/* nag_reml_hier_mixed_regsn (g02jdc) Example Program.
 *
 * Copyright 2008, Numerical Algorithms Group.
 *
 * Mark 9, 2009.
 */
/* Pre-processor includes */
#include <stdio.h>
#include <math.h>
#include <nag.h>
#include <nagx04.h>
#include <nag_stdlib.h>
#include <nagg02.h>

void print_results(Nag_OrderType order, Integer n, Integer nff, Integer nlsv,
                   Integer nrf, Integer fixed[], Integer nrndm,
                   Integer rndm[], Integer lrndm, Integer nvpr,
                   Integer vpr[], double gamma[], Integer effn,
                   Integer rnkx, Integer ncov, double like,
                   Integer id[], Integer pdid, double b[], double se[],
                   FILE *fpout);

#define RNDM(I, J) rndm[(order == Nag_ColMajor) \
                        ?((J-1)*lrndm+I-1):((I-1)*nrndm+J-1)]
#define DAT(I, J)  dat[(order == Nag_ColMajor) \
                       ?((J-1)*pddat+I-1):((I-1)*pddat+J-1)]
#define ID(I, J)   id[((J-1)*pdid+I-1)]

int main(int argc, char *argv[])
{
  /* IO file pointers */
  FILE          *fpin, *fpout;

  /* Integer scalar and array declarations */
  Integer       exit_status = 0;
  Integer       pdid, licomm, lrcomm, tdczz, lb, pdcxx, pdcxz, pdczz, pddat,
                effn, i, j, lvpr, n, ncol, ncov, lfixed, nff, nl, nlsv, nrndm,
                nrf, nv, nvpr, rnkx, lwt, size_dat, lrndm;
  Integer       *fixed = 0, *icomm = 0, *id = 0, *levels = 0, *rndm = 0;
  Integer       *vpr = 0;
  Integer       ticomm[2];

  /* NAG structures */
  NagError      fail;
  Nag_OrderType order = Nag_RowMajor;

  /* Double scalar and array declarations */
  double        like;
  double        *b = 0, *cxx = 0, *cxz = 0, *czz = 0, *dat = 0, *gamma = 0;
  double        *rcomm = 0, *se = 0, *wt = 0, *y = 0;
  double        trcomm[1];

  /* Character scalars */
  char          weight;

  /* Use the default options */
  Integer       *iopt = 0;
  Integer       liopt = 0;
  double        *ropt = 0;
  Integer       lropt = 0;

  /* Initialise the error structure */
  INIT_FAIL(fail);

  /* Check for command-line IO options */
  fpin = nag_example_file_io(argc, argv, "-data", NULL);
  fpout = nag_example_file_io(argc, argv, "-results", NULL);

  fprintf(fpout,
          "nag_reml_hier_mixed_regsn (g02jdc) Example Program Results\n\n");

  /* Skip headings in data file*/
  fscanf(fpin, "%*[^\n] ");

  /* Read in the initial arguments */
  fscanf(fpin, "%c%ld%ld%ld%ld%*[^\n] ",
         &weight, &n, &ncol, &nrndm, &nvpr);

  /* Maximum size for fixed and rndm */
  lfixed = ncol + 2;
  lrndm = 2 * ncol + 3;

  if (order == Nag_ColMajor)
    {
      pddat = n;
      size_dat = pddat * ncol;
    }
  else
    {
      pddat = ncol;
      size_dat = pddat * n;
    }

  /* Allocate some memory */
  if (!(y = NAG_ALLOC(n, double)) ||
      !(vpr = NAG_ALLOC(nvpr, Integer)) ||
      !(levels = NAG_ALLOC(ncol, Integer)) ||
      !(gamma = NAG_ALLOC(nvpr+1, double)) ||
      !(fixed = NAG_ALLOC(lfixed, Integer)) ||
      !(rndm = NAG_ALLOC(lrndm * nrndm, Integer)) ||
      !(dat = NAG_ALLOC(size_dat, double)))
    {
      fprintf(fpout, "Allocation failure\n");
      exit_status = -1;
      goto END;
    }

  /* Check whether we are supplying weights and
     allocate memory if required */
  if (weight == 'W')
    {
      lwt = n;
      if (!(wt = NAG_ALLOC(lwt, double)))
        {
          fprintf(fpout, "Allocation failure\n");
          exit_status = -1;
          goto END;
        }
    }
  else
    {
      lwt = 0;
    }

  /* Read in the number of levels associated with each of the
     independent variables */
  for (i = 0; i < ncol; i++)
    fscanf(fpin, "%ld", &levels[i]);
  fscanf(fpin, "%*[^\n] ");

  /* Read in the fixed part of the model */
  /* Skip the heading */
  fscanf(fpin, "%*[^\n] ");
  /* Number of variables */
  fscanf(fpin, "%ld%*[^\n] ", &fixed[0]);
  nv = fixed[0];
  if (nv+2 > lfixed)
    {
      fprintf(fpout, " ** Problem size too large, increase array sizes\n");
      fprintf(fpout, "LFIXED,NV+2 = %ld, %ld\n", lfixed, nv+2);
      exit_status = -1;
      goto END;
    }
  /* Intercept */
  fscanf(fpin, "%ld%*[^\n] ", &fixed[1]);
  /* Variable IDs */
  if (nv > 0)
    {
      for (i = 2; i < nv + 2; i++)
        fscanf(fpin, "%ld", &fixed[i]);
      fscanf(fpin, "%*[^\n] ");
    }

  /* Read in the random part of the model */
  lvpr = 0;
  pdid = 0;
  for (j = 1; j <= nrndm; j++)
    {
      fscanf(fpin, "%*[^\n] ");
      /* Number of variables */
      fscanf(fpin, "%ld%*[^\n] ", &RNDM(1, j));
      nv = RNDM(1, j);
      if ((nv+3) > lrndm)
        {
          fprintf(fpout, " ** Problem size too large, increase array sizes\n");
          fprintf(fpout, "LRNDM,NV+2 = %ld, %ld\n", lrndm, nv+2);
          exit_status = -1;
          goto END;
        }
      /* Intercept */
      fscanf(fpin, "%ld%*[^\n] ", &RNDM(2, j));
      /* Variable IDs */
      if (nv > 0)
        {
          for (i = 3; i <= nv + 2; i++)
            fscanf(fpin, "%ld", &RNDM(i, j));
          fscanf(fpin, "%*[^\n] ");
        }
      /* Number of subject variables */
      fscanf(fpin, "%ld%*[^\n] ", &RNDM(nv+3, j));
      nl = RNDM(nv+3, j);
      if (nv+nl+2 > lrndm)
        {
          fprintf(fpout, " ** Problem size too large, increase array sizes\n");
          fprintf(fpout, "LRNDM,NV+NL++2 = %ld, %ld\n",
                  lrndm, nv+nl+2);
          exit_status = -1;
          goto END;
        }
      /* Subject variable IDs */
      if (nl > 0)
        {
          for (i = nv+4; i <= nv + nl + 3; i++)
            fscanf(fpin, "%ld", &RNDM(i, j));
          fscanf(fpin, "%*[^\n] ");
        }
      pdid = MAX(pdid, nl);
      lvpr += RNDM(2, j) + nv;
    }
  pdid += 3;

  /* Read in the dependent and independent data */
  for (i = 1; i <= n; i++)
    {
      fscanf(fpin, "%lf", &y[i - 1]);
      for (j = 1; j <= ncol; j++)
        fscanf(fpin, "%lf", &DAT(i, j));
      if (lwt > 0)
        fscanf(fpin, "%lf", &wt[i - 1]);
      fscanf(fpin, "%*[^\n] ");
    }

  /* Read in VPR */
  for (i = 0; i < lvpr; i++)
    fscanf(fpin, "%ld", &vpr[i]);
  fscanf(fpin, "%*[^\n] ");

  /* Read in GAMMA */
  for (i = 0; i < nvpr; i++)
    fscanf(fpin, "%lf", &gamma[i]);
  fscanf(fpin, "%*[^\n] ");

  /* Get the size of the communication arrays */
  licomm = 2;
  lrcomm = 1;
  nag_hier_mixed_init(order, n, ncol, dat, pddat, levels, y, wt, fixed, lfixed,
                      nrndm, rndm, lrndm, &nff, &nlsv, &nrf, trcomm, lrcomm,
                      ticomm, licomm, &fail);
  if (fail.code != NE_NOERROR)
    {
      fprintf(fpout, "Error from nag_hier_mixed_init (g02jcc).\n%s\n",
              fail.message);
      exit_status = 1;
      goto END;
    }
  licomm = ticomm[0];
  lrcomm = ticomm[1];

  /* Allocate the communication arrays */
  if (!(icomm = NAG_ALLOC(licomm, Integer)) ||
      !(rcomm = NAG_ALLOC(lrcomm, double)))
    {
      fprintf(fpout, "Allocation failure 4\n");
      exit_status = -1;
      goto END;
    }

  /* Pre-process the data */
  nag_hier_mixed_init(order, n, ncol, dat, pddat, levels, y, wt, fixed, lfixed,
                      nrndm, rndm, lrndm, &nff, &nlsv, &nrf, rcomm, lrcomm,
                      icomm, licomm, &fail);
  if (fail.code != NE_NOERROR)
    {
      fprintf(fpout, "Error from nag_hier_mixed_init (g02jcc).\n%s\n",
              fail.message);
      exit_status = 1;
      goto END;
    }

  /* Allocate the output arrays */
  lb = nff + nrf*nlsv;
  tdczz = nrf*nlsv;
  pdcxx = nff;
  pdcxz = nff;
  pdczz = nrf;
  if (!(b = NAG_ALLOC(lb, double)) ||
      !(cxx = NAG_ALLOC(pdcxx*nff, double)) ||
      !(cxz = NAG_ALLOC(pdcxz*tdczz, double)) ||
      !(czz = NAG_ALLOC(pdczz*tdczz, double)) ||
      !(se = NAG_ALLOC(lb, double)) ||
      !(id = NAG_ALLOC(pdid*lb, Integer)))
    {
      fprintf(fpout, "Allocation failure 5\n");
      exit_status = -1;
      goto END;
    }

  /*  Perform the analysis */
  nag_reml_hier_mixed_regsn(lvpr, vpr, nvpr, gamma, &effn, &rnkx, &ncov, &like,
                            lb, id, pdid, b, se, czz, pdczz, cxx, pdcxx, cxz,
                            pdcxz, rcomm, icomm, iopt, liopt, ropt, lropt,
                            &fail);
  if (fail.code != NE_NOERROR)
    {
      fprintf(fpout, "Error from nag_reml_hier_mixed_regsn (g02jdc).\n%s\n",
              fail.message);
      exit_status = 1;
      if (fail.code != NW_NOT_CONVERGED && fail.code != NW_TOO_MANY_ITER &&
          fail.code != NW_KT_CONDITIONS && fail.code != NE_NEG_ELEMENT)
        goto END;
    }

  /* Display the output */
  print_results(order, n, nff, nlsv, nrf, fixed, nrndm, rndm, lrndm, nvpr, vpr,
                gamma, effn, rnkx, ncov, like, id, pdid, b, se, fpout);

 END:
  if (fpin != stdin && fpin != 0) fclose(fpin);
  if (fpout != stdout && fpout != 0) fclose(fpout);

  if (wt) NAG_FREE(wt);
  if (y) NAG_FREE(y);
  if (vpr) NAG_FREE(vpr);
  if (levels) NAG_FREE(levels);
  if (gamma) NAG_FREE(gamma);
  if (fixed) NAG_FREE(fixed);
  if (rndm) NAG_FREE(rndm);
  if (dat) NAG_FREE(dat);
  if (icomm) NAG_FREE(icomm);
  if (rcomm) NAG_FREE(rcomm);
  if (b) NAG_FREE(b);
  if (cxx) NAG_FREE(cxx);
  if (cxz) NAG_FREE(cxz);
  if (czz) NAG_FREE(czz);
  if (se) NAG_FREE(se);
  if (id) NAG_FREE(id);

  return exit_status;
}

void print_results(Nag_OrderType order, Integer n, Integer nff, Integer nlsv,
                   Integer nrf, Integer fixed[], Integer nrndm,
                   Integer rndm[], Integer lrndm, Integer nvpr,
                   Integer vpr[], double gamma[], Integer effn,
                   Integer rnkx, Integer ncov, double like,
                   Integer id[], Integer pdid, double b[], double se[],
                   FILE *fpout)
{
  Integer aid, i, k, l, ns, nv, p, pb, tb, tdid, vid, same;

  /* Display the output */
  fprintf(fpout, " Number of observations (N)                    =  %ld\n",
          n);
  fprintf(fpout, " Number of random factors (NRF)                =  %ld\n",
          nrf);
  fprintf(fpout, " Number of fixed factors (NFF)                 =  %ld\n",
          nff);
  fprintf(fpout, " Number of subject levels (NLSV)               =  %ld\n",
          nlsv);
  fprintf(fpout, " Rank of X (RNKX)                              =  %ld\n",
          rnkx);
  fprintf(fpout, " Effective N (EFFN)                            =  %ld\n",
          effn);
  fprintf(fpout, " Number of non-zero variance components (NCOV) =  %ld\n",
          ncov);

  fprintf(fpout, " Parameter Estimates\n");
  tdid = nff + nrf*nlsv;

  if (nrf > 0)
    {
      fprintf(fpout, "\n");
      fprintf(fpout, " Random Effects\n");
    }

  pb = -999;
  for (k = 1; k <= nrf*nlsv; k++)
    {
      tb = ID(1, k);
      if (tb != -999)
        {
          vid = ID(2, k);
          nv = RNDM(1, tb);
          ns = RNDM(3+nv, tb);

          if (pb != tb)
            {
              same = 0;
            }
          else
            {
              same = 1;
              for (l = 1; l <= ns; l++)
                {
                  if (ID(3+l, k) != ID(3+l, k-1))
                    {
                      same = 0;
                      break;
                    }
                }
            }

          if (!same)
            {
              if (k != 1) fprintf(fpout, "\n");
              fprintf(fpout, "  Subject: ");
              for (l = 1; l <= ns; l++)
                fprintf(fpout, " Variable %2ld (Level %1ld) ",
                        RNDM(3+nv+l, tb), ID(3+l, k));
              fprintf(fpout, "\n");
            }
          pb = tb;

          if (vid == 0)
            {
              /* Intercept */
              fprintf(fpout, "    Intercept                 %10.4f %10.4f\n",
                      b[k], se[k]);
            }
          else
            {
              /* VID'th variable specified in RNDM */
              aid = RNDM(2+vid, tb);
              if (ID(3, k) == 0)
                {
                  fprintf(fpout, "     Variable %2ld", aid);
                  fprintf(fpout, "               %10.4f %10.4f\n", b[k-1],
                          se[k-1]);
                }
              else
                {
                  fprintf(fpout, "     Variable %2ld", aid);
                  fprintf(fpout, " (Level %1ld)     %10.4f %10.4f\n",
                          ID(3, k), b[k-1], se[k-1]);
                }
            }
        }
    }

  if (nff > 0)
    {
      fprintf(fpout, "\n");
      fprintf(fpout, " Fixed Effects\n");
    }
  for (k = nrf*nlsv + 1; k <= tdid; k++)
    {
      vid = ID(2, k);
      if (vid != -999)
        {
          if (vid == 0)
            {
              /* Intercept */
              fprintf(fpout, "   Intercept                   %10.4f %10.4f\n",
                      b[k - 1], se[k - 1]);
            }
          else
            {
              /* VID'th variable specified in FIXED */
              aid = fixed[2+vid-1];
              if (ID(3, k) == 0)
                {
                  fprintf(fpout, "   Variable %2ld", aid);
                  fprintf(fpout, "                 %10.4f %10.4f\n", b[k - 1],
                          se[k - 1]);
                }
              else
                {
                  fprintf(fpout, "   Variable %2ld", aid);
                  fprintf(fpout, " (Level %1ld)       %10.4f %10.4f\n",
                          ID(3, k), b[k - 1], se[k - 1]);
                }
            }
        }
    }

  fprintf(fpout, "\n");
  fprintf(fpout, " Variance Components\n");
  fprintf(fpout, "  Estimate      Parameter        Subject\n");
  for (k = 1; k <= nvpr; k++)
    {
      fprintf(fpout, "%10.5f     ", gamma[k - 1]);
      p = 0;
      for (tb = 1; tb <= nrndm; tb++)
        {
          nv = RNDM(1, tb);
          ns = RNDM(3+nv, tb);
          for (i = 1; i <= nv + RNDM(2, tb); i++)
            {
              p++;
              if (vpr[p-1] == k)
                {
                  fprintf(fpout, "Variable %2ld     Variables ",
                          RNDM(2 + i, tb));
                  for (l = 1; l <= ns; l++)
                    fprintf(fpout, "%2ld ", RNDM(3 + nv + l, tb));
                }
            }
        }
      fprintf(fpout, "\n");
    }
  fprintf(fpout, "\n");
  fprintf(fpout, "SIGMA**2         = %15.5f\n", gamma[nvpr]);
  fprintf(fpout, "-2LOG LIKELIHOOD = %15.5f\n", like);
}