R/0distrModUtils.R

In distrMod: Object Oriented Implementation of Probability Models

.isUnitMatrix <- function(m){
### checks whether m is unit matrix
              m.row <- nrow(m)
              isTRUE(all.equal(m, diag(m.row), check.attributes = FALSE))
              }

.deleteDim <- function(x){
     attribs <- attributes(x)
     attribs$dim <- NULL
     attribs$dimnames <- NULL
     attributes(x) <- attribs
     x
     }

.getLogDeriv <- function(distr,
             lowerTruncQuantile = getdistrExOption("ElowerTruncQuantile"), 
             upperTruncQuantile = getdistrExOption("EupperTruncQuantile"), 
                         IQR.fac = getdistrExOption("IQR.fac")){
  low0 <- q.l(distr)(lowerTruncQuantile)
  upp0 <- q.l(distr)(upperTruncQuantile,lower.tail=FALSE)
  me <- median(distr)
  s1 <- IQR(distr)
  low1 <- me - IQR.fac * s1 
  upp1 <- me + IQR.fac * s1 
  low <- max(low0,low1); upp <- min(upp0, upp1)
  xs <- seq(low, upp, length = getdistrOption("DefaultNrGridPoints"))
  m <- getdistrOption("DefaultNrGridPoints")%/%100+1
  dxs<- -d(distr)(xs, log = TRUE)
#  plot(xs, dxs,type="l")
  x1 <- xs[1]; xn <- (rev(xs)[1])
  f2xs <- approxfun(x = xs, y = D2ss(xs,dxs)$y, rule = 2)
  f2x1 <- f2xs(x1); f2xn <- f2xs(xn);
  f1xs <- approxfun(x = xs, y = D1ss(xs,dxs))
  f1x1 <- f1xs(x1); f1xn <- f1xs(xn);
  f3xs <- approxfun(x = xs, y = D2ss(xs,f1xs(xs))$y, rule = 1)
  f3x1 <- median(f3xs(xs[1:m])); f3xn <- median(f3xs(rev(xs)[1:m]));
#  windows()
#  plot(xs, f1xs(xs),type="l")
#  print(xn); print(x0); print(f3x1); print(f3xn); print(f1x1); print(f1xn); print(f2x1); print(f2xn);
  fxs <- function(x){
       f1x0 <- f1xs(x)
       dx1 <- (x[x<x1]-x1)
       dxn <- (x[x>xn]-xn)
       f1x0[x>xn] <- f1xn + f2xn*dxn + f3xn/2*dxn^2
       f1x0[x<x1] <- f1x1 + f2x1*dx1 + f3x1/2*dx1^2
       return(f1x0)}
  return(fxs)
}

.show.with.sd <- function(est, s){
#        est <- as.numeric(est); dim(est) <- NULL
#        s <- as.numeric(s); dim(s) <- NULL
        if(is.null(names(est))) names(est) <- rep("", length.out=length(est))
  ### code borrowed from print.fitdistr in  package MASS by B.D. Ripley
        digits <- getOption("digits")
        ans <- format(base::rbind(est, s), digits=digits)
        ans[1L, ] <- sapply(ans[1L, ], function(x) paste("", x))
        ans[2L, ] <- sapply(ans[2L, ], function(x) paste("(", x, ")", sep=""))
     ## only used for digits
        dn <- dimnames(ans)
        dn[[1L]] <- rep("", 2L)
        dn[[2L]] <- paste(substring("      ", 1L,
                       (nchar(ans[2L,]) - nchar(dn[[2L]])) %/% 2), dn[[2L]])
        dn[[2L]] <- paste(dn[[2L]], substring("      ", 1L,
                       (nchar(ans[2L,]) - nchar(dn[[2L]])) %/% 2))
        dimnames(ans) <- dn
        print(ans, quote = FALSE)
        return(invisible())
        }
 ### end of borrowed code  


.validTrafo <- function(trafo, dimension, dimensionwithN){
##checks whether trafo is valid
  ret <- FALSE
  if(!is.function(trafo)){
    if((ncol(trafo) != dimension) && (ncol(trafo) != dimensionwithN))
        stop("invalid transformation:\n", 
             "number of columns of 'trafo' not equal to ", 
             "dimension of the parameter")
#    if(nrow(trafo) > dimension)
#        stop("invalid transformation:\n",
#             "number of rows of 'trafo' larger than ",
#             "dimension of the parameter")
    if(any(!is.finite(trafo)))
        stop("infinite or missing values in 'trafo'")
    ret <- (ncol(trafo) == dimensionwithN)
    }
  return(ret)
}


#------------------------------------
#### utilities copied from package distr v.2.6  svn-rev 943
#------------------------------------
.inArgs <- function(arg, fct)
          {as.character(arg) %in% names(formals(fct))}

.isEqual <- function(p0, p1, tol = min( getdistrOption("TruncQuantile")/2,
                                          .Machine$double.eps^.7
                                          ))
                abs(p0-p1)< tol

.csimpsum <- function(fx){
 l <- length(fx)
 l2 <- l%/%2
 if (l%%2 == 0) {
     fx <- c(fx[1:l2],(fx[l2]+fx[l2+1])/2,fx[(l2+1):l])
     l <- l+1}
 f.even <- fx[seq(l) %% 2 == 0]
 f.odd  <- fx[seq(l) %% 2 == 1]
 fs    <- 2 * cumsum(f.odd) - f.odd - f.odd[1]
 fsm   <- 4 * cumsum(f.even)
 ff <- c(0,(fs[2:(l2+1)]+fsm)/3 )
 ff
}

.List <- function(list0) if(is.list(list0)) list0 else list(list0)

.fillList <- function(list0, len = length(list0)){
            if(is.null(list0)) return(vector("list",len))
            list0 <- .List(list0)
            if(len == length(list0))
               return(list0)
            i <- 0
            ll0 <- length(list0)
            li0 <- vector("list",len)
            if(ll0)
            while(i < len){
               j <- 1 + ( i %% ll0)
               i <- i + 1
               li0[[i]] <- list0[[j]]
            }
           return(li0)
}

.confqq <- function(x,D, datax = TRUE, withConf.pw  = TRUE,
                    withConf.sim = TRUE, alpha,
                    col.pCI, lty.pCI, lwd.pCI, pch.pCI, cex.pCI,
                    col.sCI, lty.sCI, lwd.sCI, pch.sCI, cex.sCI,
                    n,exact.sCI=(n<100),exact.pCI=(n<100), nosym.pCI = FALSE,
                    with.legend = TRUE, legend.bg = "white",
                    legend.pos = "topleft", legend.cex = 0.8,
                    legend.pref = "", legend.postf = "",
                    legend.alpha = alpha, qqb0=NULL, transf0=NULL, debug = FALSE){

   x <- sort(unique(x))
   if("gaps" %in% names(getSlots(class(D))))
       {if(!is.null(gaps(D)))
            x <- sort(unique(c(x, gaps(D))))
       }
   SI <- .SingleDiscrete(x,D)
#   print(SI)
   SI.in <- SI<4
   SIi <- SI[SI.in]
   SI.c <- SIi>0
   x.in <- x[SI.in]
   x.c <- x.in[SI.c]
   x.d <- x.in[!SI.c]
   tx.c <- if(is.null(transf0)) x.c else transf0(x.c)
   tx.d <- if(is.null(transf0)) x.d else transf0(x.d)


   qqb <- if(is.null(qqb0)) qqbounds(x,D,alpha,n,withConf.pw, withConf.sim,
                   exact.sCI,exact.pCI,nosym.pCI, debug) else qqb0

   qqb$crit <- qqb$crit[SI.in,]

   if(qqb$err["pw"]){
      if(sum(SI.c)>0){
         if(!datax){
            lines(tx.c, qqb$crit[SI.c,"pw.right"],
               col=col.pCI,lty=lty.pCI,lwd=lwd.pCI)
            lines(tx.c, qqb$crit[SI.c,"pw.left"],
               col=col.pCI,lty=lty.pCI,lwd=lwd.pCI)
         }else{
            lines(qqb$crit[SI.c,"pw.right"], tx.c,
               col=col.pCI,lty=lty.pCI,lwd=lwd.pCI)
            lines(qqb$crit[SI.c,"pw.left"], tx.c,
               col=col.pCI,lty=lty.pCI,lwd=lwd.pCI)
         }
      }
      if(sum(!SI.c)>0){
         if(!datax){
            points(tx.d, qqb$crit[!SI.c,"pw.right"],
               col=col.pCI, pch=pch.pCI, cex = cex.pCI)
            points(tx.d, qqb$crit[!SI.c,"pw.left"],
               col=col.pCI, pch=pch.pCI, cex = cex.pCI)
         }else{
            points(qqb$crit[!SI.c,"pw.right"], tx.d,
               col=col.pCI, pch=pch.pCI, cex = cex.pCI)
            points(qqb$crit[!SI.c,"pw.left"], tx.d,
               col=col.pCI, pch=pch.pCI, cex = cex.pCI)
         }
      }
   }
   if(qqb$err["sim"]){
      if(sum(SI.c)>0){
         if(!datax){
            lines(tx.c, qqb$crit[SI.c,"sim.right"],
               col=col.sCI,lty=lty.sCI,lwd=lwd.sCI)
            lines(tx.c, qqb$crit[SI.c,"sim.left"],
               col=col.sCI,lty=lty.sCI,lwd=lwd.sCI)
         }else{
            lines(qqb$crit[SI.c,"sim.right"], tx.c,
               col=col.sCI,lty=lty.sCI,lwd=lwd.sCI)
            lines(qqb$crit[SI.c,"sim.left"], tx.c,
               col=col.sCI,lty=lty.sCI,lwd=lwd.sCI)
         }
      }
      if(sum(!SI.c)>0){
         if(!datax){
            points(tx.d, qqb$crit[!SI.c,"sim.right"],
                col=col.sCI, pch=pch.sCI, cex = cex.sCI)
            points(tx.d, qqb$crit[!SI.c,"sim.left"],
                col=col.sCI, pch=pch.sCI, cex = cex.sCI)
         }else{
            points(qqb$crit[!SI.c,"sim.right"], tx.d,
                col=col.sCI, pch=pch.sCI, cex = cex.sCI)
            points(qqb$crit[!SI.c,"sim.left"], tx.d,
                col=col.sCI, pch=pch.sCI, cex = cex.sCI)
         }
      }
   }
   if(with.legend){
      if( qqb$err["pw"] ||  qqb$err["sim"] ){
         expression1 <- substitute(
            legpf~nosym0~"pointw."~ex.p~alpha==alpha0~"%- conf. interval"~legpof,
            list(legpf = legend.pref, legpof = legend.postf,
                 ex.p = if(exact.pCI) "exact" else "asympt.",
                 alpha0 = round(legend.alpha*100,2),
                 nosym0 = if(nosym.pCI&&exact.pCI) "shortest asymm." else "symm"))
         expression2 <- substitute(
            legpf~"simult."~ex.s~alpha==alpha0~"%- conf. interval"~legpof,
            list(legpf = legend.pref, legpof = legend.postf,
                 ex.s = if(exact.sCI) "exact" else "asympt.",
                 alpha0 = round(legend.alpha*100,2)))

         lcl <- list()
         if(!qqb$err["sim"]){
            expression3 <- expression1
            lcl$pch <- if(sum(!SI.c)>0) pch.pCI else NULL
            lcl$lty <- if(sum(SI.c)>0)  lty.pCI else NULL
            lcl$col <- col.pCI
            lcl$lwd <- if(sum(SI.c)>0)  2 else NULL
         }
         if(!qqb$err["pw"]){
            expression3 <- expression2
            lcl$pch <- if(sum(!SI.c)>0) pch.sCI else NULL
            lcl$lty <- if(sum(SI.c)>0)  lty.sCI else NULL
            lcl$col <- col.sCI
            lcl$lwd <- if(sum(SI.c)>0)  2 else NULL
         }
         if( qqb$err["pw"] && qqb$err["sim"]){
            expression3 <- eval(substitute(expression(expression1, expression2)))
            lcl$pch <- if(sum(!SI.c)>0) c(pch.pCI, pch.sCI) else NULL
            lcl$lty <- if(sum(SI.c)>0)  c(lty.pCI, lty.sCI) else NULL
            lcl$col <- c(col.pCI,col.sCI)
            lcl$lwd <- if(sum(SI.c)>0)  2 else NULL
         }
         do.call(legend, c(list(legend.pos, legend = expression3, bg = legend.bg,
                                merge = FALSE, cex = legend.cex), lcl))
      }
   }
  return(invisible(qqb))
}

.deleteItemsMCL <- function(mcl){
    mcl$datax <- mcl$n <- NULL
    mcl$col.IdL <- mcl$alpha.CI <- mcl$lty.IdL <-  NULL
    mcl$col.NotInSupport <- mcl$check.NotInSupport <- NULL
    mcl$exact.sCI <- mcl$exact.pCI <- NULL
    mcl$withConf <- mcl$withConf.sim <- mcl$withConf.pw <- NULL
    mcl$withIdLine <- mcl$distance <- NULL
    mcl$col.pCI <- mcl$lty.pCI <- mcl$col.sCI <- mcl$lty.sCI <- NULL
    mcl$lwd.IdL <- mcl$lwd.pCI <- mcl$lwd.sCI <- NULL
    mcl$withLab <- mcl$lab.pts <- mcl$which.lbs <- NULL
    mcl$which.Order <- mcl$order.traf  <- NULL
    mcl$col.pch <- mcl$cex.pch  <- mcl$jit.fac <- NULL
    mcl$col.lbl <- mcl$cex.lbl  <- mcl$adj.lbl <- NULL
    mcl$col.lbs <- mcl$cex.lbs  <- mcl$adj.lbs <- NULL
    mcl$exp.cex2.pch <- mcl$exp.cex2.lbl <- mcl$exp.cex2.lbs <- NULL
    mcl$exp.fadcol.pch <- mcl$exp.fadcol.lbl <- mcl$exp.fadcol.lbs <- NULL
    mcl$nosym.pCI <- mcl$n.CI <- mcl$n.adj <- NULL
    mcl$legend.cex <- mcl$with.legend <- mcl$legend.bg <- NULL
    mcl$legend.pos <- mcl$legend.pref <- mcl$legend.postf <- NULL
    mcl$legend.alpha <- NULL
    mcl$withSweave <- NULL
    mcl$mfColRow <- NULL
    mcl$debug <- mcl$with.lab <- mcl$MaxOrPOT <- NULL
    mcl$added.points.CI <- NULL
    mcl$pch.pts <- mcl$pch.npts <- mcl$cex.pts <- mcl$cex.npts <- NULL
    mcl$col.pts <- mcl$col.npts <- mcl$which.nonlbs <- mcl$attr.pre <- NULL
mcl}

## helpers
.inGaps <- function(x,gapm){
  if(is.null(gapm)) return(rep(FALSE,length(x)))
  fct <- function(x,m){ m[,2]>=x & m[,1]<=x}
  sapply(x, function(y) length(which(fct(y,gapm)))>0)
}

.isReplicated <- function(x, tol=.Machine$double.eps){
  tx <- table(x)
  rx <- as.numeric(names(tx[tx>1]))
  sapply(x, function(y) any(abs(y-rx)<tol))
}

.NotInSupport <- function(x,D){
  if(length(x)==0) return(logical(0))
  nInSupp <- which(x < q.l(D)(0))
  nInSupp <- unique(sort(c(nInSupp,which(x > q.l(D)(1)))))

  nInSuppo <-
      if("support" %in% names(getSlots(class(D))))
         which( ! x %in% support(D)) else numeric(0)
  if("gaps" %in% names(getSlots(class(D)))){
         InGap <- which( .inGaps(x,gaps(D)))
         if("support" %in% names(getSlots(class(D))))
            nInSupp <- unique(sort(c(nInSupp, intersect(InGap,nInSuppo))))
         else
            nInSupp <- unique(sort(c(nInSupp, InGap)))
  }else{
         nInSupp <- unique(sort(c(nInSupp, nInSuppo)))
  }
  return((1:length(x)) %in% nInSupp)
}

.SingleDiscrete <- function(x,D){
  ## produces a logical vector of
  ##     0  : discrete mass point
  ##     1  : within continuous support
  ##     2  : left gap point
  ##     3  : right gap point
  ##     4  : not in support
  lx <- x * 0

  lx[.NotInSupport(x,D)] <- 4

  idx.0 <- ((x>q.l(D)(1)) | (x<q.l(D)(0)))
  iG <- rep(FALSE,length(x))

  if(is(D, "DiscreteDistribution")){
     return(lx)
  }
  if("gaps" %in% names(getSlots(class(D)))){
     if(!is.null(gaps(D))){
        lx[apply(sapply(gaps(D)[,1], function(u) .isEqual(u,x)),1,any)] <- 2
        lx[apply(sapply(gaps(D)[,2], function(u) .isEqual(u,x)),1,any)] <- 3
        iG <- .inGaps(x,gaps(D))
        lx[!idx.0 & !iG] <- 1
     }else{
        lx[!idx.0 & !iG] <- 1
     }
  }
  if("support" %in% names(getSlots(class(D)))){
     idx <- x %in% support(D)
     if("acPart" %in% names(getSlots(class(D))))
         idx.0 <- ((x>q.ac(D)(1)) | (x<q.ac(D)(0)))
     lx[idx & (idx.0|iG)] <- 0
  }

  return(lx)
}


.makeLenAndOrder <- function(x,ord){
   n <- length(ord)
   x <- rep(x, length.out=n)
   x[ord]
}

#------------------------------------------------------------------------------
# .presubs : for titles etc
#------------------------------------------------------------------------------

.presubs <- function(inp, frompat, topat){
### replaces in an expression or a string all frompat patterns to topat patterns

logic <- FALSE
inCx <- sapply(inp,
   function(inpx){
      inC <- deparse(inpx)
      l <- length(frompat)
      for(i in 1:l)
         { if (is.language(topat[[i]])){
               totxt <- deparse(topat[[i]])
               totxt <- gsub("expression\\(", "\", ", gsub("\\)$",", \"",totxt))
               if (length(grep(frompat[i],inC))) logic <<- TRUE
               inC <- gsub(frompat[i],totxt,inC)
           }else inC <- gsub(frompat[i], topat[[i]], inC)
         }
      return(inC)
    })
if(length(grep("expression",inCx))>0)
   inCx <- gsub("expression\\(", "", gsub("\\)$","",inCx))
if (length(inCx) > 1) {
   inCx <- paste(inCx, c(rep(",", length(inCx)-1), ""),
                 sep = "", collapse = "\"\\n\",")
   if ( any(as.logical(c(lapply(inp,is.language)))) | logic )
      inCx <- paste("expression(paste(", gsub("\\\\n"," ", inCx), "))", sep ="")
   else
      inCx <- paste("paste(",inCx,")", sep ="")
}else inCx <- paste("expression(paste(",inCx,"))",sep="")
outC <- eval(parse(text = eval(inCx)))
return(outC)
}

.panel.mingle <- function(dots, element){
  pF <- dots[[element]]
  if(is.list(pF)) return(pF)
  pFr <- if(typeof(pF)=="symbol") eval(pF) else{
     pFc <- as.call(pF)
     if(as.list(pFc)[[1]] == "list"){
        lis <- vector("list",length(as.list(pFc))-1)
        for(i in 1:length(lis)){
            lis[[i]] <- pFc[[i+1]]
        }
        lis
     }else pF
  }
  return(pFr)
}


#---------------------------------------------------
### from packages stats:
#---------------------------------------------------
.format_perc <- function (probs, digits)
paste(format(100 * probs, trim = TRUE, scientific = FALSE, digits = digits),
    "%")