Rcgminb <- function(par, fn, gr, lower, upper, bdmsk = NULL, control = list(), ...) {
    ## An R version of the conjugate gradient minimization
    ## using the Dai-Yuan ideas
    #
    # Input:
    #  par  = a vector containing the starting point
    # fn = objective function (assumed to be sufficeintly
    #   differentiable)
    #  gr = gradient of objective function
    #  lower = vector of lower bounds on parameters
    #  upper = vector of upper bounds on parameters
    # Note: free parameters outside bounds will be adjusted to
    #   bounds.
    # bdmsk = control vector for bounds and masks. Parameters
    #   for which bdmsk are 1
    # are unconstrained or 'free', those with bdmsk 0 are
    #   masked i.e., fixed.
    # For historical reasons, we use the same array as an
    #   indicator that a
    #         parameter is at a lower bound (-3) or upper bound (-1)
    #  control = list of control parameters
    #           maxit = a limit on the number of iterations (default 500)
    #           maximize = TRUE to maximize the function (default FALSE)
    #           trace = 0 (default) for no output,
    #                  >0 for output (bigger => more output)
    # eps=1.0e-7 (default) for use in computing numerical
    #   gradient approximations.
    # dowarn=TRUE by default. Set FALSE to suppress warnings.
    #
    # Output:
    #    A list with components:
    #
    #     par: The best set of parameters found.
    #
    #   value: The value of 'fn' corresponding to 'par'.
    #
    # counts: A two-element integer vector giving the number of
    #   calls to
    # 'fn' and 'gr' respectively. This excludes those calls
    #   needed
    # to compute the Hessian, if requested, and any calls to
    #   'fn'
    # to compute a finite-difference approximation to the
    #   gradient.
    #
    # convergence: An integer code. '0' indicates successful
    #   convergence.
    #          Error codes are
    #          '0' converged
    # '1' indicates that the function evaluation count
    #   'maxfeval'
    #               was reached.
    #          '2' indicates initial point is infeasible
    #
    # message: A character string giving any additional
    #   information returned
    #          by the optimizer, or 'NULL'.
    #
    # bdmsk: Returned index describing the status of bounds and
    #   masks at the
    # proposed solution. Parameters for which bdmsk are 1 are
    #   unconstrained
    # or 'free', those with bdmsk 0 are masked i.e., fixed. For
    #   historical
    # reasons, we indicate a parameter is at a lower bound
    #   using -3
    #          or upper bound using -1.
    #
    #
    #  Author:  John C Nash
    #  Date:  April 2, 2009; revised July 28, 2009
    #################################################################
    # control defaults -- idea from spg
    ctrl <- list(maxit = 500, maximize = FALSE, trace = 0, eps = 1e-07, 
        dowarn = TRUE, tol=0)
    namc <- names(control)
    if (!all(namc %in% names(ctrl))) 
        stop("unknown names in control: ", namc[!(namc %in% names(ctrl))])
    ctrl[namc] <- control
    npar<-length(par)
    if (ctrl$tol == 0) tol <- npar * (npar * .Machine$double.eps)  # for gradient test.  Note -- integer overflow if n*n*d.eps
    else tol<-ctrl$tol
    maxit <- ctrl$maxit  # limit on function evaluations
    maximize <- ctrl$maximize  # TRUE to maximize the function
    trace <- ctrl$trace  # 0 for no output, >0 for output (bigger => more output)
    if (trace > 2) cat("trace = ", trace, "\n")
    eps <- ctrl$eps
    fargs <- list(...)  # the ... arguments that are extra function / gradient data
    grNULL <- is.null(gr)
    dowarn <- ctrl$dowarn  #
    #############################################
    if (maximize) {
       warning("Rcgmin no longer supports maximize 111121 -- see documentation")
       msg<-"Rcgmin no longer supports maximize 111121"
       ans <- list(par, NA, c(0, 0), 9999, msg, bdmsk)
       return(ans)
    }
    #############################################
    # gr MUST be provided
    if (is.null(gr)) {  # if gr function is not provided STOP (Rvmmin has definition)
       stop("A gradient calculation (analytic or numerical) MUST be provided for Rcgmin") 
    }
    if ( is.character(gr) ) {
       # Convert string to function call, assuming it is a numerical gradient function
       mygr<-function(par=par, userfn=fn, ...){
           do.call(gr, list(par, userfn, ...))
       }
    } else { mygr<-gr }
   ############# end test gr ####################
    ## Set working parameters (See CNM Alg 22)
    if (trace > 0) {
        cat("Rcgmin -- J C Nash 2009 - bounds constraint version of new CG\n")
        cat("an R implementation of Alg 22 with Yuan/Dai modification\n")
    }
    bvec <- par  # copy the parameter vector
    n <- length(bvec)  # number of elements in par vector
    maxfeval <- round(sqrt(n + 1) * maxit)  # change 091219
    ig <- 0  # count gradient evaluations
    ifn <- 1  # count function evaluations (we always make 1 try below)
    stepredn <- 0.15  # Step reduction in line search
    acctol <- 1e-04  # acceptable point tolerance
    reltest <- 100  # relative equality test
    ceps <- .Machine$double.eps * reltest
    pceps <- ceps*max(abs(bvec))
    accpoint <- as.logical(FALSE)  # so far do not have an acceptable point
    cyclimit <- min(2.5 * n, 10 + sqrt(n))  #!! upper bound on when we restart CG cycle
    fargs <- list(...)  # function arguments
    if (trace > 2) {
        cat("Extra function arguments:")
        print(fargs)
    }
    # set default masks if not defined
    if (is.null(bdmsk)) {
        bdmsk <- rep(1, n)
    }
    if (trace > 2) {
        cat("bdmsk:")
        print(bdmsk)
    }
    # Routine should NOT be called directly without bounds.
    # Still do checks to get nolower, noupper, bounds
    if (is.null(lower) || !any(is.finite(lower))) 
        nolower = TRUE
    else nolower = FALSE
    if (is.null(upper) || !any(is.finite(upper))) 
        noupper = TRUE
    else noupper = FALSE
    if (nolower && noupper && all(bdmsk == 1)) 
        bounds = FALSE
    else bounds = TRUE
    if (trace > 2) 
        cat("Bounds: nolower = ", nolower, "  noupper = ", noupper, 
            " bounds = ", bounds, "\n")
    if (nolower) 
        lower <- rep(-Inf, n)
    if (noupper) 
        upper <- rep(Inf, n)
    ######## check bounds and masks #############
    ## NOTE: do this inline to avoid call to external routine
    if (bounds) {
        # Make sure to expand lower and upper
        if (!nolower & (length(lower) < n)) 
            {
                ## tmp<-readline('Check length lower ')
                if (length(lower) == 1) {
                  lower <- rep(lower, n)
                }
                else {
                  stop("1<length(lower)<n")
                }
            }  # else lower OK
        if (!noupper & (length(upper) < n)) 
            {
                if (length(upper) == 1) {
                  upper <- rep(upper, n)
                }
                else {
                  stop("1<length(upper)<n")
                }
            }  # else upper OK
        # At this point, we have full bounds in play
        # This implementation as a loop, but try later to vectorize
        for (i in 1:n) {
            #       cat('i = ',i,'\n')
            if (bdmsk[i] == 0) {
                # NOTE: we do not change masked parameters, even if out of bounds
                if (!nolower) {
                  if (bvec[i] < lower[i]) {
                    wmsg <- paste(bvec[i], " = MASKED x[", i, 
                      "] < lower bound = ", lower[i], sep = "")
                    if (dowarn) 
                      warning(wmsg)
                  }
                }
                if (!noupper) {
                  if (bvec[i] > upper[i]) {
                    wmsg <- paste(bvec[i], " = MASKED x[", i, 
                      "] > upper bound = ", upper[i], sep = "")
                    if (dowarn) 
                      warning(wmsg)
                  }
                }
            }
            else {
                # not masked, so must be free or active constraint
                if (!nolower) {
                  if (bvec[i] <= lower[i]) {
                    # changed 090814 to ensure bdmsk is set
                    wmsg <- paste("x[", i, "], set ", bvec[i], 
                      " to lower bound = ", lower[i], sep = "")
                    if (dowarn && (bvec[i] != lower[i])) 
                      warning(wmsg)
                    bvec[i] <- lower[i]
                    bdmsk[i] <- -3  # active lower bound
                  }
                }
                if (!noupper) {
                  if (bvec[i] >= upper[i]) {
                    # changed 090814 to ensure bdmsk is set
                    wmsg <- paste("x[", i, "], set ", bvec[i], 
                      " to upper bound = ", upper[i], sep = "")
                    if (dowarn && (bvec[i] != upper[i])) 
                      warning(wmsg)
                    bvec[i] <- upper[i]
                    bdmsk[i] <- -1  # active upper bound
                  }
                }
            }  # end not masked
        }  # end loop for bound/mask check
    } else stop("Do not call Rcgminb without bounds")
    ############## end bounds check #############
    # Initial function value -- may NOT be at initial point
    #   specified by user.
    if (trace > 2) {
        cat("Try function at initial point:")
        print(bvec)
    }
    f <- try(fn(bvec, ...), silent = TRUE)  # Compute the function at initial point.
    if (trace > 0) {
        cat("Initial function value=", f, "\n")
    }
    if (inherits(f,"try-error")) {
        msg <- "Initial point is infeasible."
        if (trace > 0) 
            cat(msg, "\n")
        ans <- list(par, NA, c(ifn, 0), 2, msg, bdmsk)
        names(ans) <- c("par", "value", "counts", "convergence", 
            "message", "bdmsk")
        return(ans)
    }
    fmin <- f
    if (trace > 0) 
        cat("Initial fn=", f, "\n")
    if (trace > 2) 
        print(bvec)
    # Start the minimization process
    keepgoing <- TRUE
    msg <- "not finished"  # in case we exit somehow
    oldstep <- 0.8  #!! 2/3 #!!? WHY?
    ####################################################################
    fdiff <- NA  # initially no decrease
    cycle <- 0  # !! cycle loop counter
    while (keepgoing) {
        # main loop -- must remember to break out of it!!
        t <- as.vector(rep(0, n))  # zero step vector
        c <- t  # zero 'last' gradient
        while (keepgoing && (cycle < cyclimit)) {
            ## cycle loop
            cycle <- cycle + 1
            if (trace > 0) 
                cat(ifn, " ", ig, " ", cycle, " ", fmin, "  last decrease=", 
                  fdiff, "\n")
            if (trace > 1) {
                print(bvec)
                cat("\n")
            }
            if (ifn > maxfeval) {
                msg <- paste("Too many function evaluations (> ", 
                  maxfeval, ") ", sep = "")
                if (trace > 0) 
                  cat(msg, "\n")
                ans <- list(par, fmin, c(ifn, ig), 1, msg, bdmsk)  # 1 indicates not converged in function limit
                names(ans) <- c("par", "value", "counts", "convergence", 
                  "message", "bdmsk")
                return(ans)
            }
            par <- bvec  # save best parameters
            ig <- ig + 1
            if (ig > maxit) {
                msg <- paste("Too many gradient evaluations (> ", 
                  maxit, ") ", sep = "")
                if (trace > 0) 
                  cat(msg, "\n")
                ans <- list(par, fmin, c(ifn, ig), 1, msg, bdmsk)  # 1 indicates not converged in function or gradient limit
                names(ans) <- c("par", "value", "counts", "convergence", 
                  "message", "bdmsk")
                return(ans)
            }
            g <- mygr(bvec, ...)
            if (bounds) 
                {
                  ## Bounds and masks adjustment of gradient ##
                  ## first try with looping -- later try to vectorize
                  if (trace > 2) {
                    cat("bdmsk:")
                    print(bdmsk)
                  }
                  for (i in 1:n) {
                    if ((bdmsk[i] == 0)) {
                      # masked, so gradient component is zero
                      g[i] <- 0
                    }
                    else {
                      if (bdmsk[i] == 1) {
                        if (trace > 1) 
                          cat("Parameter ", i, " is free\n")
                      }
                      else {
                        if ((bdmsk[i] + 2) * g[i] < 0) {
                          # test for -ve gradient at upper bound, +ve at lower bound
                          g[i] <- 0  # in which case active mask or constraint and zero gradient component
                        }
                        else {
                          bdmsk[i] <- 1  # freeing parameter i
                          if (trace > 1) 
                            cat("freeing parameter ", i, "\n")
                        }
                      }
                    }
                  }  # end masking loop on i
                  if (trace > 2) {
                    cat("bdmsk adj:\n")
                    print(bdmsk)
                    cat("proj-g:\n")
                    print(g)
                  }
                }  # end if bounds
            ## end bounds and masks adjustment of gradient
            g1 <- sum(g * (g - c))  # gradient * grad-difference
            g2 <- sum(t * (g - c))  # oldsearch * grad-difference
            gradsqr <- sum(g * g)
            if (trace > 1) {
                cat("Gradsqr = ", gradsqr, " g1, g2 ", g1, " ", 
                  g2, " fmin=", fmin, "\n")
            }
            c <- g  # save last gradient
            g3 <- 1  # !! Default to 1 to ensure it is defined -- t==0 on first cycle
            if (gradsqr > tol * (abs(fmin) + reltest)) {
                if (g2 > 0) {
                  betaDY <- gradsqr/g2
                  betaHS <- g1/g2
                  g3 <- max(0, min(betaHS, betaDY))  # g3 is our new 'beta' !! Dai/Yuan 2001, (4.2)
                }
            }
            else {
                msg <- paste("Very small gradient -- gradsqr =", 
                  gradsqr, sep = " ")
                if (trace > 0) 
                  cat(msg, "\n")
                keepgoing <- FALSE  # done loops -- should we break?
                break  # to leave inner loop
            }
            if (trace > 2) 
                cat("Betak = g3 = ", g3, "\n")
            if (g3 == 0 || cycle >= cyclimit) {
                # we are resetting to gradient in this case
                if (trace > 0) {
                  if (cycle < cyclimit) 
                    cat("Yuan/Dai cycle reset\n")
                  else cat("Cycle limit reached -- reset\n")
                }
                fdiff <- NA
                cycle <- 0
                break  #!!
            }
            else {
                # drop through if not Yuan/Dai cycle reset
                t <- t * g3 - g  # t starts at zero, later is step vector
                gradproj <- sum(t * g)  # gradient projection
                if (trace > 1) 
                  cat("Gradproj =", gradproj, "\n")
                if (bounds) 
                  {
                    ## Adjust search direction for masks
                    if (trace > 2) {
                      cat("t:\n")
                      print(t)
                    }
                    t[which(bdmsk <= 0)] <- 0  # apply mask constraint
                    if (trace > 2) {
                      cat("adj-t:\n")
                      print(t)
                    }
                    ## end adjust search direction for masks
                  }  # end if bounds
                # Why do we not check gradproj size?
                ########################################################
                ####                  Line search                   ####
                OKpoint <- FALSE
                if (trace > 2) 
                  cat("Start linesearch with oldstep=", oldstep, 
                    "\n")
                steplength <- oldstep * 1.5  #!! try a bit bigger
                f <- fmin
                changed <- TRUE  # Need to set so loop will start
                while ((f >= fmin) && changed) {
                  if (bounds) 
                    {
                      # Box constraint -- adjust step length
                      for (i in 1:n) {
                        # loop on parameters -- vectorize?
                        if ((bdmsk[i] == 1) && (abs(t[i]) > pceps)) 
                        {
                            # only concerned with free parameters and non-zero search
                            #   dimension
                            if (t[i] < 0) {
                              # going down. Look at lower bound
                              trystep <- (lower[i] - par[i])/t[i]  # t[i] < 0 so this is positive
                            }
                            else {
                              # going up, check upper bound
                              trystep <- (upper[i] - par[i])/t[i]  # t[i] > 0 so this is positive
                            }
                            if (trace > 3) 
                              cat("steplength, trystep:", steplength, 
                                trystep, "\n")
                            steplength <- min(steplength, trystep)  # reduce as necessary
                        }  # end steplength reduction
                        else {t[i] <- 0} # small dirn gets set to zero just in case 
                      }  # end loop on i to reduce step length
                      if (trace > 1) 
                        cat("reset steplength=", steplength, "\n")
                      # end box constraint adjustment of step length
                    }  # end if bounds
                  bvec <- par + steplength * t
                  if (trace > 1) {cat("trial bvec:"); print(bvec)}
                  changed <- (!identical((bvec + reltest), (par + reltest)))
                  if (changed) {
                    # compute newstep, if possible
                    f <- fn(bvec, ...)  # Because we need the value for linesearch, don't use try()
                    # instead preferring to fail out, which will hopefully be
                    #   unlikely.
                    ifn <- ifn + 1
                    if (is.na(f) || (!is.finite(f))) {
                      warning("Rcgmin - undefined function")
                      f <- .Machine$double.xmax
                    }
                    if (f < fmin) { f1 <- f } # Hold onto value
                    else {
                      savestep<-steplength
                      steplength <- steplength * stepredn
                      if (steplength >=savestep) changed<-FALSE
                      if (trace > 0) cat("*")
                    }
                  }
                }  # end while
                changed1 <- changed  # Change in parameters occured in step reduction
                if (changed1) {
                  ## Should we check for reduction? or is this done in if (newstep >0) ?
                  newstep <- 2 * (f - fmin - gradproj * steplength)  # JN 081219 change
# ?? Explain! 
                  if (newstep > 0) {
                     newstep = -(gradproj * steplength * steplength/newstep)
                  } # ?? what if NOT positive
                  if (bounds) {
                        # Box constraint -- adjust step length
                        for (i in 1:n) {
                          # loop on parameters -- vectorize?
                          if ((bdmsk[i] == 1) && (t[i] != 0)) 
                            {
                              # only concerned with free parameters and non-zero search dimension
                              if (t[i] < 0) {
                                # going down. Look at lower bound
                                trystep <- (lower[i] - par[i])/t[i]  # t[i] < 0 so this is positive
                              }
                              else {
                                # going up, check upper bound
                                trystep <- (upper[i] - par[i])/t[i]  # t[i] > 0 so this is positive
                              }
                              if (trace > 3) 
                                cat("newstep, trystep:", newstep, trystep, "\n")
                              newstep <- min(newstep, trystep)  # reduce as necessary
                            }  # end newstep reduction
                        }  # end loop on i to reduce step length
                        if (trace > 2) 
                          cat("reset newstep=", newstep, "\n")
                        # end box constraint adjustment of step length
                      }  # end if bounds
                    bvec <- par + newstep * t
                    changed <- (!identical((bvec + reltest), 
                      (par + reltest)))
                    if (changed) {
                      f <- fn(bvec, ...)
                      ifn <- ifn + 1
                    }
                    if (trace > 2) 
                      cat("fmin, f1, f: ", fmin, f1, f, "\n")
                    if (f < min(fmin, f1)) {
                      # success
                      OKpoint <- TRUE
                      accpoint <- (f <= fmin + gradproj * newstep * 
                        acctol)
                      fdiff <- (fmin - f)  # check decrease
                      fmin <- f
                      oldstep <- newstep  # !! save it
                    }
                    else {
                      if (f1 < fmin) {
                        bvec <- par + steplength * t  # reset best point
                        accpoint <- (f1 <= fmin + gradproj * 
                          steplength * acctol)
                        OKpoint <- TRUE  # Because f1 < fmin
                        fdiff <- (fmin - f1)  # check decrease
                        fmin <- f1
                        oldstep <- steplength  #!! save it
                      }
                      else {
                        # no reduction
                        fdiff <- NA
                        accpoint <- FALSE
                      }  # f1<?fmin
                    }  # f < min(f1, fmin)
                    if (trace > 1) 
                      cat("accpoint = ", accpoint, " OKpoint = ", 
                        OKpoint, "\n")
                    if (!accpoint) {
                      msg <- "No acceptable point -- exit loop"
                      if (trace > 0) 
                        cat("\n", msg, "\n")
                      keepgoing <- FALSE
                      break  #!!
                    }
                  }  # changed1
                else {
                  # not changed on step redn
                  if (cycle == 1) {
                    msg <- " Converged -- no progress on new CG cycle"
                    if (trace > 0) 
                      cat("\n", msg, "\n")
                    keekpgoing <- FALSE
                    break  #!!
                  }
                }  # end else
            }  # end of test on Yuan/Dai condition
            #### End line search ####
            if (bounds) {
               ## Reactivate constraints? -- should check for infinite bounds!!?
               for (i in 1:n) {
                 if (bdmsk[i] == 1) { # only interested in free parameters
                   if (is.finite(lower[i])) {# JN091020 -- need to use abs in case bounds negative
                     if ((bvec[i] - lower[i]) < ceps * (abs(lower[i]) + 1)) { # are we near or lower than lower bd
                       if (trace > 2) cat("(re)activate lower bd ", i, " at ", lower[i], "\n")
                       bdmsk[i] <- -3
                     }  # end lower bd reactivate
                   }
                   if (is.finite(upper[i])) { # JN091020 -- need to use abs in case bounds negative
                     if ((upper[i] - bvec[i]) < ceps * (abs(upper[i]) + 1)) { # are we near or above upper bd
                       if (trace > 2) cat("(re)activate upper bd ", i, " at ", upper[i], "\n")
                       bdmsk[i] <- -1
                     }  # end upper bd reactivate
                   }
                 }  # end test on free params
               }  # end reactivate constraints loop
            }  # end if bounds
        }  # end of inner loop (cycle)
        if (oldstep < acctol) {
            oldstep <- acctol
        }
        #   steplength
        if (oldstep > 1) {
            oldstep <- 1
        }
        if (trace > 1) 
            cat("End inner loop, cycle =", cycle, "\n")
    }  # end of outer loop
    msg <- "Rcgmin seems to have converged"
    if (trace > 0) 
        cat(msg, "\n")
    #  par: The best set of parameters found.
    #  value: The value of 'fn' corresponding to 'par'.
    #  counts: number of calls to 'fn' and 'gr' (2 elements)
    # convergence: An integer code. '0' indicates successful
    #   convergence.
    #  message: A character string or 'NULL'.
#    if (maximize) 
#        fmin <- -fmin
    ans <- list(par, fmin, c(ifn, ig), 0, msg, bdmsk)
    names(ans) <- c("par", "value", "counts", "convergence", 
        "message", "bdmsk")
    return(ans)
}  ## end of Rcgmin
