# fields, Tools for spatial data
# Copyright 2004-2007, Institute for Mathematics Applied Geosciences
# University Corporation for Atmospheric Research
# Licensed under the GPL -- www.gpl.org/licenses/gpl.html
Krig.check.xY <- function(x, Y, Z, weights, na.rm, 
    verbose = FALSE) {
    #
    # check for missing values in Y or X.
    #
    # save logical indicating where there are NA's
    # and check for NA's
    #
    ind <- is.na(Y)
    if (any(ind) & !na.rm) {
        stop("Need to remove missing values or use: na.rm=TRUE in the call")
    }
    #
    # coerce x to be a matrix
    x <- as.matrix(x)
    #
    # coerce Y to be a vector
    #
    Y <- as.matrix(Y)
    if (ncol(Y) != 1) {
        stop("Krig can handle matrix Y data")
    }
    #
    #default weights ( reciprocal variance of errors).
    #
    if (is.null(weights)) 
        weights <- rep(1, length(Y))
    #
    # check that dimensions agree
    #
    if (length(Y) != nrow(x)) {
        stop(" length of y and number of rows of x differ")
    }
    if (length(Y) != length(weights)) {
        stop(" length of y and weights differ")
    }
    #  if Z is not NULL coerce to be  a matrix
    # and check  # of rows
    if (verbose) {
        print(Z)
    }
    if (!is.null(Z)) {
        if (!is.matrix(Z)) {
            Z <- matrix(c(Z), ncol = 1)
        }
        if (length(Y) != nrow(Z)) {
            stop(" length of y and number of rows of Z differ")
        }
    }
    # if NAs can be removed then remove them and warn the user
    if (na.rm) {
        ind <- is.na(Y)
        if (any(ind)) {
            Y <- Y[!ind]
            x <- as.matrix(x[!ind, ])
            if (!is.null(Z)) {
                Z <- Z[!ind, ]
            }
            weights <- weights[!ind]
            #            warning('NA's have been removed from Y ')
        }
    }
    #
    # check for NA's in x matrix -- there should not be any to proceed!
    if (any(c(is.na(x)))) {
        stop(" NA's in x matrix")
    }
    #
    # check for NA's in Z matrix
    if (!is.null(Z)) {
        if (any(c(is.na(Z)))) {
            stop(" NA's in Z matrix")
        }
    }
    #
    # verbose block
    if (verbose) {
        cat("Y:", fill = TRUE)
        print(Y)
        cat("x:", fill = TRUE)
        print(x)
        cat("weights:", fill = TRUE)
        cat(weights, fill = TRUE)
    }
    #
    # save x, weights  and Y w/o NAs
    N <- length(Y)
    return(list(N = N, y = Y, x = x, weights = weights, Z = Z, 
        NA.ind = ind))
}