R/family.rcim.R

In VGAM: Vector Generalized Linear and Additive Models

# These functions are
# Copyright (C) 1998-2024 T.W. Yee, University of Auckland.
# All rights reserved.















 rcim <-
  function(y,
           family = poissonff,
           Rank = 0,
           M1 = NULL,
           weights = NULL,
           which.linpred = 1,
   Index.corner = ifelse(is.null(str0), 0, max(str0)) + 1:Rank,
           rprefix = "Row.",
           cprefix = "Col.",
           iprefix = "X2.",
           offset = 0,

           str0 = if (Rank) 1 else NULL,  # Ignored if Rank == 0
           summary.arg = FALSE, h.step = 0.0001,
           rbaseline = 1, cbaseline = 1,

           has.intercept = TRUE,

           M = NULL,

           rindex = 2:nrow(y),  # Row index
           cindex = 2:ncol(y),  # Col index
           iindex = 2:nrow(y),  # Interaction index



           ...) {





  rindex <- unique(sort(rindex))
  cindex <- unique(sort(cindex))
  iindex <- unique(sort(iindex))


  if (Rank == 0 && !has.intercept)
    warning("probably 'has.intercept == TRUE' is better for ",
            "a rank-0 model")



  ncoly <- ncol(y)


  noroweffects <- FALSE
  nocoleffects <- FALSE

  if (!is.Numeric(which.linpred, length.arg = 1,
                  integer.valued = TRUE, positive = TRUE))
    stop("bad input for argument 'which.linpred'")

  if (!is.character(rprefix))
    stop("argument 'rprefix' must be character")
  if (!is.character(cprefix))
    stop("argument 'cprefix' must be character")

  if (is.character(family))
    family <- get(family)
  if (is.function(family))
    family <- ((family)())
  if (!inherits(family, "vglmff")) {
    stop("'family = ", family, "' is not a VGAM family function")
  }
  efamily <- family


  if (!is.Numeric(M1)) {
    iefamily <- efamily@infos

    if (is.function(iefamily))
      M1 <- (iefamily())$M1
      if (is.Numeric(M1))
        M1 <- abs(M1)
  }
  if (!is.Numeric(M1)) {
    if (!is.Numeric(M))
      warning("cannot determine the value of 'M1'.",
              "Assuming the value one.")
    M1 <- 1
  }



  M <- if (is.null(M)) M1 * ncol(y) else M

  special <- (M > 1) && (M1 == 1)



  object.save <- y
  y <- if (is(y, "rrvglm")) {
    depvar(object.save)
  } else {
    as(as.matrix(y), "matrix")
  }
  if (length(dim(y)) != 2 || nrow(y) < 3 || ncol(y) < 3)
    stop("argument 'y' must be a matrix with >= 3 rows & ",
         "columns, or a rrvglm() object")


  .rcim.df <-
    if (!noroweffects)
      data.frame("Row.2" = I.col(2, nrow(y))) else  # See below
    if (!nocoleffects)
      data.frame("Col.2" = I.col(2, nrow(y))) else  # See below
      stop("at least one of 'noroweffects' and 'nocoleffects' ",
           "must be FALSE")


  min.row.val <- rindex[1]  # == min(rindex) since its sorted
  min.col.val <- cindex[1]  # == min(cindex) since its sorted
  if (!noroweffects) {
    colnames( .rcim.df ) <-
      paste(rprefix, as.character(min.row.val),  # "2",
            sep = "")  # Overwrite "Row.2"
  } else if (!nocoleffects) {
    colnames( .rcim.df ) <-
      paste(cprefix, as.character(min.col.val),  # "2",
            sep = "")  # Overwrite "Col.2"
  }



  yn1 <- if (length(dimnames(y)[[1]])) dimnames(y)[[1]] else
             param.names(iprefix, nrow(y))
  warn.save <- options()$warn
  options(warn = -3)  # Suppress warnings (hopefully temporarily)
  if (any(!is.na(as.numeric(substring(yn1, 1, 1)))))
    yn1 <- param.names(iprefix, nrow(y))
  options(warn = warn.save)


  nrprefix <- as.name(rprefix)
  ncprefix <- as.name(cprefix)


  assign(rprefix, factor(1:nrow(y)))
  modmat.row <- substitute(
           model.matrix( ~ .rprefix ), list( .rprefix = nrprefix ))

  LLL <- ifelse(special, M, ncol(y))
  assign(cprefix, factor(1:LLL))


  modmat.col <- substitute(
           model.matrix( ~ .cprefix ), list( .cprefix = ncprefix ))
  modmat.row <- eval( modmat.row )
  modmat.col <- eval( modmat.col )




  Hlist <-
    if (has.intercept) {
      list("(Intercept)" = matrix(1, LLL, 1))
    } else {
      temp <- list("Row.2" = matrix(1, LLL, 1))
      names(temp) <- paste(rprefix,
                           as.character(min.row.val), sep = "")
      temp
    }


  if (!noroweffects)
    for (ii in rindex) {
         Hlist[[paste(rprefix, ii, sep = "")]] <- matrix(1, LLL, 1)
      .rcim.df[[paste(rprefix, ii, sep = "")]] <- modmat.row[, ii]
    }


  if (!nocoleffects)
    for (ii in cindex) {
      temp6.mat <- modmat.col[, ii, drop = FALSE]
         Hlist[[paste(cprefix, ii, sep = "")]] <- temp6.mat
      .rcim.df[[paste(cprefix, ii, sep = "")]] <- rep_len(1, nrow(y))
    }


  if (Rank > 0) {
    for (ii in iindex) {

      Hlist[[yn1[ii]]] <- diag(LLL)

      .rcim.df[[yn1[ii]]] <- I.col(ii, nrow(y))
    }
  }


  dimnames(.rcim.df) <- list(if (length(dimnames(y)[[1]]))
                               dimnames(y)[[1]] else
                               as.character(iindex),
                             dimnames( .rcim.df )[[2]])

    str1 <- paste0(if (has.intercept)
                   "~ 1 + " else "~ -1 + ", rprefix,
                   as.character(min.row.val))  # "2"


  if (nrow(y) > 2)
    str1 <- paste(str1,
                  paste(rprefix, rindex[-1], sep = "",
                        collapse = " + "),
                  sep = " + ")


    str1 <- paste(str1,
                  paste(cprefix, cindex, sep = "",
                        collapse = " + "),
                  sep = " + ")




  str2 <- paste("y", str1)
  if (Rank > 0) {
    str2 <- paste(str2,
                  paste(yn1[iindex], sep = "", collapse = " + "),
                  sep = " + ")
  }




    controlfun <- if (Rank == 0)
                    vglm.control else rrvglm.control  # orig.


  mycontrol <- controlfun(Rank = Rank,
                          Index.corner = Index.corner,
                          str0 = str0, ...)

  if (mycontrol$trace) {
  }



  if ((mindim <- min(nrow(y), ncol(y))) <= Rank) {
    stop("argument 'Rank' is too high. Must be a value from 0 ",
         "to ", mindim - 1, " inclusive")
  }



  if (Rank > 0)
    mycontrol$noRRR <- as.formula(str1)  # Overwrite this

  assign(".rcim.df", .rcim.df, envir = VGAM::VGAMenv)

  warn.save <- options()$warn
  options(warn = -3)  # Suppress warnings (hopefully temporarily)

  if (mycontrol$trace) {
  }


  if (M1 > 1) {
    orig.Hlist <- Hlist

    kmat1 <- matrix(0, nrow = M1, ncol = 1)
    kmat1[which.linpred, 1] <- 1
    kmat0 <- (diag(M1))[, -which.linpred, drop = FALSE]

    for (ii in seq_along(Hlist)) {
      Hlist[[ii]] <- kronecker(Hlist[[ii]], kmat1)
    }
    if (has.intercept)
      Hlist[["(Intercept)"]] <-
         cbind(Hlist[["(Intercept)"]],
               kronecker(matrix(1, ncoly, 1), kmat0))

    if (mycontrol$trace) {
    }
  }



  offset.matrix <-
    matrix(offset, nrow = nrow(y),
                   ncol = M)  # byrow = TRUE



  answer <- if (Rank > 0) {
    if (is(object.save, "rrvglm")) object.save else
      rrvglm(as.formula(str2),
             family = family,
             constraints = Hlist,
             offset = offset.matrix,
             weights = if (length(weights))
                       weights else rep_len(1, nrow(y)),
             ...,
             control = mycontrol, data = .rcim.df )
  } else {
    if (is(object.save, "vglm")) object.save else
        vglm(as.formula(str2),
             family = family,
             constraints = Hlist,
             offset = offset.matrix,
             weights = if (length(weights))
                       weights else rep_len(1, nrow(y)),
             ...,
             control = mycontrol, data = .rcim.df )
  }

  options(warn = warn.save)  # Restore warnings to prior state


  answer <- if (summary.arg) {
    if (Rank > 0) {
      summary.rrvglm(as(answer, "rrvglm"), h.step = h.step)
    } else {
      summary(answer)
    }
  } else {
    as(answer, ifelse(Rank > 0, "rcim",  "rcim0"))
  }


  answer@misc$rbaseline     <- rbaseline
  answer@misc$cbaseline     <- cbaseline
  answer@misc$which.linpred <- which.linpred
  answer@misc$offset        <- offset.matrix

  answer
}








summaryrcim <- function(object, ...) {
  rcim(depvar(object), summary.arg = TRUE, ...)
}









 setClass("rcim0", representation(not.needed = "numeric"),
          contains = "vglm")  # Added 20110506

 setClass("rcim", representation(not.needed = "numeric"),
          contains = "rrvglm")


setMethod("summary", "rcim0",
          function(object, ...)
          summaryrcim(object, ...))


setMethod("summary", "rcim",
          function(object, ...)
          summaryrcim(object, ...))










 Rcim <- function(mat, rbaseline = 1, cbaseline = 1) {

  mat <- as.matrix(mat)
  RRR <- dim(mat)[1]
  CCC <- dim(mat)[2]

  rnames <- if (is.null(rownames(mat))) {
    param.names("X", RRR)
  } else {
    rownames(mat)
  }

  cnames <- if (is.null(colnames(mat))) {
    param.names("Y", CCC)
  } else {
    colnames(mat)
  }

  r.index <-
    if (is.character(rbaseline))
      which(rownames(mat) == rbaseline) else
    if (is.numeric(rbaseline)) rbaseline else
      stop("argement 'rbaseline' must be numeric",
           "or character of the level of row")

  c.index <-
    if (is.character(cbaseline))
       which(colnames(mat) == cbaseline) else
    if (is.numeric(cbaseline)) cbaseline else
       stop("argement 'cbaseline' must be numeric",
            "or character of the level of row")

  if (length(r.index) != 1)
    stop("Could not match with argument 'rbaseline'")

  if (length(c.index) != 1)
    stop("Could not match with argument 'cbaseline'")


  yswap <- rbind(mat[r.index:RRR, ],
                 if (r.index > 1) mat[1:(r.index - 1),] else
                 NULL)
  yswap <- cbind(yswap[, c.index:CCC],
                 if (c.index > 1) yswap[, 1:(c.index - 1)] else
                 NULL)

  new.rnames <- rnames[c(r.index:RRR,
                         if (r.index > 1) 1:(r.index - 1) else
                         NULL)]
  new.cnames <- cnames[c(c.index:CCC,
                         if (c.index > 1) 1:(c.index - 1) else
                         NULL)]
  colnames(yswap) <- new.cnames
  rownames(yswap) <- new.rnames

  yswap
}













 plotrcim0  <- function(object,
     centered = TRUE, which.plots = c(1, 2),
     hline0 = TRUE, hlty = "dashed",
     hcol = par()$col, hlwd = par()$lwd,
     rfirst = 1, cfirst = 1,
     rtype = "h", ctype = "h",
     rcex.lab = 1, rcex.axis = 1,  # rlabels = FALSE,
     rtick = FALSE,
     ccex.lab = 1, ccex.axis = 1,  # clabels = FALSE,
     ctick = FALSE,
     rmain = "Row effects", rsub = "",
     rxlab = "", rylab = "Row effects",
     cmain = "Column effects", csub = "",
     cxlab = "", cylab = "Column effects",
     rcol = par()$col, ccol = par()$col,
     no.warning = FALSE,
     ...) {


  nparff <- if (is.numeric(object@family@infos()$M1)) {
    object@family@infos()$M1
  } else {
    1
  }



  if (!no.warning &&
      is.numeric(object@control$Rank) &&
      object@control$Rank != 0)
    warning("argument 'object' is not Rank-0")


  n.lm  <- nrow(object@y)

  cobj <- coefficients(object)

  upperbound <- if (!is.numeric(object@control$Rank) ||
                   object@control$Rank == 0) length(cobj) else
               length(object@control$colx1.index)

 orig.roweff <- c("Row.1" = 0,
                  cobj[(nparff + 1) : (nparff + n.lm - 1)])
 orig.coleff <- c("Col.1" = 0,
                  cobj[(nparff + n.lm) : upperbound])
  last.r <- length(orig.roweff)
  last.c <- length(orig.coleff)


  orig.raxisl  <- rownames(object@y)
  orig.caxisl  <- colnames(object@y)
  if (is.null(orig.raxisl))
    orig.raxisl <- as.character(1:nrow(object@y))
  if (is.null(orig.caxisl))
    orig.caxisl <- as.character(1:ncol(object@y))

  roweff.orig <-
  roweff <- orig.roweff[c(rfirst:last.r,
                          if (rfirst > 1) 1:(rfirst-1) else NULL)]
  coleff.orig <-
  coleff <- orig.coleff[c(cfirst:last.c,
                          if (cfirst > 1) 1:(cfirst-1) else NULL)]

  if (centered) {
    roweff <- scale(roweff, scale = FALSE)  # Center it only
    coleff <- scale(coleff, scale = FALSE)  # Center it only
  }

  raxisl <- orig.raxisl[c(rfirst:last.r,
                          if (rfirst > 1) 1:(rfirst-1) else NULL)]

  caxisl <- orig.caxisl[c(cfirst:last.c,
                          if (cfirst > 1) 1:(cfirst-1) else NULL)]


  if (any(which.plots == 1, na.rm = TRUE)) {
    plot(roweff, type = rtype,
         axes = FALSE, col = rcol, main = rmain,
         sub  = rsub, xlab = rxlab, ylab = rylab, ...)

    axis(1, at = seq_along(raxisl),
         cex.lab = rcex.lab,
         cex.axis = rcex.axis,
         labels = raxisl)
    axis(2, cex.lab = rcex.lab, ...)  # las = rlas)

    if (hline0)
      abline(h = 0, lty = hlty, col = hcol, lwd = hlwd)
  }


  if (any(which.plots == 2, na.rm = TRUE)) {
    plot(coleff, type = ctype,
         axes = FALSE, col = ccol, main = cmain,
         sub  = csub, xlab = cxlab, ylab = cylab, ...)

    axis(1, at = seq_along(caxisl),
         cex.lab = ccex.lab,
         cex.axis = ccex.axis,
         labels = caxisl)
    axis(2, cex.lab = ccex.lab, ...)  # las = clas)

    if (hline0)
      abline(h = 0, lty = hlty, col = hcol, lwd = hlwd)
  }




  object@post$row.effects = roweff
  object@post$col.effects = coleff
  object@post$raw.row.effects = roweff.orig
  object@post$raw.col.effects = coleff.orig

  invisible(object)
}





setMethod("plot", "rcim0",
          function(x, y, ...)
          plotrcim0(object = x, ...))


setMethod("plot", "rcim",
          function(x, y, ...)
          plotrcim0(object = x, ...))













 moffset <-
  function(mat, roffset = 0, coffset = 0, postfix = "",
           rprefix = "Row.",
           cprefix = "Col."
          ) {





  if ((is.numeric(roffset) && (roffset == 0)) &&
      (is.numeric(coffset) && (coffset == 0)))
    return(mat)


  vecmat <- c(unlist(mat))
  ind1 <-
    if (is.character(roffset))
      which(rownames(mat) == roffset) else
      if (is.numeric(roffset)) roffset + 1 else
      stop("argument 'roffset' not matched (character).",
           " It must be numeric, ",
           "else character and match the ",
           "row names of the response")
  ind2 <- if (is.character(coffset))
             which(colnames(mat) == coffset) else
                   if (is.numeric(coffset)) coffset + 1 else
             stop("argument 'coffset' not matched (character).",
                           " It must be numeric, ",
                           "else character and match the ",
                           "column names of the response")

  if (!is.Numeric(ind1, positive = TRUE,
                  integer.valued = TRUE, length.arg = 1) ||
      !is.Numeric(ind2, positive = TRUE,
                  integer.valued = TRUE, length.arg = 1))
    stop("bad input for arguments 'roffset' and/or 'coffset'")
  if (ind1 > nrow(mat))
    stop("too large a value for argument 'roffset'")
  if (ind2 > ncol(mat))
    stop("too large a value for argument 'coffset'")


  start.ind <- (ind2 - 1)* nrow(mat) + ind1


  svecmat <- vecmat[c(start.ind:(nrow(mat) * ncol(mat)),
                     0:(start.ind - 1))]

  rownames.mat <- rownames(mat)
  if (length(rownames.mat) != nrow(mat))
    rownames.mat <- param.names(rprefix, nrow(mat))

  colnames.mat <- colnames(mat)
  if (length(colnames.mat) != ncol(mat))
    colnames.mat <- param.names(cprefix, ncol(mat))


  newrn <- if (roffset > 0)
            c(rownames.mat[c(ind1:nrow(mat))],
    paste(rownames.mat[0:(ind1-1)], postfix, sep = "")) else
          rownames.mat

  newcn <- c(colnames.mat[c(ind2:ncol(mat), 0:(ind2 - 1))])
  if (roffset > 0)
    newcn <- paste(newcn, postfix, sep = "")

  newmat <- matrix(svecmat, nrow(mat), ncol(mat),
                  dimnames = list(newrn, newcn))
  newmat
}



















Confint.rrnb <- function(rrnb2, level = 0.95) {



  if (!is(rrnb2, "rrvglm"))
      stop("argument 'rrnb2' does not appear to be a ",
           "rrvglm() object")

  if (!any(rrnb2@family@vfamily == "negbinomial"))
      stop("argument 'rrnb2' does not appear to be a ",
           "negbinomial() fit")

  if (rrnb2@control$Rank != 1)
    stop("argument 'rrnb2' is not Rank-1")

  if (rrnb2@misc$M != 2)
    stop("argument 'rrnb2' does not have M = 2")

  if (!all(rrnb2@misc$link == "loglink"))
    stop("argument 'rrnb2' does not have log links for ",
         "both parameters")

  a21.hat <- (Coef(rrnb2)@A)["loglink(size)", 1]
  beta11.hat <- Coef(rrnb2)@B1["(Intercept)", "loglink(mu)"]
  beta21.hat <- Coef(rrnb2)@B1["(Intercept)", "loglink(size)"]
  delta1.hat <- exp(a21.hat * beta11.hat - beta21.hat)
  delta2.hat <- 2 - a21.hat

  SE.a21.hat <-
    sqrt(vcovrrvglm(rrnb2)["I(latvar.mat)", "I(latvar.mat)"])


  ci.a21 <- a21.hat +
            c(-1, 1) * qnorm(1 - (1 - level)/2) * SE.a21.hat
  (ci.delta2 <- 2 - rev(ci.a21))  # e.g., the 95 percent CI

  list(a21.hat    = a21.hat,
       beta11.hat = beta11.hat,
       beta21.hat = beta21.hat,
       CI.a21     = ci.a21,
       CI.delta2  = ci.delta2,
       delta1     = delta1.hat,
       delta2     = delta2.hat,
       SE.a21.hat = SE.a21.hat)
}





Confint.nb1 <- function(nb1, level = 0.95) {




  if (!is(nb1, "vglm"))
    stop("argument 'nb1' does not appear to be a vglm() object")

  if (!any(nb1@family@vfamily == "negbinomial"))
    stop("argument 'nb1' does not appear to be a ",
         "negbinomial() fit")

  if (!all(unlist(constraints(nb1)[-1]) == 1))
    stop("argument 'nb1' does not appear to ",
         "have 'parallel = TRUE'")

  if (!all(unlist(constraints(nb1)[1]) == c(diag(nb1@misc$M))))
    stop("argument 'nb1' does not have 'parallel = FALSE' ",
         "for the intercept")

  if (nb1@misc$M != 2)
    stop("argument 'nb1' does not have M = 2")

  if (!all(nb1@misc$link == "loglink"))
    stop("argument 'nb1' does not have log links ",
         "for both parameters")

  cnb1 <- coefficients(as(nb1, "vglm"), matrix = TRUE)
  mydiff <- (cnb1["(Intercept)", "loglink(size)"] -
             cnb1["(Intercept)", "loglink(mu)"])
  delta0.hat <- exp(mydiff)
  (phi0.hat <- 1 + 1 / delta0.hat)  # MLE of phi0


  myvcov <- vcov(as(nb1, "vglm"))  # Not great; improve this!



  myvec <- cbind(c(-1, 1, rep_len(0, nrow(myvcov) - 2)))
  se.mydiff <- c(sqrt(t(myvec) %*% myvcov %*% myvec))

  ci.mydiff <- mydiff +
    c(-1, 1) * qnorm(1 - (1 - level)/2) * se.mydiff

  ci.delta0 <- ci.exp.mydiff <- exp(ci.mydiff)
  (ci.phi0 <- 1 + 1 / rev(ci.delta0))

  list(CI.phi0    = ci.phi0,
       CI.delta0  = ci.delta0,
       delta0     = delta0.hat,
       phi0       = phi0.hat)
}






plota21 <- function(rrvglm2, show.plot = TRUE, nseq.a21 = 31,
                    se.eachway = c(5, 5),  # == c(LHS, RHS),
                    trace.arg = TRUE,
                    lwd = 2, ...) {





  if (!is(rrvglm2, "rrvglm"))
      stop("argument 'rrvglm2' does not appear to ",
           "be a rrvglm() object")

  if (rrvglm2@control$Rank != 1)
    stop("argument 'rrvglm2' is not Rank-1")

  if (rrvglm2@misc$M != 2)
    stop("argument 'rrvglm2' does not have M = 2")


  loglik.orig <- logLik(rrvglm2)
  temp1 <- Confint.rrnb(rrvglm2)  # zz

  a21.hat <- (Coef(rrvglm2)@A)[2, 1]
  SE.a21.hat <- temp1$SE.a21.hat


    SE.a21.hat <-
        sqrt(vcov(rrvglm2)["I(latvar.mat)", "I(latvar.mat)"])


  big.ci.a21 <- a21.hat +  c(-1, 1) * se.eachway * SE.a21.hat
  seq.a21 <- seq(big.ci.a21[1], big.ci.a21[2], length = nseq.a21)
  Hlist.orig <- constraints.vlm(rrvglm2, type = "term")


  alreadyComputed <- !is.null(rrvglm2@post$a21.matrix)


  a21.matrix <- if (alreadyComputed) rrvglm2@post$a21.matrix else
                cbind(a21 = seq.a21, loglikelihood = 0)
  prev.etastart <- predict(rrvglm2)  # Halves the computing time
  funname <- "vglm"
  listcall <- as.list(rrvglm2@call)


  if (!alreadyComputed)
  for (ii in 1:nseq.a21) {
    if (trace.arg)
      print(ii)
    argslist <- vector("list", length(listcall) - 1)
    for (kay in 2:(length(listcall)))
      argslist[[kay - 1]] <- listcall[[kay]]

    names(argslist) <- c(names(listcall)[-1])

    argslist$trace       <- trace.arg
    argslist$etastart    <- prev.etastart
    argslist$constraints <- Hlist.orig


    for (kay in 2:length(argslist[["constraints"]])) {
      argslist[["constraints"]][[kay]] <-
        rbind(1, a21.matrix[ii, 1])
    }


    fitnew <- do.call(what = funname, args = argslist)

    a21.matrix[ii, 2] <- logLik(fitnew)

    prev.etastart <- predict(fitnew)
  }



  if (show.plot) {
    plot(a21.matrix[ ,1], a21.matrix[ ,2], type = "l",
            col = "blue", cex.lab = 1.1,
            xlab = expression(a[21]), ylab = "Log-likelihood")  # ...

    abline(v = (Hlist.orig[[length(Hlist.orig)]])[2, 1],
           col = "darkorange", lty = "dashed")

    abline(h = loglik.orig,
           col = "darkorange", lty = "dashed")

    abline(h = loglik.orig -
               qchisq(0.95, df = 1) / 2,
           col = "darkorange", lty = "dashed")

    abline(v = a21.hat +  c(-1, 1) * 1.96 * SE.a21.hat,
           col = "gray50", lty = "dashed", lwd = lwd)

  }  # End of (show.plot)

  rrvglm2@post <- list(a21.matrix = a21.matrix)
  invisible(rrvglm2)
}














 Qvar <- function(object,
                  factorname = NULL,
                  which.linpred = 1,
                  coef.indices = NULL,
                  labels = NULL, dispersion = NULL,
                  reference.name = "(reference)",
                  estimates = NULL
                 ) {








  if (!is.Numeric(which.linpred, length.arg = 1,
                  integer.valued = TRUE, positive = TRUE))
    stop("argument 'which.linpred' must be a positive integer")



  coef.indices.saved <- coef.indices

  if (!is.matrix(object)) {
    model <- object
    if (is.null(factorname) && is.null(coef.indices)) {
      stop("arguments 'factorname' and 'coef.indices' are ",
           "both NULL")
    }


    if (is.null(coef.indices)) {

      M <- npred(model)
      if (M < which.linpred)
          stop("argument 'which.linpred' must be a value ",
               "from the set 1:",
             M)


      newfactorname <- if (M > 1) {
        clist <- constraints(model, type = "term")

        Hk <- clist[[factorname]]
        Mdot <- ncol(Hk)
        Hk.row <- Hk[which.linpred, ]
        if (sum(Hk.row != 0) > 1)
          stop("cannot handle rows of constraint matrices ",
               "with more than one nonzero value")

        foo <- function(ii)
          switch(as.character(ii), '1'="1st", '2'="2nd", '3'="3rd",
                 paste(ii, "th", sep = ""))
        if (sum(Hk.row != 0) == 0)
          stop("factor '", factorname, "' is not used the ",
               foo(which.linpred), " eta (linear predictor)")

        row.index <- (1:Mdot)[Hk.row != 0]

        all.labels <- vlabel(factorname, ncolHlist = Mdot, M = M)
        all.labels[row.index]
      } else {
        factorname
      }

      colptr <- attr(model.matrix(object, type = "vlm"),
                     "vassign")
      colptr <- if (M > 1) {
        colptr[newfactorname]
      } else {
        colptr[[newfactorname]]
      }

      coef.indices <- colptr

      contmat <- if (length(model@xlevels[[factorname]]) ==
                     length(coef.indices)) {
        diag(length(coef.indices))
      } else {
        eval(call(model@contrasts[[factorname]],
                  model@xlevels  [[factorname]]))
      }
      rownames(contmat) <- model@xlevels[[factorname]]

      if (is.null(estimates)) {
        if (M > 1) {
          estimates <- matrix(-1, nrow(contmat), 1)
          ii <- 1
          estimates[, ii] <- contmat %*%
                      (coefvlm(model)[(coef.indices[[ii]])])
        } else {
          estimates <- contmat %*% (coefvlm(model)[coef.indices])
        }
      }




      Covmat <- vcov(model, dispersion = dispersion)



      covmat <- Covmat[unlist(coef.indices),
                       unlist(coef.indices), drop = FALSE]
      covmat <- if (M > 1) {
        ii <- 1
        ans <- contmat %*% Covmat[(colptr[[ii]]),
                                  (colptr[[ii]])] %*% t(contmat)
        ans
      } else {
        contmat %*% covmat %*% t(contmat)
      }
    } else { # ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
      kk <- length(coef.indices)
      refPos <- numeric(0)
      if (0 %in% coef.indices) {
        refPos <- which(coef.indices == 0)
        coef.indices <- coef.indices[-refPos]
      }




      covmat <- vcov(model, dispersion = dispersion)




      covmat <- covmat[coef.indices, coef.indices, drop = FALSE]

      if (is.null(estimates))
        estimates <- coefvlm(model)[coef.indices]

      if (length(refPos) == 1) {
        if (length(estimates) != kk)
          estimates <- c(0, estimates)
        covmat <- rbind(0, cbind(0, covmat))
        names(estimates)[1] <-
        rownames(covmat)[1] <-
        colnames(covmat)[1] <- reference.name
        if (refPos != 1) {
          perm <- if (refPos == kk) c(2:kk, 1) else
                  c(2:refPos, 1, (refPos + 1):kk)
          estimates <- estimates[perm]
          covmat <- covmat[perm, perm, drop = FALSE]
        }
      }
    }  # ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,


    return(Recall(covmat,
                  factorname = factorname,
                  which.linpred = which.linpred,
                  coef.indices = coef.indices.saved,
                  labels = labels,
                  dispersion = dispersion,
                  estimates = estimates
                  )
           )
  } else { # ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

    covmat <- object
    if (length(labels))
      rownames(covmat) <- colnames(covmat) <- labels
    if ((LLL <- dim(covmat)[1]) <= 2)
      stop("This function works only for factors with 3 ",
           "or more levels")
  }  # ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;




  allvcov <- covmat
  for (ilocal in 1:LLL)
    for (jlocal in ilocal:LLL)
      allvcov[ilocal, jlocal] <-
      allvcov[jlocal, ilocal] <- covmat[ilocal, ilocal] +
                                 covmat[jlocal, jlocal] -
                                 covmat[ilocal, jlocal] * 2

  diag(allvcov) <- rep_len(1.0, LLL)  # Any positive value should do


  wmat   <- matrix(1.0, LLL, LLL)
  diag(wmat) <- sqrt( .Machine$double.eps )


  logAllvcov <- log(allvcov)
  attr(logAllvcov, "Prior.Weights") <- wmat
  attr(logAllvcov, "estimates")     <- estimates
  attr(logAllvcov, "coef.indices")  <- coef.indices
  attr(logAllvcov, "factorname")    <- factorname
  attr(logAllvcov, "regularVar")    <- diag(covmat)
  attr(logAllvcov, "which.linpred") <- which.linpred

  logAllvcov
}  # End of Qvar()








WorstErrors <- function(qv.object) {
  stop("20110729; does not work")

  reducedForm <- function(covmat, qvmat) {
    nlevels <- dim(covmat)[1]
    firstRow <- covmat[1, ]
    ones <- rep_len(1, nlevels)
    J <- outer(ones, ones)
    notzero <- 2:nlevels
    r.covmat <- covmat + (firstRow[1]*J) -
                         outer(firstRow, ones) -
                         outer(ones, firstRow)
    r.covmat <- r.covmat[notzero, notzero]
    qv1 <- qvmat[1, 1]
    r.qvmat <- (qvmat + qv1*J)[notzero, notzero]
    list(r.covmat, r.qvmat)
  }
  covmat <- qv.object$covmat
  qvmat <- diag(qv.object$qvframe$quasiVar)
  r.form <- reducedForm(covmat, qvmat)
  r.covmat <- r.form[[1]]
  r.qvmat <- r.form[[2]]
  inverse.sqrt <- solve(chol(r.covmat))
  evalues <- eigen(t(inverse.sqrt) %*% r.qvmat %*% inverse.sqrt,
                   symmetric = TRUE)$values
  sqrt(c(min(evalues), max(evalues))) - 1
}




IndentPrint <- function(object, indent = 4, ...) {
  stop("20110729; does not work")

  zz <- ""
  tc <- textConnection("zz", "w", local = TRUE)
  sink(tc)
  try(print(object, ...))
  sink()
  close(tc)
  indent <- paste(rep_len(" ", indent), sep = "", collapse = "")
  cat(paste(indent, zz, sep = ""), sep = "\n")
}



Print.qv <- function(x, ...) {
  stop("20110729; does not work")

}




summary.qvar <- function(object, ...) {


  relerrs <- 1 - sqrt(exp(residuals(object, type = "response")))
  diag(relerrs) <- NA

  minErrSimple <- round(100 * min(relerrs, na.rm = TRUE), 1)
  maxErrSimple <- round(100 * max(relerrs, na.rm = TRUE), 1)



  estimates <- c(object@extra$attributes.y$estimates)
  if (!length(names(estimates)) &&
      is.matrix(object@extra$attributes.y$estimates))
    names( estimates) <-
      rownames(object@extra$attributes.y$estimates)
  if (!length(names(estimates)))
    names( estimates) <- param.names("Level", length(estimates))


  regularVar <- c(object@extra$attributes.y$regularVar)
  QuasiVar <- exp(diag(fitted(object))) / 2
  QuasiSE  <- sqrt(QuasiVar)


  structure(list(estimate = estimates,
                 SE            = sqrt(regularVar),
                 minErrSimple  = minErrSimple,
                 maxErrSimple  = maxErrSimple,
                 quasiSE  = QuasiSE,
                 object   = object,
                 quasiVar = QuasiVar),
            class = "summary.qvar")
}




print.summary.qvar <- function(x, ...) {

  object <- x$object
  minErrSimple  <- x$minErrSimple
  maxErrSimple  <- x$maxErrSimple

  x$minErrSimple <- NULL
  x$maxErrSimple <- NULL
  x$object <- NULL


  if (length(cl <- object@call)) {
      cat("Call:\n")
      dput(cl)
  }


  facname <- c(object@extra$attributes.y$factorname)
  if (length(facname))
    cat("Factor name: ", facname, "\n")


  if (length(object@dispersion))
    cat("\nDispersion: ", object@dispersion, "\n\n")

  x <- as.data.frame(c(x))
  print.data.frame(x)


    cat("\nWorst relative errors in SEs of simple contrasts (%): ",
        minErrSimple, ", ", maxErrSimple, "\n")

  invisible(x)
}




qvar <- function(object, se = FALSE, ...) {



  if (!inherits(object, "rcim") && !inherits(object, "rcim0"))
      warning("argument 'object' should be an 'rcim' or ",
              "'rcim0' object. ",
            "This call may fail.")

  if (!(object@family@vfamily %in% c("uninormal", "normal1")))
    warning("argument 'object' does not seem to have used ",
            "a 'uninormal' family.")

  if (!any(object@misc$link == "explink"))
    warning("argument 'object' does not seem to have used ",
            "a 'explink' link function.")

  quasiVar <- diag(predict(object)[, c(TRUE, FALSE)]) / 2
  if (se) sqrt(quasiVar) else quasiVar
}








plotqvar <-
qvplot   <-
  function(object,
           interval.width = 2,
           ylab = "Estimate",
           xlab = NULL,  # x$factorname,
           ylim = NULL,
           main = "",
           level.names = NULL,
           conf.level = 0.95,
           warn.ratio = 10,
           border = "transparent",  # None
           points.arg = TRUE,
           length.arrows = 0.25, angle = 30,
           lwd = par()$lwd,
           scol = par()$col,
           slwd = par()$lwd,
           slty = par()$lty,
           ...) {




  if (!is.numeric(interval.width) &&
      !is.numeric(conf.level))
    stop("at least one of arguments 'interval.width' and ",
         "'conf.level' ",
         "should be numeric")





  if (!any("uninormal" %in% object@family@vfamily))
    stop("argument 'object' dos not appear to be a ",
         "rcim(, uninormal) object")

  estimates <- c(object@extra$attributes.y$estimates)
  if (!length(names(estimates)) &&
      is.matrix(object@extra$attributes.y$estimates))
    names(estimates) <-
      rownames(object@extra$attributes.y$estimates)


  if (length(level.names) == length(estimates)) {
    names(estimates) <- level.names
  } else if (!length(names(estimates)))
    names(estimates) <- param.names("Level", length(estimates))




  QuasiVar <- exp(diag(fitted(object))) / 2
  QuasiSE  <- sqrt(QuasiVar)

  if (!is.numeric(estimates))
    stop("Cannot plot, because there are no 'proper' ",
          "parameter estimates")
  if (!is.numeric(QuasiSE))
    stop("Cannot plot, because there are no ",
         "quasi standard errors")



  faclevels <- factor(names(estimates), levels = names(estimates))


  xvalues <- seq(along = faclevels)
  tops  <- estimates + interval.width * QuasiSE
  tails <- estimates - interval.width * QuasiSE




  if (is.numeric(conf.level)) {
    zedd <- abs(qnorm((1 - conf.level) / 2))
    lsd.tops  <- estimates + zedd * QuasiSE / sqrt(2)
    lsd.tails <- estimates - zedd * QuasiSE / sqrt(2)
    if (max(QuasiSE) / min(QuasiSE) > warn.ratio)
      warning("Quasi SEs appear to be quite different... the ",
              "LSD intervals may not be very accurate")
  } else {
    lsd.tops  <- NULL
    lsd.tails <- NULL
  }




  if (is.null(ylim))
    ylim <- range(c(tails, tops, lsd.tails, lsd.tops),
                  na.rm = TRUE)

  if (is.null(xlab))
    xlab <- "Factor level"

  plot(faclevels, estimates,
       border = border,
       ylim = ylim, xlab = xlab, ylab = ylab,
       lwd = lwd,
       main = main, ...)


  if (points.arg)
    points(estimates, ...)


  if (is.numeric(interval.width)) {
    segments(xvalues, tails, xvalues, tops,
             col = scol, lty = slty, lwd = slwd)
  }


  if (is.numeric(conf.level)) {
    arrows(xvalues, lsd.tails, xvalues, lsd.tops,
           col = scol, lty = slty, lwd = slwd, code = 3,
           length = length.arrows, angle = angle)

  }




  if (any(slotNames(object) == "post")) {
    object@post$estimates  <- estimates
    object@post$xvalues    <- xvalues
    if (is.numeric(interval.width)) {
      object@post$tails <- tails
      object@post$tops  <- tops
    }
    if (is.numeric(conf.level)) {
      object@post$lsd.tails <- lsd.tails
      object@post$lsd.tops  <- lsd.tops
    }
  }


  invisible(object)
}