
length(T)==0)
if (coord_system != new_coord_system && new_coord_system != "keep")
stop("coordinate systems differ")
if (is.list(distances)) {
L <- list()
for (i in 1:length(x))
L[[i]] <- do.call("CheckXT", list(distances=distances[[i]], dim=dim))
class(L) <- "CheckXT"
return(L)
}
if (class(distances) == "dist") {
x <- as.vector(distances)
len <- length(distances)
} 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
} else {
stop("'distances' not of required format.")
}
if (ex.red && len > ex.red^2 / 2) {
LEN <- as.integer(ex.red)
len <- as.integer(LEN * (LEN - 1) / 2)
x <- if (is.matrix(x)) x[1:len ,] else x[1:len]
} else {
LEN <- as.integer(1e-9 + 0.5 * (1 + sqrt(1 + 8 * len)))
if (LEN * (LEN-1) / 2 != len) LEN <- NaN
}
## keep exactly the sequence up to 'distances'
if (storage.mode(x) != "double") storage.mode(x) <- "double"
L <- list(x = as.matrix(x), #0
y = double(0), #1
T= double(0), #2
grid = FALSE, #3
spatialdim=as.integer(dim),#4
Zeit=FALSE, #5
dist.given = TRUE, #6
restotal = LEN, ## number of points
l = LEN, ## ?? physical length??
coordunits = curunits,
new_coordunits = newunits
)
class(L) <- "CheckXT"
return(L)
}
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$spatialdim > 1)
message("Grid detected. If it is not a grid, set grid=FALSE.\n")
}
}
return(if (grid) new else {
CheckXT(x, y, z, T, grid=FALSE, distances,
if (!missing(distances) && length(distances) > 0) dim=1,
length.data = length.data,
printlevel = printlevel) }
)
} # if (missing(grid) && !missing(length.data))
gridtriple <- FALSE
if (is.GridTopology <- is(x, "GridTopology")){
x <- rbind(x@cellcentre.offset,
x@cellsize,
x@cells.dim)
if ((missing(grid) || length(grid) == 0)) grid <- TRUE else stopifnot(grid)
gridtriple <- TRUE
}
##else {
## is.GridTopology <- FALSE
##}
if (is.data.frame(x)) {
if (ncol(x)==1) x <- as.vector(x) else x <- as.matrix(x)
}
stopifnot(length(x) != 0)
# stopifnot(all(unlist(lapply(as.list(x), FUN=function(li) is.numeric(li))))) ## wann benoetigt???
stopifnot(is.numeric(x))# um RFsimulte(model, data) statt data=data abzufangen
# stopifnot(all(is.finite(x)), all(is.finite(y)), all(is.finite(z))) ; s.u. unlist
if (is.matrix(x)) {
if (!is.numeric(x)) stop("x is not numeric.")
if (length(z)!=0) stop("If x is a matrix, then z may not be given")
if (length(y)!=0) {
if (!y.ok) stop("If x is a matrix, then y may not be given")
if (length(T)!=0)
stop("If x is a matrix and y is given, then T may not be given")
if (!is.matrix(y) || ncol(y) != ncol(x) ||
nrow(x)==3 && nrow(y)!=3 && ((missing(grid) || length(grid) == 0) ||
grid))
stop("y does not match x (it must be a matrix)")
}
if (coord_system == COORD_SYS_NAMES[coord_auto + 1] && ncol(x) >= 2
&& ncol(x) <= 3 && !is.null(n <- dimnames(x)[[2]])) {
if (any(idx <- earth_coordinate_names(n))) {
if (length(idx) == 2 && !all(idx == 1:2))
stop("earth coordinates not in order longitude/latitude")
cur <- curunits[1]
newunits <- RFopt$coords$new_coordunits
curunits <- RFopt$coords$coordunits
curunits[1:2] <- ZF_EARTHCOORD_NAMES[1:2]
if (newunits[1] == "") newunits[1] <- UNITS_NAMES[units_km + 1]
newunits[2:3] <- newunits[1]
if (RFopt$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$warn_oldstyle) {
message("x was interpreted as a gridtriple; the new gridtriple notation is:\n 1st row of x is interpreted as starting values of sequences,\n 2nd row as step,\n 3rd row as number of points (i.e. length),\n in each of the ", ncol(x), " directions.")
}
} else len <- rep(len, times=spatialdim) # Alex 8.10.2011
}
if (grid && !gridtriple) {
## list with columns as list elements -- easier way to
## do it??
x <- lapply(apply(x, 2, list), function(r) r[[1]])
if (length(y) != 0) y <- lapply(apply(y, 2, list), function(r) r[[1]])
}
} else { ## x, y, z given separately
if (length(y)==0 && length(z)!=0) stop("y is not given, but z")
xyzT <- list(x=if (!missing(x)) x, y=y, z=z, T=T)
for (i in 1:4) {
if (!is.null(xyzT[[i]]) && !is.numeric(xyzT[[i]])) {
if (printlevel>PL_IMPORTANT)
message(names(xyzT)[i],
" not being numeric it is converted to numeric")
assign(names(xyzT)[i], as.numeric(xyzT[[i]]))
}
}
remove(xyzT)
spatialdim <- 1 + (length(y)!=0) + (length(z)!=0)
if (spatialdim==1 && ((missing(grid) || length(grid) == 0) || !grid)) {
## ueberschreibt Einstellung des Nutzers im Falle d=1
if (length(x) <= 2) newgrid <- TRUE
else {
dx <- diff(x)
newgrid <- max(abs(diff(dx))) < dx[1] * RFopt$general$gridtolerance
}
if ((missing(grid) || length(grid) == 0)) grid <- newgrid
else if (xor(newgrid, grid) && RFopt$internal$warn_on_grid) {
RFoptions(internal.warn_on_grid = FALSE)
message("coordinates", if (grid) " do not",
" seem to be on a grid, but grid = ", grid)
}
}
len <- c(length(x), length(y), length(z))[1:spatialdim]
if (!(missing(grid) || length(grid) == 0) && !grid) { ## sicher nicht grid, ansonsten ausprobieren
if (any(diff(len) != 0)) stop("some of x, y, z differ in length")
x <- cbind(x, y, z)
## make a matrix out of the list
len <- len[1]
} else {
if ((missing(grid) || length(grid) == 0) && any(len != len[1]))
grid <- TRUE
x <- list(x, y, z)[1:spatialdim]
}
y <- z <- NULL ## wichtig dass y = NULL ist, da unten die Abfrage
} ## end of x, y, z given separately
if (!all(is.finite(unlist(x)))) {
stop("coordinates are not all finite")
}
if ((missing(grid) || length(grid) == 0) || grid) {
if (gridtriple) {
if (len != 3)
stop("In case of simulating a grid with option gridtriple, exactly 3 numbers are needed for each direction")
lr <- x[3,] # apply(x, 2, function(r) length(seq(r[1], r[2], r[3])))
##x[2,] <- x[1,] + (lr - 0.999) * x[3,] ## since own algorithm recalculates
## the sequence, this makes sure that
## I will certainly get the result of seq
## altough numerical errors may occurs
restotal <- prod(x[3, ])
if (length(y)!=0 && !all(y[3,] == x[3,]))
stop("the grids of x and y do not match ")
} else {
xx <- seq2grid(x, "x", grid,
RFopt$internal$warn_ambiguous, RFopt$general$gridtolerance)
if (length(y)!=0) {
yy <- seq2grid(y, "y", grid,
RFopt$internal$warn_ambiguous,
RFopt$general$gridtolerance)
if (xor(is.logical(xx), is.logical(yy)) ||
(!is.logical(xx) && !all(yy[3,] == xx[3,])))
stop("the grids for x and y do not match")
}
if (missing(grid) || length(grid) == 0) grid <- !is.logical(xx)
if (grid) {
x <- xx
if (length(y) != 0) y <- yy
restotal <- prod(len)
len <- 3
} else {
x <- sapply(x, function(z) z)
if (length(y) != 0) y <- sapply(y, function(z) z)
}
}
if (grid && any(x[3, ] <= 0))
stop(paste("step must be postive. Got as steps",
paste(x[3,], collapse=",")))
##if (len == 1) stop("Use grid=FALSE if only a single point is simulated")
}
if (!grid) { ## not grid
restotal <- nrow(x)
if (length(y)==0) {
if (restotal < 200 && any(as.double(dist(x)) == 0)) {## 2000
d <- as.matrix(dist(x))
diag(d) <- 1
idx <- which(as.matrix(d) ==0)
if (printlevel>PL_ERRORS)
Print(x, dim(d), idx , cbind( 1 + ((idx-1)%% nrow(d)), #
1 + as.integer((idx - 1) / nrow(d))) )
warning("locations are not distinguishable")
}
## fuer hoehere Werte con total ist ueberpruefung nicht mehr praktikabel
}
}
if (coord_system == "earth") {
# if (ncol(x) > 4) stop("earth coordinates have maximal 3 components")
opt <- RFoptions()$coords ## muss nochmals neu sein
global.units <- opt$new_coordunits[1]
if (global.units[1] == "") global.units <- "km"
Raumdim <- ncol(x) #if (grid) ncol(x) else
new_is_cartesian <- new_coord_system %in% CARTESIAN_SYSTEMS
if (new_is_cartesian) {
if (sum(idx <- is.na(opt$zenit))) {
zenit <- (if (grid) x[1, 1:2] + x[2, 1:2] * (x[3, 1:2] - 1) else
if (opt$zenit[!idx] == 1) colMeans(x[, 1:2]) else
if (opt$zenit[!idx] == Inf) colMeans(apply(x[, 1:2], 2, range)) else
stop("unknown value of zenit"))
RFoptions(zenit = zenit)
}
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 (length(y) != 0)
y <- RFfctn(RMtrafo(new=code), y, 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 <- length(T)!=0) {
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.")
}
if (ex.red) {
if (grid) {
x[3, ] <- pmin(x[3, ], ex.red)
if (length(y) > 0) y[3, ] <- pmin(y[3, ], ex.red)
restotal <- as.integer(prod(x[3, ]))
} else {
len <- restotal <- as.integer(min(nrow(x), ex.red^spatialdim))
x <- x[1:len, , drop=FALSE]
if (length(y) > 0) y <- y[1:len, , drop=FALSE]
}
if (Zeit) {
T[3] <- min(T[3], 3)
restotal <- as.integer(restotal * T[3])
}
}
## keep exactly the sequence up to 'grid'
if (length(x) > 0) {
if (storage.mode(x) != "double") storage.mode(x) <- "double"
} else x <- double(0)
if (length(y) > 0) {
if (storage.mode(y) != "double") storage.mode(y) <- "double"
} else y <- double(0)
L <- list(x=x, #0
y=y, #1
T=as.double(T), #2
grid=as.logical(grid), #3
spatialdim=as.integer(spatialdim), #4
Zeit=Zeit, #5
dist.given=FALSE, #6
restotal=as.integer(restotal), ## 7, nr of locations
l=as.integer(len), ## 8, physical "length/rows" of input
coordunits = curunits, #9
new_coordunits = newunits) #10
class(L) <- "CheckXT"
return(L)
}
trafo.to.C_CheckXT <- function(new) {
if (is.list(new[[1]])) {
for(i in 1:length(new)) {
if (length(new[[i]]$x)>0 && !new[[i]]$grid) new[[i]]$x = t(new[[i]]$x)
if (length(new[[i]]$y)>0 && !new[[i]]$grid) new[[i]]$y = t(new[[i]]$y)
}
} else {
if (length(new$x)>0 && !new$grid) new$x = t(new$x)
if (length(new$y)>0 && !new$grid) new$y = t(new$y)
}
new
}
C_CheckXT <- function(x, y=NULL, z=NULL, T=NULL, grid, distances=NULL,
dim=NULL, # == spatialdim!
length.data,
y.ok = FALSE,
printlevel = RFoptions()$general$printlevel){
neu <- CheckXT(x=x, y=y, z=z, T=T, grid=grid, distances=distances,
dim=dim, length.data=length.data, y.ok=y.ok,
printlevel = printlevel)
return(trafo.to.C_CheckXT(neu))
}
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, ...))
}
## used by RFratiotest, fitgauss, Crossvalidation, likelihood-ratio, RFempir
StandardizeData <- function(model,
x, y=NULL, z=NULL, T=NULL,
grid, data, distances=NULL,
RFopt, mindist_pts=2,
dim=NULL, allowFirstCols=TRUE, vdim = NULL, ...) {
#if (missing(x)) Print(data, T) else Print(data, T, x)
RFoptions(internal.examples_reduced=FALSE)
#Print(data); if (!missing(x)) print(x); Print(missing(x), y, z, T, missing(dim), missing(grid), missing(distances))
if (missing(dim)) dim <- NULL
if (missing(grid)) grid <- NULL
dist.given <- !missing(distances) && length(distances)>0
matrix.indep.of.x.assumed <- FALSE
rangex <- neu <- gridlist <- RFsp.coord <- gridTopology <- data.RFparams <-
mindist <- data.col <- NULL
if (missing(data)) stop("missing data")
missing.x <- missing(x)
if (isSpObj(data)) data <- sp2RF(data)
if (isRFsp <- is(data, "RFsp") || (is.list(data) && is(data[[1]], "RFsp"))){
## ||(is.list(data) && is(data[[1]], "RFsp")))
if ( (!missing.x && length(x)!=0) || length(y)!=0 || length(z) != 0 ||
length(T) != 0 || dist.given || length(dim)!=0 || length(grid) != 0)
stop("data object already contains information about the locations. So, none of 'x' 'y', 'z', 'T', 'distance', 'dim', 'grid' should be given.")
if (!is.list(data)) data <- list(data)
sets <- length(data)
x <- RFsp.coord <- gridTopology <- data.RFparams <- vector("list", sets)
if (!is.null(data[[1]]@.RFparams)) {
if (length(vdim) > 0) stopifnot( vdim == data[[1]]@.RFparams$vdim)
else vdim <- data[[1]]@.RFparams$vdim
}
dimdata <- NULL
dimensions <- (if (isGridded(data[[1]])) data[[1]]@grid@cells.dim
else nrow(data[[1]]@data))
dimensions <- c(dimensions, data[[1]]@.RFparams$vdim)
for (i in 1:length(data)) {
xi <- list()
xi$grid <- isGridded(data[[i]])
compareGridBooleans(grid, xi$grid)
data[[i]] <- selectDataAccordingFormula(data[[i]], model=model)
data.RFparams[[i]] <- data[[i]]@.RFparams
gridTopology[[i]] <- if (xi$grid) data[[i]]@grid else NULL
RFsp.coord[[i]] <- if (!xi$grid) data[[i]]@coords else NULL
dimensions <- if (xi$grid) data[[i]]@grid@cells.dim else nrow(data[[i]]@data)
dimensions <- c(dimensions, data[[i]]@.RFparams$vdim)
if (RFopt$general$vdim_close_together) dimensions <- rev(dimensions)
dimdata <- rbind(dimdata, c(dimensions, data[[i]]@.RFparams$n))
tmp <- rfspDataFrame2conventional(data[[i]])
xi$x <- tmp$x
if (!is.null(tmp$T)) xi$T <- tmp$T
data[[i]] <- as.matrix(tmp$data)
x[[i]] <- xi
}
idx <- if (RFopt$general$vdim_close_together) 1 else length(dimensions)
if (all(dimdata[, idx] == 1))
dimdata <- dimdata[, -idx, drop=FALSE]
if (all(dimdata[, ncol(dimdata)] == 1)) # repet
dimdata <- dimdata[, -ncol(dimdata), drop=FALSE]
# Print(x); #pppp
} else { # !isRFsp
## dimdata wird spaeter bestimmt
if (dist.given) {
stopifnot(missing(x) || length(x)==0, length(y)==0, length(z)==0)
if (!is.list(distances)) {
distances <- list(distances)
if (is.list(data))
stop("if list of data is given then also for distances ")
data <- list(as.matrix(data))
} else if (!is.list(data)) {
stop("if list of distances is given then also for data ")
if (length(data) != length(distances))
stop("length of distances does not match length of data")
}
for (i in 1:length(distances)) {
if (any(is.na(data)))
stop("missing data are not allowed if distances are used.")
}
stopifnot(missing(T) || length(T)==0)
if (is.matrix(distances[[1]])) {
dimensions <- sapply(distances, nrow)
spatialdim <- tsdim <- xdimOZ <- dimensions[1]
if (length(dim) > 0 && dim != spatialdim)
stop("unclear specification of the distances: either the distances is given as a vector or distance vectors should given, where the number of rows matches the spatial dimension")
lcc <- sapply(distances, function(x) 0.5 * (1 + sqrt(1 + 8 * ncol(x))) )
if (!all(diff(dimensions) == 0))
stop("sets of distances show different dimensions")
range_distSq <- function(M) range(apply(M, 2, function(z) sum(z^2)))
rangex <- sqrt(range(sapply(distances, range_distSq)))
} else {
xdimOZ <- 1
spatialdim <- tsdim <- as.integer(dim)
lcc <- sapply(distances, function(x) if (is.matrix(x)) -1
else 0.5 * (1 + sqrt(1 + 8* length(x))))
rangex <- range(sapply(distances, range))
}
# Print(mindist, rangex, RFopt$nugget$tol)
mindist <- min(rangex)
if (is.na(mindist)) mindist <- 1 ## nur 1 pkt gegeben, arbitraerer Wert
if (mindist <= RFopt$nugget$tol) {
if (!RFopt$general$allowdistanceZero)
stop("distance with value 0 identified -- use allowdistanceZero=T?")
mindist <- 1e-15 * (RFopt$nugget$tol == 0) + 2 * RFopt$nugget$tol
for (i in 1:length(distances))
if (is.vector(distances[[i]]))
distances[[i]][distances[[i]] == 0] <- mindist
else distances[[i]][1, apply(distances[[i]], 2,
function(z) sum(z^2))] <- mindist
}
len <- as.integer(lcc)
if (any(len != lcc)) stop("number of distances not of form k(k-1)/2")
neu <- distances
coordunits <- RFopt$coords$coordunits
Zeit <- FALSE
} else { ## distances not given
if (is.data.frame(data) || !is.list(data)) {
# Print(missing(x), x, data, is.data.frame(data), !is.list(data))
if (!missing(x) && is.list(x) && !is.data.frame(x) &&
(length(x$grid)==0 || length(x$restot)==0))
stop("either both coordinates and data must be lists or none")
data <- list(data)
}
sets <- length(data)
for (i in 1:sets) {
if (is.data.frame(data[[i]]) || is.vector(data[[i]]))
data[[i]] <- as.matrix(data[[i]])
}
sel <- try(selectAccordingFormula(data[[1]], model), silent=TRUE)
if (is(sel, "try-error")) sel <- NULL
if (missing(x)) { ## dec 2012: matrix.indep.of.x.assumed
if (!is.null(dnames <- colnames(data[[1]]))) {
if ((!any(is.na(xi <- RFopt$coord$coordnames))) ||
(length(xi <- earth_coordinate_names(dnames)) == 2) ||
(length(xi <- cartesian_coordinate_names(dnames)) > 0) ||
(length(xi <- general_coordinate_names(dnames)) > 0) ) {
x <- list()
for (i in 1:sets) {
xx <- data[[i]][ , xi, drop=FALSE]
storage.mode(xx) <- "numeric"
x[[i]] <- list(x=xx, grid = FALSE)
if (length(sel) == 0) sel <- -xi
}
}
}
if (missing(x)) { ## if still missing
data.col <- try(data.columns(data[[1]], xdim=dim,
force=allowFirstCols,
halt=!allowFirstCols))
x <- list()
if (is(data.col, "try-error")) {
if (length(sel) > 0){
for (i in 1:sets) {
x[[i]] <- data[[i]][ , !sel, drop=FALSE]
storage.mode(x[[i]]) <- "numeric"
}
if (length(dim) == 0) {
warning("better give 'dim' explicitely.")
}
if (length(dim) > 0 && ncol(x[[i]]) != dim)
stop("'dim' does not match the recognized coordindates")
} else {
sel <- TRUE
data.col <- NULL
matrix.indep.of.x.assumed <- TRUE
for (i in 1:sets) {
x[[i]] <- 1:nrow(as.matrix(data[[i]]))
storage.mode(x[[i]]) <- "numeric"
}
}
### x[1] <- 0 ## so no grid ! ## why forbidding ?? 15.5.2015
} else {
for (i in 1:sets) {
xx <- data[[i]][, data.col$x, drop=FALSE]
storage.mode(xx) <- "numeric"
x[[i]] <- list(x=xx, grid=FALSE)
if (length(sel) == 0) sel <- data.col$data
}
}
}
for (i in 1:sets) {
data[[i]] <- data[[i]][ , sel, drop=FALSE]
storage.mode(data[[i]]) <- "numeric"
}
} ## xgiven; KEIN ELSE, auch wenn nachfolgend z.T. gedoppelt wird
if (is.data.frame(x)) x <- as.matrix(x)
if (is.list(x)) {
if (length(y)!=0 || length(z)!=0 || length(T)!=0)
stop("if x is alist 'y', 'z', 'T' may not be given")
if (!is.list(x[[1]])) {
if (length(data) == 1) x <- list(x)
else stop("number of sets of 'x' and 'data' differ")
}
} else {
x <- list(x=x)
if (length(y)!=0) {
stopifnot(!is.list(y))
x$y <- y
}
if (length(z)!=0) {
stopifnot(!is.list(z))
x$z <- z
}
if (length(T)!=0) {
stopifnot(!is.list(T))
x$T <- T
}
if (!is.null(grid))
x$grid <- grid
if (!is.list(data)) data <- list(as.matrix(data))
x <- list(x)
}
##}
} # ! distance
sets <- length(data)
dimdata <- matrix(nrow=sets, ncol=length(base::dim(data[[1]])))
for (i in 1:sets) dimdata[i, ] <- base::dim(data[[i]])
} # !isRFsp
if (!dist.given) { ## x coordinates, not distances
neu <- CheckXT(x=x) #, y=y, z=z, T=T, grid=grid, distances=distances,
# dim=dim, length) # , length.data=length(data[[i]]), printlevel = 0)
if (!is.list(neu[[1]])) neu <- list(neu)
coordunits<- neu[[1]]$coordunits
spatialdim <- as.integer(neu[[1]]$spatialdim)
Zeit <- neu[[1]]$Zeit
tsdim <- as.integer(spatialdim + Zeit)
len <- sapply(neu, function(x)
(if (x$grid) prod(x$x[3, ]) else nrow(x$x)) *
(if (Zeit) x$T[3] else 1))
getrange <- function(x)
if (x$grid) rbind(x$x[1, ], x$x[1, ] + x$x[2, ] * (x$x[3, ] - 1))
else apply(x$x, 2, range)
rangex <- t(sapply(neu, getrange))
base::dim(rangex) <- c(length(rangex) / spatialdim, spatialdim)
rangex <- apply(rangex, 2, range)
getmindistSq <- function(x) {
if (x$grid) sum(x$x[2,]^2)
else if (nrow(x$x) < 2) NA
else if (nrow(x$x) <= mindist_pts) min(dist(x$x))
else min(dist(x$x[sample(nrow(x$x), mindist_pts), ]))
}
if (Zeit && any(sapply(neu, function(x) x$T[2]) <= RFopt$nugget$tol))
stop("step of time component smaller than nugget tolerance 'tol'")
if (any(sapply(neu, function(x) x$grid && any(x$x[2, ]<=RFopt$nugget$tol))))
stop("step of some spatial component smaller than nugget tolerance 'tol'")
zaehler <- 0
repeat {
mindist <- sqrt(min(sapply(neu, getmindistSq)))
if (is.na(mindist)) mindist <- 1 ## nur 1 pkt gegeben, arbitraerer Wert
if (mindist <= RFopt$nugget$tol) {
if (!RFopt$general$allowdistanceZero)
stop("Distance with value 0 identified -- use allowdistanceZero=T?")
if ((zaehler <- zaehler + 1) > 10)
stop("unable to scatter point pattern")
for (i in 1:length(neu)) if (!neu[[i]]$grid)
neu[[i]]$x <- neu[[i]]$x + rnorm(length(neu[[i]]$x), 0,
10 * RFopt$nugget$tol)
} else break;
}
xdimOZ <- ncol(neu[[1]]$x)
}
if (length(dim) > 0) stopifnot(dim == tsdim)
varnames <- try(colnames(data[[1]]))
## geht x[[1]]$x immer gut ??
names <- GetDataNames(model=model, coords=x[[1]]$x, locinfo=neu[[1]]) #ohne data!
if (is.null(names$varnames))
names$varnames <-
if (class(varnames) == "try-error") NULL else varnames
restotal <- sapply(neu, function(x) x$restotal)
ldata <- sapply(data, length)
if (length(vdim) == 0) {
if (all(sapply(data, function(x) is.vector(x) || ncol(x) == 1)))
vdim <- 1
else if (!missing(model)) {
vdim <- rfInit(list("Cov", PrepareModel2(model=model, ...,
x=trafo.to.C_CheckXT(neu))),
x=x, y=y, z=z, T=T, grid=grid, distances=distances,
dim=dim, reg=MODEL_AUX, dosimulate=FALSE)[1]
} else vdim <- NA
}
repetitions <- as.integer(ldata / (restotal * vdim))
# Print(data, ldata, repetitions, restotal, vdim, neu, dist.given)
if (!is.na(vdim) && any(ldata != repetitions * restotal * vdim))
stop("mismatch of data dimensions")
RFoptions(internal.examples_reduced=RFopt$internal$examples_red)
return(list(
## coord = expandiertes neu # #
model = if (missing(model)) NULL else
PrepareModel2(model, ..., x=trafo.to.C_CheckXT(neu)),
orig.model = if (missing(model)) NULL else model,
data=data, dimdata=dimdata, isRFsp = isRFsp,
RFsp.coord = RFsp.coord,
coord = neu,
dist.given=dist.given,
gridTopology = gridTopology,
data.RFparams = data.RFparams,
spatialdim=spatialdim,
tsdim=tsdim,
rangex = as.matrix(rangex),
coordunits=coordunits,
Zeit = Zeit,
matrix.indep.of.x.assumed = matrix.indep.of.x.assumed,
len = len,
mindist = mindist,
xdimOZ = xdimOZ,
vdim = vdim,
coordnames=names$coordnames,
varnames=if (length(names$varnames)==0) ""
else names$varnames,
data.col = data.col,
repetitions = repetitions
))
}
