The R Project SVN R

/*
 *  R : A Computer Language for Statistical Data Analysis
 *  Copyright (C) 1995, 1996  Robert Gentleman and Ross Ihaka
 *  Copyright (C) 1998-2001   The R Development Core Team
 *  Copyright (C) 2002--2005  The R Foundation
 *
 *  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 2 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.
 *
 *  A copy of the GNU General Public License is available via WWW at
 *  http://www.gnu.org/copyleft/gpl.html.  You can also obtain it by
 *  writing to the Free Software Foundation, Inc., 59 Temple Place,
 *  Suite 330, Boston, MA  02111-1307  USA.
 */

/* <UTF8> Only ASCII values */

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <Defn.h>
#include <Rmath.h>
#include <R_ext/RS.h>     /* for Calloc/Free */
#include <R_ext/Applic.h> /* for dgemm */

/* "GetRowNames" and "GetColNames" are utility routines which
 * locate and return the row names and column names from the
 * dimnames attribute of a matrix.  They are useful because
 * old versions of R used pair-based lists for dimnames
 * whereas recent versions use vector based lists.

 * These are now very old, plus
 * ``When the "dimnames" attribute is
 *   grabbed off an array it is always adjusted to be a vector.''
*/
SEXP GetRowNames(SEXP dimnames)
{
    if (TYPEOF(dimnames) == VECSXP)
    return VECTOR_ELT(dimnames, 0);
    else
    return R_NilValue;
}

SEXP GetColNames(SEXP dimnames)
{
    if (TYPEOF(dimnames) == VECSXP)
    return VECTOR_ELT(dimnames, 1);
    else
    return R_NilValue;
}

SEXP do_matrix(SEXP call, SEXP op, SEXP args, SEXP rho)
{
    SEXP vals, snr, snc;
    int nr, nc, byrow, lendat;

    checkArity(op, args);
    vals = CAR(args);
    snr = CADR(args);
    snc = CADDR(args);
    byrow = asLogical(CADR(CDDR(args)));
    if (byrow == NA_INTEGER)
    error(_("matrix: invalid 'byrow' value"));

    /* R wrapper does as.vector
    if (isVector(vals) || isList(vals)) {
    if (length(vals) < 0)  (sic! cannot happen)
       errorcall(call, "argument has length zero");
    }
    else errorcall(call, "invalid matrix element type"); */

    if (!isNumeric(snr) || !isNumeric(snc))
    error(_("non-numeric matrix extent"));

    lendat = length(vals);
    nr = asInteger(snr);
    if (nr == NA_INTEGER) /* This is < 0 */
    error(_("matrix: invalid 'nrow' value (too large or NA)"));
    if (nr < 0)
    error(_("matrix: invalid 'nrow' value (< 0)"));
    nc = asInteger(snc);
    if (nc < 0)
    error(_("matrix: invalid 'ncol' value (< 0)"));
    if (nc == NA_INTEGER)
    error(_("matrix: invalid 'ncol' value (too large or NA)"));
    if (nc < 0)
    error(_("matrix: invalid 'ncol' value (< 0)"));

    if(lendat > 0 ) {
    if (lendat > 1 && (nr * nc) % lendat != 0) {
        if (((lendat > nr) && (lendat / nr) * nr != lendat) ||
        ((lendat < nr) && (nr / lendat) * lendat != nr))
        warning(_("data length [%d] is not a sub-multiple or multiple of the number of rows [%d] in matrix"), lendat, nr);
        else if (((lendat > nc) && (lendat / nc) * nc != lendat) ||
             ((lendat < nc) && (nc / lendat) * lendat != nc))
        warning(_("data length [%d] is not a sub-multiple or multiple of the number of columns [%d] in matrix"), lendat, nc);
    }
    else if ((lendat > 1) && (nr * nc == 0)){
        warning(_("data length exceeds size of matrix"));
    }
    }

    if ((double)nr * (double)nc > INT_MAX)
    error(_("matrix: too many elements specified"));

    PROTECT(snr = allocMatrix(TYPEOF(vals), nr, nc));
    if(lendat) {
    if (isVector(vals))
        copyMatrix(snr, vals, byrow);
    else
        copyListMatrix(snr, vals, byrow);
    } else if (isVector(vals)) { /* fill with NAs */
    int i, j;
    switch(TYPEOF(vals)) {
    case STRSXP:
        for (i = 0; i < nr; i++)
        for (j = 0; j < nc; j++)
            SET_STRING_ELT(snr, i + j * nr, NA_STRING);
        break;
    case LGLSXP:
        for (i = 0; i < nr; i++)
        for (j = 0; j < nc; j++)
            LOGICAL(snr)[i + j * nr] = NA_LOGICAL;
        break;
    case INTSXP:
        for (i = 0; i < nr; i++)
        for (j = 0; j < nc; j++)
            INTEGER(snr)[i + j * nr] = NA_INTEGER;
        break;
    case REALSXP:
        for (i = 0; i < nr; i++)
        for (j = 0; j < nc; j++)
            REAL(snr)[i + j * nr] = NA_REAL;
        break;
    case CPLXSXP:
        {
        Rcomplex na_cmplx;
        na_cmplx.r = NA_REAL;
        na_cmplx.i = 0;
        for (i = 0; i < nr; i++)
            for (j = 0; j < nc; j++)
            COMPLEX(snr)[i + j * nr] = na_cmplx;
        }
        break;
    case RAWSXP:
        for (i = 0; i < nr; i++)
        for (j = 0; j < nc; j++)
            RAW(snr)[i + j * nr] = 0;
        break;
    default:
        /* don't fill with anything */
        ;
    }
    }
    UNPROTECT(1);
    return snr;
}


SEXP allocMatrix(SEXPTYPE mode, int nrow, int ncol)
{
    SEXP s, t;
    int n;

    if (nrow < 0 || ncol < 0)
    error(_("negative extents to matrix"));
    if ((double)nrow * (double)ncol > INT_MAX)
    error(_("allocMatrix: too many elements specified"));
    n = nrow * ncol;
    PROTECT(s = allocVector(mode, n));
    PROTECT(t = allocVector(INTSXP, 2));
    INTEGER(t)[0] = nrow;
    INTEGER(t)[1] = ncol;
    setAttrib(s, R_DimSymbol, t);
    UNPROTECT(2);
    return s;
}


SEXP allocArray(SEXPTYPE mode, SEXP dims)
{
    SEXP array;
    int i, n;
    double dn;

    dn = n = 1;
    for (i = 0; i < LENGTH(dims); i++) {
    dn *= INTEGER(dims)[i];
    if(dn > INT_MAX)
        error(_("allocArray: too many elements specified by 'dims'"));
    n *= INTEGER(dims)[i];
    }

    PROTECT(dims = duplicate(dims));
    PROTECT(array = allocVector(mode, n));
    setAttrib(array, R_DimSymbol, dims);
    UNPROTECT(2);
    return array;
}

/* DropDims strips away redundant dimensioning information. */
/* If there is an appropriate dimnames attribute the correct */
/* element is extracted and attached to the vector as a names */
/* attribute.  Note that this function mutates x. */
/* Duplication should occur before this is called. */

SEXP DropDims(SEXP x)
{
    SEXP q, dims, dimnames, newnames = R_NilValue;
    int i, n, ndims;

    PROTECT(x);
    dims = getAttrib(x, R_DimSymbol);
    dimnames = getAttrib(x, R_DimNamesSymbol);

    /* Check that dropping will actually do something. */
    /* (1) Check that there is a "dim" attribute. */

    if (dims == R_NilValue) {
    UNPROTECT(1);
    return x;
    }
    ndims = LENGTH(dims);

    /* (2) Check whether there are redundant extents */
    n = 0;
    for (i = 0; i < ndims; i++)
    if (INTEGER(dims)[i] != 1) n++;
    if (n == ndims) {
    UNPROTECT(1);
    return x;
    }

    if (n <= 1) {
    /* We have reduced to a vector result. */
    if (dimnames != R_NilValue) {
        n = length(dims);
        if (TYPEOF(dimnames) == VECSXP) {
        for (i = 0; i < n; i++) {
            if (INTEGER(dims)[i] != 1) {
            newnames = VECTOR_ELT(dimnames, i);
            break;
            }
        }
        }
        else {
        q = dimnames;
        for (i = 0; i < n; i++) {
            if (INTEGER(dims)[i] != 1) {
            newnames = CAR(q);
            break;
            }
            q = CDR(q);
        }
        }
    }
    PROTECT(newnames);
    setAttrib(x, R_DimNamesSymbol, R_NilValue);
    setAttrib(x, R_DimSymbol, R_NilValue);
    setAttrib(x, R_NamesSymbol, newnames);
    UNPROTECT(1);
    }
    else {
    /* We have a lower dimensional array. */
    SEXP newdims, dnn, newnamesnames = R_NilValue;
    dnn = getAttrib(dimnames, R_NamesSymbol);
    PROTECT(newdims = allocVector(INTSXP, n));
    for (i = 0, n = 0; i < ndims; i++)
        if (INTEGER(dims)[i] != 1)
        INTEGER(newdims)[n++] = INTEGER(dims)[i];
    if (!isNull(dimnames)) {
        int havenames = 0;
        for (i = 0; i < ndims; i++)
        if (INTEGER(dims)[i] != 1 &&
            VECTOR_ELT(dimnames, i) != R_NilValue)
            havenames = 1;
        if (havenames) {
        PROTECT(newnames = allocVector(VECSXP, n));
        PROTECT(newnamesnames = allocVector(STRSXP, n));
        for (i = 0, n = 0; i < ndims; i++) {
            if (INTEGER(dims)[i] != 1) {
            if(!isNull(dnn))
                SET_STRING_ELT(newnamesnames, n,
                       STRING_ELT(dnn, i));
            SET_VECTOR_ELT(newnames, n++, VECTOR_ELT(dimnames, i));
            }
        }
        }
        else dimnames = R_NilValue;
    }
    PROTECT(dimnames);
    setAttrib(x, R_DimNamesSymbol, R_NilValue);
    setAttrib(x, R_DimSymbol, newdims);
    if (dimnames != R_NilValue)
    {
        if(!isNull(dnn))
        setAttrib(newnames, R_NamesSymbol, newnamesnames);
        setAttrib(x, R_DimNamesSymbol, newnames);
        UNPROTECT(2);
    }
    UNPROTECT(2);
    }
    UNPROTECT(1);
    return x;
}

SEXP do_drop(SEXP call, SEXP op, SEXP args, SEXP rho)
{
    SEXP x, xdims;
    int i, n, shorten;

    checkArity(op, args);
    x = CAR(args);
    if ((xdims = getAttrib(x, R_DimSymbol)) != R_NilValue) {
    n = LENGTH(xdims);
    shorten = 0;
    for (i = 0; i < n; i++)
        if (INTEGER(xdims)[i] == 1) shorten = 1;
    if (shorten) {
        if (NAMED(x)) x = duplicate(x);
        x = DropDims(x);
    }
    }
    return x;
}

/* Length of Primitive Objects */

SEXP do_length(SEXP call, SEXP op, SEXP args, SEXP rho)
{
    SEXP ans;
    R_len_t len;

    if (length(args) != 1)
    error(_("incorrect number of args to 'length'"));

    if( isObject(CAR(args)) && DispatchOrEval(call, op, "length", args,
                          rho, &ans, 0, 1))
      return(ans);

    ans = allocVector(INTSXP, 1);
    len = length(CAR(args));
    INTEGER(ans)[0] = (len < INT_MAX) ? len : NA_INTEGER;
    return ans;
}


SEXP do_rowscols(SEXP call, SEXP op, SEXP args, SEXP rho)
{
    SEXP ans;
    int i, j, nr, nc;

    if (length(args) != 1)
    error(_("incorrect number of arguments to 'row/col'"));
    if (!isMatrix(CAR(args)))
    error(_("a matrix is required as argument to 'row/col'"));

    nr = nrows(CAR(args));
    nc = ncols(CAR(args));

    ans = allocMatrix(INTSXP, nr, nc);

    switch (PRIMVAL(op)) {
    case 1:
    for (i = 0; i < nr; i++)
        for (j = 0; j < nc; j++)
        INTEGER(ans)[i + j * nr] = i + 1;
    break;
    case 2:
    for (i = 0; i < nr; i++)
        for (j = 0; j < nc; j++)
        INTEGER(ans)[i + j * nr] = j + 1;
    break;
    }
    return ans;
}

static void matprod(double *x, int nrx, int ncx,
            double *y, int nry, int ncy, double *z)
{
    char *transa = "N", *transb = "N";
    int i,  j, k;
    double one = 1.0, zero = 0.0, sum;
    Rboolean have_na = FALSE;

    if (nrx > 0 && ncx > 0 && nry > 0 && ncy > 0) {
    /* Don't trust the BLAS to handle NA/NaNs correctly: PR#4582
     * The test is only O(n) here
     */
    for (i = 0; i < nrx*ncx; i++)
        if (ISNAN(x[i])) {have_na = TRUE; break;}
    if (!have_na)
        for (i = 0; i < nry*ncy; i++)
        if (ISNAN(y[i])) {have_na = TRUE; break;}
    if (have_na) {
        for (i = 0; i < nrx; i++)
        for (k = 0; k < ncy; k++) {
            sum = 0.0;
            for (j = 0; j < ncx; j++)
            sum += x[i + j * nrx] * y[j + k * nry];
            z[i + k * nrx] = sum;
        }
    } else
        F77_CALL(dgemm)(transa, transb, &nrx, &ncy, &ncx, &one,
                x, &nrx, y, &nry, &zero, z, &nrx);
    } else /* zero-extent operations should return zeroes */
    for(i = 0; i < nrx*ncy; i++) z[i] = 0;
}

#ifdef HAVE_FORTRAN_DOUBLE_COMPLEX
/* ZGEMM - perform one of the matrix-matrix operations    */
/* C := alpha*op( A )*op( B ) + beta*C */
extern void
F77_NAME(zgemm)(const char *transa, const char *transb, const int *m,
        const int *n, const int *k, const Rcomplex *alpha,
        const Rcomplex *a, const int *lda,
        const Rcomplex *b, const int *ldb,
        const Rcomplex *beta, Rcomplex *c, const int *ldc);
#endif

static void cmatprod(Rcomplex *x, int nrx, int ncx,
             Rcomplex *y, int nry, int ncy, Rcomplex *z)
{
#ifdef HAVE_FORTRAN_DOUBLE_COMPLEX
    char *transa = "N", *transb = "N";
    int i;
    Rcomplex one, zero;

    one.r = 1.0; one.i = zero.r = zero.i = 0.0;
    if (nrx > 0 && ncx > 0 && nry > 0 && ncy > 0) {
        F77_CALL(zgemm)(transa, transb, &nrx, &ncy, &ncx, &one,
            x, &nrx, y, &nry, &zero, z, &nrx);
    } else { /* zero-extent operations should return zeroes */
    for(i = 0; i < nrx*ncy; i++) z[i].r = z[i].i = 0;
    }
#else
    int i, j, k;
    double xij_r, xij_i, yjk_r, yjk_i, sum_i, sum_r;

    for (i = 0; i < nrx; i++)
    for (k = 0; k < ncy; k++) {
        z[i + k * nrx].r = NA_REAL;
        z[i + k * nrx].i = NA_REAL;
        sum_r = 0.0;
        sum_i = 0.0;
        for (j = 0; j < ncx; j++) {
        xij_r = x[i + j * nrx].r;
        xij_i = x[i + j * nrx].i;
        yjk_r = y[j + k * nry].r;
        yjk_i = y[j + k * nry].i;
        if (ISNAN(xij_r) || ISNAN(xij_i)
            || ISNAN(yjk_r) || ISNAN(yjk_i))
            goto next_ik;
        sum_r += (xij_r * yjk_r - xij_i * yjk_i);
        sum_i += (xij_r * yjk_i + xij_i * yjk_r);
        }
        z[i + k * nrx].r = sum_r;
        z[i + k * nrx].i = sum_i;
    next_ik:
        ;
    }
#endif
}

static void symcrossprod(double *x, int nr, int nc, double *z)
{
    char *trans = "T", *uplo = "U";
    double one = 1.0, zero = 0.0;
    int i, j;
    if (nr > 0 && nc > 0) {
        F77_CALL(dsyrk)(uplo, trans, &nc, &nr, &one, x, &nr, &zero, z, &nc);
    for (i = 1; i < nc; i++)
        for (j = 0; j < i; j++) z[i + nc *j] = z[j + nc * i];
    } else { /* zero-extent operations should return zeroes */
    for(i = 0; i < nc*nc; i++) z[i] = 0;
    }

}

static void crossprod(double *x, int nrx, int ncx,
              double *y, int nry, int ncy, double *z)
{
    char *transa = "T", *transb = "N";
    double one = 1.0, zero = 0.0;
    if (nrx > 0 && ncx > 0 && nry > 0 && ncy > 0) {
        F77_CALL(dgemm)(transa, transb, &ncx, &ncy, &nrx, &one,
            x, &nrx, y, &nry, &zero, z, &ncx);
    }
    else { /* zero-extent operations should return zeroes */
    int i;
    for(i = 0; i < ncx*ncy; i++) z[i] = 0;
    }
}

static void ccrossprod(Rcomplex *x, int nrx, int ncx,
               Rcomplex *y, int nry, int ncy, Rcomplex *z)
{
    char *transa = "T", *transb = "N";
    Rcomplex one, zero;

    one.r = 1.0; one.i = zero.r = zero.i = 0.0;
    if (nrx > 0 && ncx > 0 && nry > 0 && ncy > 0) {
        F77_CALL(zgemm)(transa, transb, &ncx, &ncy, &nrx, &one,
            x, &nrx, y, &nry, &zero, z, &ncx);
    }
    else { /* zero-extent operations should return zeroes */
    int i;
    for(i = 0; i < ncx*ncy; i++) z[i].r = z[i].i = 0;
    }
}
/* "%*%" (op = 0)  or  crossprod (op = 1) : */
SEXP do_matprod(SEXP call, SEXP op, SEXP args, SEXP rho)
{
    int ldx, ldy, nrx, ncx, nry, ncy, mode;
    SEXP x = CAR(args), y = CADR(args), xdims, ydims, ans;
    Rboolean sym;

    if(R_has_methods(op)) {
      SEXP value;
      value = R_possible_dispatch(call, op, args, rho);
      if(value) return value;
    }

    sym = isNull(y);
    if (sym && (PRIMVAL(op) == 1)) y = x;
    if ( !(isNumeric(x) || isComplex(x)) || !(isNumeric(y) || isComplex(y)) )
    errorcall(call, _("requires numeric matrix/vector arguments"));

    xdims = getAttrib(x, R_DimSymbol);
    ydims = getAttrib(y, R_DimSymbol);
    ldx = length(xdims);
    ldy = length(ydims);

    if (ldx != 2 && ldy != 2) {     /* x and y non-matrices */
    if (PRIMVAL(op) == 0) {
        nrx = 1;
        ncx = LENGTH(x);
    }
    else {
        nrx = LENGTH(x);
        ncx = 1;
    }
    nry = LENGTH(y);
    ncy = 1;
    }
    else if (ldx != 2) {        /* x not a matrix */
    nry = INTEGER(ydims)[0];
    ncy = INTEGER(ydims)[1];
    nrx = 0;
    ncx = 0;
    if (PRIMVAL(op) == 0) {
        if (LENGTH(x) == nry) { /* x as row vector */
        nrx = 1;
        ncx = LENGTH(x);
        }
        else if (nry == 1) {    /* x as col vector */
        nrx = LENGTH(x);
        ncx = 1;
        }
    }
    else { /* crossprod */
        if (LENGTH(x) == nry) { /* x is a row vector */
        nrx = LENGTH(x);
        ncx = 1;
        }
    }
    }
    else if (ldy != 2) {        /* y not a matrix */
    nrx = INTEGER(xdims)[0];
    ncx = INTEGER(xdims)[1];
    nry = 0;
    ncy = 0;
    if (PRIMVAL(op) == 0) {
        if (LENGTH(y) == ncx) { /* y as col vector */
        nry = LENGTH(y);
        ncy = 1;
        }
        else if (ncx == 1) {    /* y as row vector */
        nry = 1;
        ncy = LENGTH(y);
        }
    }
    else {
        if (LENGTH(y) == nrx) { /* y is a row vector */
        nry = LENGTH(y);
        ncy = 1;
        }
    }
    }
    else {              /* x and y matrices */
    nrx = INTEGER(xdims)[0];
    ncx = INTEGER(xdims)[1];
    nry = INTEGER(ydims)[0];
    ncy = INTEGER(ydims)[1];
    }
    /* nr[ow](.) and nc[ol](.) are now defined for x and y */

    if (PRIMVAL(op) == 0) {
    if (ncx != nry)
        errorcall(call, _("non-conformable arguments"));
    }
    else {
    if (nrx != nry)
        errorcall(call, _("non-conformable arguments"));
    }

    if (isComplex(CAR(args)) || isComplex(CADR(args)))
    mode = CPLXSXP;
    else
    mode = REALSXP;
    SETCAR(args, coerceVector(CAR(args), mode));
    SETCADR(args, coerceVector(CADR(args), mode));

    if (PRIMVAL(op) == 0) {         /* op == 0 : matprod() */

    PROTECT(ans = allocMatrix(mode, nrx, ncy));
    if (mode == CPLXSXP)
        cmatprod(COMPLEX(CAR(args)), nrx, ncx,
             COMPLEX(CADR(args)), nry, ncy, COMPLEX(ans));
    else
        matprod(REAL(CAR(args)), nrx, ncx,
            REAL(CADR(args)), nry, ncy, REAL(ans));

    PROTECT(xdims = getAttrib(CAR(args), R_DimNamesSymbol));
    PROTECT(ydims = getAttrib(CADR(args), R_DimNamesSymbol));

    if (xdims != R_NilValue || ydims != R_NilValue) {
        SEXP dimnames, dimnamesnames, dnx=R_NilValue, dny=R_NilValue;

        /* allocate dimnames and dimnamesnames */

        PROTECT(dimnames = allocVector(VECSXP, 2));
        PROTECT(dimnamesnames = allocVector(STRSXP, 2));
        if (xdims != R_NilValue) {
        if (ldx == 2 || ncx == 1) {
            SET_VECTOR_ELT(dimnames, 0, VECTOR_ELT(xdims, 0));
            dnx = getAttrib(xdims, R_NamesSymbol);
            if(!isNull(dnx))
            SET_STRING_ELT(dimnamesnames, 0, STRING_ELT(dnx, 0));
        }
        }

#define YDIMS_ET_CETERA                         \
        if (ydims != R_NilValue) {                  \
        if (ldy == 2) {                     \
            SET_VECTOR_ELT(dimnames, 1, VECTOR_ELT(ydims, 1));  \
            dny = getAttrib(ydims, R_NamesSymbol);      \
            if(!isNull(dny))                    \
            SET_STRING_ELT(dimnamesnames, 1, STRING_ELT(dny, 1)); \
        } else if (nry == 1) {                  \
            SET_VECTOR_ELT(dimnames, 1, VECTOR_ELT(ydims, 0));  \
            dny = getAttrib(ydims, R_NamesSymbol);      \
            if(!isNull(dny))                    \
            SET_STRING_ELT(dimnamesnames, 1, STRING_ELT(dny, 0)); \
        }                           \
        }                               \
                                    \
        /* We sometimes attach a dimnames attribute         \
         * whose elements are all NULL ...              \
         * This is ugly but causes no real damage.          \
         * Now (2.1.0 ff), we don't anymore: */         \
        if (VECTOR_ELT(dimnames,0) != R_NilValue ||         \
        VECTOR_ELT(dimnames,1) != R_NilValue) {         \
        if (dnx != R_NilValue || dny != R_NilValue)     \
            setAttrib(dimnames, R_NamesSymbol, dimnamesnames);  \
        setAttrib(ans, R_DimNamesSymbol, dimnames);     \
        }                               \
        UNPROTECT(2)

        YDIMS_ET_CETERA;
    }
    }

    else {                  /* op == 1: crossprod() */

    PROTECT(ans = allocMatrix(mode, ncx, ncy));
    if (mode == CPLXSXP)
        if(sym)
        ccrossprod(COMPLEX(CAR(args)), nrx, ncx,
               COMPLEX(CAR(args)), nry, ncy, COMPLEX(ans));
        else
        ccrossprod(COMPLEX(CAR(args)), nrx, ncx,
               COMPLEX(CADR(args)), nry, ncy, COMPLEX(ans));
    else {
        if(sym)
        symcrossprod(REAL(CAR(args)), nrx, ncx, REAL(ans));
        else
        crossprod(REAL(CAR(args)), nrx, ncx,
              REAL(CADR(args)), nry, ncy, REAL(ans));
    }

    PROTECT(xdims = getAttrib(CAR(args), R_DimNamesSymbol));
    if (sym)
        PROTECT(ydims = xdims);
    else
        PROTECT(ydims = getAttrib(CADR(args), R_DimNamesSymbol));

    if (xdims != R_NilValue || ydims != R_NilValue) {
        SEXP dimnames, dimnamesnames, dnx=R_NilValue, dny=R_NilValue;

        /* allocate dimnames and dimnamesnames */

        PROTECT(dimnames = allocVector(VECSXP, 2));
        PROTECT(dimnamesnames = allocVector(STRSXP, 2));

        if (xdims != R_NilValue) {
        if (ldx == 2) {/* not nrx==1 : .. fixed, ihaka 2003-09-30 */
            SET_VECTOR_ELT(dimnames, 0, VECTOR_ELT(xdims, 1));
            dnx = getAttrib(xdims, R_NamesSymbol);
            if(!isNull(dnx))
            SET_STRING_ELT(dimnamesnames, 0, STRING_ELT(dnx, 1));
        }
        }

        YDIMS_ET_CETERA;
    }
    }
    UNPROTECT(3);
    return ans;
}
#undef YDIMS_ET_CETERA

SEXP do_transpose(SEXP call, SEXP op, SEXP args, SEXP rho)
{
    SEXP a, r, dims, dimnames, dimnamesnames=R_NilValue,
    ndimnamesnames, rnames, cnames;
    int i, ldim, len = 0, ncol=0, nrow=0;

    checkArity(op, args);
    a = CAR(args);

    if (isVector(a)) {
    dims = getAttrib(a, R_DimSymbol);
    ldim = length(dims);
    rnames = R_NilValue;
    cnames = R_NilValue;
    switch(ldim) {
    case 0:
        nrow = len = length(a);
        ncol = 1;
        rnames = getAttrib(a, R_NamesSymbol);
        break;
    case 1:
        nrow = len = length(a);
        ncol = 1;
        dimnames = getAttrib(a, R_DimNamesSymbol);
        if (dimnames != R_NilValue) {
        rnames = VECTOR_ELT(dimnames, 0);
        dimnamesnames = getAttrib(dimnames, R_NamesSymbol);
        }
        break;
    case 2:
        ncol = ncols(a);
        nrow = nrows(a);
        len = length(a);
        dimnames = getAttrib(a, R_DimNamesSymbol);
        if (dimnames != R_NilValue) {
        rnames = VECTOR_ELT(dimnames, 0);
        cnames = VECTOR_ELT(dimnames, 1);
        dimnamesnames = getAttrib(dimnames, R_NamesSymbol);
        }
        break;
    default:
        goto not_matrix;
    }
    }
    else
    goto not_matrix;
    PROTECT(r = allocVector(TYPEOF(a), len));
    switch (TYPEOF(a)) {
    case LGLSXP:
    case INTSXP:
    for (i = 0; i < len; i++)
        INTEGER(r)[i] = INTEGER(a)[(i / ncol) + (i % ncol) * nrow];
    break;
    case REALSXP:
    for (i = 0; i < len; i++)
        REAL(r)[i] = REAL(a)[(i / ncol) + (i % ncol) * nrow];
    break;
    case CPLXSXP:
    for (i = 0; i < len; i++)
        COMPLEX(r)[i] = COMPLEX(a)[(i / ncol) + (i % ncol) * nrow];
    break;
    case STRSXP:
    for (i = 0; i < len; i++)
        SET_STRING_ELT(r, i,
               STRING_ELT(a, (i / ncol) + (i % ncol) * nrow));
    break;
    case VECSXP:
    for (i = 0; i < len; i++)
        SET_VECTOR_ELT(r, i,
               VECTOR_ELT(a, (i / ncol) + (i % ncol) * nrow));
    break;
    case RAWSXP:
    for (i = 0; i < len; i++)
        RAW(r)[i] = RAW(a)[(i / ncol) + (i % ncol) * nrow];
    break;
    default:
    goto not_matrix;
    }
    PROTECT(dims = allocVector(INTSXP, 2));
    INTEGER(dims)[0] = ncol;
    INTEGER(dims)[1] = nrow;
    setAttrib(r, R_DimSymbol, dims);
    UNPROTECT(1);
    if(rnames != R_NilValue || cnames != R_NilValue) {
    PROTECT(dimnames = allocVector(VECSXP, 2));
    SET_VECTOR_ELT(dimnames, 0, cnames);
    SET_VECTOR_ELT(dimnames, 1, rnames);
    if(!isNull(dimnamesnames)) {
        PROTECT(ndimnamesnames = allocVector(VECSXP, 2));
        SET_STRING_ELT(ndimnamesnames, 1, STRING_ELT(dimnamesnames, 0));
        SET_STRING_ELT(ndimnamesnames, 0,
               (ldim == 2) ? STRING_ELT(dimnamesnames, 1):
               R_BlankString);
        setAttrib(dimnames, R_NamesSymbol, ndimnamesnames);
        UNPROTECT(1);
    }
    setAttrib(r, R_DimNamesSymbol, dimnames);
    UNPROTECT(1);
    }
    copyMostAttrib(a, r);
    UNPROTECT(1);
    return r;
 not_matrix:
    errorcall(call, _("argument is not a matrix"));
    return call;/* never used; just for -Wall */
}

/*
 New version of aperm, using strides for speed.
 Jonathan Rougier <J.C.Rougier@durham.ac.uk>

 v1.0 30.01.01

 M.Maechler : expanded  all ../include/Rdefines.h macros
 */

/* this increments iip and sets j using strides */

#define CLICKJ                      \
    for (itmp=0; itmp<n; itmp++)            \
    if (iip[itmp] == INTEGER(dimsr)[itmp]-1)    \
        iip[itmp] = 0;              \
    else {                      \
        iip[itmp]++;                \
        break;                  \
    }                       \
    for (j=0, itmp=0; itmp<n; itmp++)           \
    j += iip[itmp] * stride[itmp];

/* aperm (a, perm, resize = TRUE) */
SEXP do_aperm(SEXP call, SEXP op, SEXP args, SEXP rho)
{
    SEXP a, perm, resize, r, dimsa, dimsr, dna;
    int i, j, n, len, itmp;
    int *pp, *iip, *stride;
    char *vmax;

    checkArity(op, args);

    a = CAR(args);
    if (!isArray(a))
    errorcall(call, _("invalid first argument, must be an array"));

    PROTECT(dimsa = getAttrib(a, R_DimSymbol));
    n = LENGTH(dimsa);

    /* check the permutation */

    PROTECT(perm = coerceVector(CADR(args), INTSXP));
    vmax = vmaxget();
    pp = (int *) R_alloc(n, sizeof(int));
    if (length(perm) == 0) {
    for (i=0; i<n; i++)
        pp[i] = n-1-i;
    } else if (length(perm) == n) {
    for (i=0; i<n; i++)
        pp[i] = INTEGER(perm)[i] - 1; /* no offset! */
    } else
    errorcall(call, _("'perm' is of wrong length"));

    iip = (int *) R_alloc(n, sizeof(int));
    for (i=0; i<n; iip[i++] = 0);
    for (i=0; i<n; i++)
    if (pp[i] >= 0 && pp[i] < n)
        iip[pp[i]]++;
    else
        errorcall(call, _("value out of range in 'perm'"));
    for (i=0; i<n; i++)
    if (iip[i]==0)
        errorcall(call, _("invalid permutation ('perm')"));

    /* create the stride object and permute */

    stride = (int *) R_alloc(n, sizeof(int));

    for (iip[0] = 1, i = 1; i<n; i++)
    iip[i] = iip[i-1] * INTEGER(dimsa)[i-1];

    for (i=0; i<n; i++)
    stride[i] = iip[pp[i]];

    /* also need to have the dimensions of r */

    PROTECT(dimsr = allocVector(INTSXP,n));
    for (i=0; i<n; i++)
    INTEGER(dimsr)[i] = INTEGER(dimsa)[pp[i]];

    /* and away we go! iip will hold the incrementer */

    len = LENGTH(a);
    len = length(a);
    PROTECT(r = allocVector(TYPEOF(a), len));

    for (i=0; i<n; iip[i++] = 0);

    switch (TYPEOF(a)) {

    case INTSXP:
    case LGLSXP:
    for (j=0, i=0; i<len; i++) {
        INTEGER(r)[i] = INTEGER(a)[j];
        CLICKJ;
    }
    break;

    case REALSXP:
    for (j=0, i=0; i<len; i++) {
        REAL(r)[i] = REAL(a)[j];
        CLICKJ;
    }
    break;

    case CPLXSXP:
    for (j=0, i=0; i<len; i++) {
        COMPLEX(r)[i].r = COMPLEX(a)[j].r;
        COMPLEX(r)[i].i = COMPLEX(a)[j].i;
        CLICKJ;
    }
    break;

    case STRSXP:
    for (j=0, i=0; i<len; i++) {
        SET_STRING_ELT(r, i, STRING_ELT(a, j));
        CLICKJ;
    }
    break;

    case VECSXP:
    for (j=0, i=0; i<len; i++) {
        SET_VECTOR_ELT(r, i, VECTOR_ELT(a, j));
        CLICKJ;
    }
    break;

    case RAWSXP:
    for (j=0, i=0; i<len; i++) {
        RAW(r)[i] = RAW(a)[j];
        CLICKJ;
    }
    break;

    default:
    UNIMPLEMENTED_TYPE("aperm", a);
    }

    /* handle the resize */
    PROTECT(resize = coerceVector(CADDR(args), INTSXP));
    if (LOGICAL(resize)[0])
    setAttrib(r, R_DimSymbol, dimsr);
    else
    setAttrib(r, R_DimSymbol, dimsa);

    /* and handle the dimnames */

    PROTECT(dna = getAttrib(a, R_DimNamesSymbol));

    if (LOGICAL(resize)[0] && dna != R_NilValue) {

    SEXP dnna, dnr, dnnr;

    PROTECT(dnna = getAttrib(dna, R_NamesSymbol));
    PROTECT(dnnr = allocVector(STRSXP,n));
    PROTECT(dnr  = allocVector(VECSXP,n));

    for (i=0; i<n; i++) {
        SET_VECTOR_ELT(dnr, i, VECTOR_ELT(dna, pp[i]));
        if (dnna != R_NilValue)
        SET_STRING_ELT(dnnr, i, STRING_ELT(dnna, pp[i]));
    }

    if (dnna != R_NilValue)
        setAttrib(dnr, R_NamesSymbol, dnnr);
    setAttrib(r, R_DimNamesSymbol, dnr);
    UNPROTECT(3); /* dnna, dnr, dnnr */
    }
    /* free temporary memory */
    vmaxset(vmax);

    UNPROTECT(6); /* dimsa, perm, r, dimsr, resize, dna */
    return r;
}

/* colSums(x, n, p, na.rm) and friends */
SEXP do_colsum(SEXP call, SEXP op, SEXP args, SEXP rho)
{
    SEXP x, ans = R_NilValue;
    int OP, n, p, cnt = 0, i, j, type;
    Rboolean NaRm, keepNA;
    int *ix;
    double *rx, sum = 0.0;

    checkArity(op, args);
    x = CAR(args); args = CDR(args);
    n = asInteger(CAR(args)); args = CDR(args);
    p = asInteger(CAR(args)); args = CDR(args);
    NaRm = asLogical(CAR(args));
    if (n == NA_INTEGER || n < 0)
    errorcall(call, _("invalid value of 'n'"));
    if (p == NA_INTEGER || p < 0)
    errorcall(call, _("invalid value of 'p'"));
    if (NaRm == NA_LOGICAL) errorcall(call, _("invalid value of 'na.rm'"));
    keepNA = !NaRm;

    OP = PRIMVAL(op);
    switch (type = TYPEOF(x)) {
    case LGLSXP: break;
    case INTSXP: break;
    case REALSXP: break;
    default:
    errorcall(call, _("'x' must be numeric"));
    }

    if (OP == 0 || OP == 1) { /* columns */
    cnt = n;
    PROTECT(ans = allocVector(REALSXP, p));
    for (j = 0; j < p; j++) {
        switch (type) {
        case REALSXP:
        rx = REAL(x) + n*j;
        if (keepNA)
            for (sum = 0., i = 0; i < n; i++) sum += *rx++;
        else {
            for (cnt = 0, sum = 0., i = 0; i < n; i++, rx++)
            if (!ISNAN(*rx)) {cnt++; sum += *rx;}
            else if (keepNA) {sum = NA_REAL; break;}
        }
        break;
        case INTSXP:
        ix = INTEGER(x) + n*j;
        for (cnt = 0, sum = 0., i = 0; i < n; i++, ix++)
            if (*ix != NA_INTEGER) {cnt++; sum += *ix;}
            else if (keepNA) {sum = NA_REAL; break;}
        break;
        case LGLSXP:
        ix = LOGICAL(x) + n*j;
        for (cnt = 0, sum = 0., i = 0; i < n; i++, ix++)
            if (*ix != NA_LOGICAL) {cnt++; sum += *ix;}
            else if (keepNA) {sum = NA_REAL; break;}
        break;
        default:
        /* we checked the type above, but be sure */
        UNIMPLEMENTED_TYPEt("do_colsum", type);
        }
        if (OP == 1) {
        if (cnt > 0) sum /= cnt; else sum = NA_REAL;
        }
        REAL(ans)[j] = sum;
    }
    }

    if (OP == 2 || OP == 3) { /* rows */
    cnt = p;
    PROTECT(ans = allocVector(REALSXP, n));

    /* reverse summation order to improve cache hits */
    if (type == REALSXP) {
        double *rans = REAL(ans), *ra = rans;
        int *Cnt = NULL, *c;
        rx = REAL(x);
        if (!keepNA && OP == 3) Cnt = Calloc(n, int);
        memset(rans, 0, n*sizeof(double));
        for (j = 0; j < p; j++) {
        ra = rans;
        if (keepNA)
            for (i = 0; i < n; i++) *ra++ += *rx++;
        else
            for (c = Cnt, i = 0; i < n; i++, ra++, rx++, c++)
            if (!ISNAN(*rx)) {
                *ra += *rx;
                if (OP == 3) (*c)++;
            }
        }
        if (OP == 3) {
        if (keepNA)
            for (ra = rans, i = 0; i < n; i++) *ra++ /= p;
        else {
            for (ra = rans, c = Cnt, i = 0; i < n; i++, c++)
            if (*c > 0) *ra++ /= *c; else *ra++ = NA_REAL;
            Free(Cnt);
        }
        }
        UNPROTECT(1);
        return ans;
    }

    for (i = 0; i < n; i++) {
        switch (type) {
        case REALSXP: /* this cannot be reached */
        rx = REAL(x) + i;
        if (keepNA)
            for (sum = 0., j = 0; j < p; j++, rx += n) sum += *rx;
        else {
            for (cnt = 0, sum = 0., j = 0; j < p; j++, rx += n)
            if (!ISNAN(*rx)) {cnt++; sum += *rx;}
            else if (keepNA) {sum = NA_REAL; break;}
        }
        break;
        case INTSXP:
        ix = INTEGER(x) + i;
        for (cnt = 0, sum = 0., j = 0; j < p; j++, ix += n)
            if (*ix != NA_INTEGER) {cnt++; sum += *ix;}
            else if (keepNA) {sum = NA_REAL; break;}
        break;
        case LGLSXP:
        ix = LOGICAL(x) + i;
        for (cnt = 0, sum = 0., j = 0; j < p; j++, ix += n)
            if (*ix != NA_LOGICAL) {cnt++; sum += *ix;}
            else if (keepNA) {sum = NA_REAL; break;}
        break;
        default:
        /* we checked the type above, but be sure */
        UNIMPLEMENTED_TYPEt("do_colsum", type);
        }
        if (OP == 3) {
        if (cnt > 0) sum /= cnt; else sum = NA_REAL;
        }
        REAL(ans)[i] = sum;
    }
    }

    UNPROTECT(1);
    return ans;
}