From noreply at r-forge.r-project.org  Wed Feb  3 21:00:58 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  3 Feb 2016 21:00:58 +0100 (CET)
Subject: [R-gregmisc-commits] r2072 - pkg/gdata/R
Message-ID: <20160203200058.86F78187D2D@r-forge.r-project.org>

Author: warnes
Date: 2016-02-03 21:00:57 +0100 (Wed, 03 Feb 2016)
New Revision: 2072

Modified:
   pkg/gdata/R/rename.vars.R
Log:
Improve logging and error reporting for remove.vars()

Modified: pkg/gdata/R/rename.vars.R
===================================================================
--- pkg/gdata/R/rename.vars.R	2015-11-24 17:58:02 UTC (rev 2071)
+++ pkg/gdata/R/rename.vars.R	2016-02-03 20:00:57 UTC (rev 2072)
@@ -44,14 +44,20 @@
 }
 
 
-# GRW 2004-04-01
 remove.vars <- function( data, names, info=TRUE)
+{
+  dsn <- deparse(substitute(data))
+  if (info) cat('\nChanging in',dsn, "\n")
+  
+  
+  flag <- names %in% colnames(data)
+  if(any(!flag))
+    warning("Variable(s) not found: ", paste(names[!flag], collapse=", ") )
+  if(any(flag))
   {
-    for( i in names )
-      {
-        if(info)
-          cat("Removing variable '", i, "'\n", sep="")
-        data[[i]] <- NULL
-      }
-    data
+    if(info) cat("Dropping variables:", paste(names[flag], collapse=", "), "\n\n")
+    for(var in names[flag])
+      data[[var]] <- NULL
   }
+  data
+}
\ No newline at end of file


From noreply at r-forge.r-project.org  Wed Feb  3 21:13:50 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  3 Feb 2016 21:13:50 +0100 (CET)
Subject: [R-gregmisc-commits] r2073 - in pkg/gdata: R man
Message-ID: <20160203201350.6DD80186BFF@r-forge.r-project.org>

Author: warnes
Date: 2016-02-03 21:13:49 +0100 (Wed, 03 Feb 2016)
New Revision: 2073

Modified:
   pkg/gdata/R/first.R
   pkg/gdata/man/first.Rd
Log:
Add assignment versions of first() and last()

Modified: pkg/gdata/R/first.R
===================================================================
--- pkg/gdata/R/first.R	2016-02-03 20:00:57 UTC (rev 2072)
+++ pkg/gdata/R/first.R	2016-02-03 20:13:49 UTC (rev 2073)
@@ -1,3 +1,16 @@
 # Simply call 'first' or 'last' with a different default value for 'n'.
 first <- function(x, n=1, ...) head(x, n=n, ...)
 last  <- function(x, n=1, ...) tail(x, n=n, ...)
+
+"first<-" <- function(x, n=1, ..., value )
+{
+  x[1:n] <- value[1:n]
+  x
+}
+
+"last<-" <- function(x, n=1, ..., value )
+{
+  index <- seq( length(x)-n+1, length(x) )
+  x[index] <- value[1:n]
+  x
+}

Modified: pkg/gdata/man/first.Rd
===================================================================
--- pkg/gdata/man/first.Rd	2016-02-03 20:00:57 UTC (rev 2072)
+++ pkg/gdata/man/first.Rd	2016-02-03 20:13:49 UTC (rev 2073)
@@ -1,6 +1,8 @@
 \name{first}
 \alias{first}
 \alias{last}
+\alias{first<-}
+\alias{last<-}
 \title{Return first or last element of an object}
 \description{
   Return first or last element of an object.  These functions are convenience
@@ -9,6 +11,8 @@
 \usage{
 first(x, n=1, ...)
 last(x, n=1, ...)
+first(x, n=1, ...) <- value
+last(x, n=1, ...) <- value
 }
 \arguments{
   \item{x}{data object}
@@ -17,6 +21,7 @@
           matrix or data frame or lines for a function. If negative,
           all but the 'n' last/first number of elements of 'x'.}
    \item{...}{arguments to be passed to or from other methods.}
+   \item{value}{a vector of values to be assigned (should be of length \code{n})}
 }
 \value{
   An object (usually) like 'x' but generally smaller.
@@ -36,20 +41,37 @@
 first(v)
 last(v)
 
+first(v) <- 9
+v
+
+last(v) <- 20
+v
+
 ## and for lists
 l <- list(a=1, b=2, c=3)
 first(l)
 last(l)
 
+first(l) <- "apple"
+last(l)  <- "bannana"
+l
+
 ## and data.frames
 df <- data.frame(a=1:2, b=3:4, c=5:6)
 first(df)
 last(df)
 
+first(df) <- factor(c("red","green"))
+last(df) <- list(c(20,30)) # note the enclosing list!
+df
+
 ## and matrixes
 m <- as.matrix(df)
 first(m)
 last(m)
 
+first(m) <- "z"
+last(m)  <- "q"
+m
 }
 \keyword{ manip }


From noreply at r-forge.r-project.org  Wed Feb  3 21:15:02 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  3 Feb 2016 21:15:02 +0100 (CET)
Subject: [R-gregmisc-commits] r2074 - in pkg/gdata: R man
Message-ID: <20160203201502.6D213186DFC@r-forge.r-project.org>

Author: warnes
Date: 2016-02-03 21:15:02 +0100 (Wed, 03 Feb 2016)
New Revision: 2074

Added:
   pkg/gdata/R/update.data.frame.R
   pkg/gdata/R/update.list.R
   pkg/gdata/man/update.list.Rd
Log:
Add update() methods for lists and data frames

Added: pkg/gdata/R/update.data.frame.R
===================================================================
--- pkg/gdata/R/update.data.frame.R	                        (rev 0)
+++ pkg/gdata/R/update.data.frame.R	2016-02-03 20:15:02 UTC (rev 2074)
@@ -0,0 +1,33 @@
+# This function replace rows in 'x' by corresponding rows in 'y' the have 
+# the same value for 'by'
+update.data.frame <- function(x, y, by, by.x=by, by.y=by, append=TRUE, verbose=TRUE, ...)
+{
+  retval <- x
+  x.by <- x[[by.x]]
+  y.by <- y[[by.y]]
+  
+  matches.x <- match(y.by, x.by)
+  matches.y <- which(!is.na(matches.x))
+  nomatch.y <- which(is.na(matches.x))
+  matches.x <- matches.x[!is.na(matches.x)]
+  
+  if(length(matches.x)>0)
+    retval[matches.x, ] <- y[matches.y,]
+  
+  if(length(nomatch.y) && append)  
+    retval <- rbind(retval, y[nomatch.y,])
+  
+  if(verbose)
+  {
+    cat("\n")    
+    cat("Number of rows in x     :", nrow(x),           "\n")
+    cat("Number of rows in y     :", nrow(y),           "\n")
+    cat("\n")
+    cat("Number of rows replaced :", length(matches.x), "\n")
+    cat("Number of rows appended :", length(nomatch.y), "\n")
+    cat("\n")
+    cat("Number of rows in result:", nrow(retval),      "\n")
+    cat("\n")
+  }
+  retval
+}

Added: pkg/gdata/R/update.list.R
===================================================================
--- pkg/gdata/R/update.list.R	                        (rev 0)
+++ pkg/gdata/R/update.list.R	2016-02-03 20:15:02 UTC (rev 2074)
@@ -0,0 +1,20 @@
+## this function updates the elements of list 'object' to contain all of the elements
+## of 'new', overwriting elements with the same name, and (optionally) copying unnamed
+## elements.
+update.list <- function(object, new, unnamed=FALSE, ...)
+{
+  retval <- object
+
+  for(name in names(new))
+    retval[[name]] <- new[[name]]
+
+  if(unnamed)
+  {
+    if(is.null(names(new)))
+      names(new) <- rep("", length=length(new))
+    for(i in (1:length(new))[names(new)==""] )
+        retval <- append(retval, new[[i]])
+  }
+
+  retval
+}
\ No newline at end of file

Added: pkg/gdata/man/update.list.Rd
===================================================================
--- pkg/gdata/man/update.list.Rd	                        (rev 0)
+++ pkg/gdata/man/update.list.Rd	2016-02-03 20:15:02 UTC (rev 2074)
@@ -0,0 +1,45 @@
+\name{update.list}
+\alias{update.list}
+\title{
+  Update the elements of a list
+}
+\description{
+ Function to update the elements of a list to contain all of the named elements
+ of a new list, overwriting elements with the same name, and (optionally) copying unnamed
+ elements.
+ }
+\usage{
+update.list(object, new, unnamed=FALSE, ...)
+\method{update}{list}(object, new, unnamed=FALSE, ...)
+}
+\arguments{
+  \item{object}{List to be updated.}
+  \item{new}{List containing new elements.}
+  \item{unnamed}{Logical. If \code{TRUE}, unnamed elements of \code{new} will be appended to \code{object}}
+}
+\note{
+  This method can be called directly, or as via the S3 base method for \code{update}.
+}
+\value{
+A constructed from the elements of \code{object}, with named elements of \code{new} replacing corresponding named elements from \code{object}, and non-corresponding elements of \code{new} appended.   If \code{unnamed=TRUE}, unnamed elements of \code{new} will be appended.
+}
+\author{
+Gregory R. Warnes \email{greg at warnes.net}
+}
+\seealso{
+\code{\link[stats]{update}}, \code{\link[base]{merge}}
+}
+\examples{
+old <- list(a=1,b="red",c=1.37)
+new <- list(b="green",c=2.4)
+
+update(old, new)
+update.list(old,new)  # equivalent
+
+older <- list(a=0, b="orange", 4, 5, 6)
+newer <- list(b="purple", 7, 8, 9)
+update(older, newer)               # ignores unnamed elements of newer
+update(older, newer, unnamed=TRUE) # appends unnamed elements of newer
+}
+\keyword{data}
+\keyword{manip}


From noreply at r-forge.r-project.org  Wed Feb  3 21:17:22 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  3 Feb 2016 21:17:22 +0100 (CET)
Subject: [R-gregmisc-commits] r2075 - pkg/gdata
Message-ID: <20160203201722.40C4C186DFC@r-forge.r-project.org>

Author: warnes
Date: 2016-02-03 21:17:21 +0100 (Wed, 03 Feb 2016)
New Revision: 2075

Modified:
   pkg/gdata/NAMESPACE
Log:
- Add update() methods list and data.frame
- Add 'first<-' and 'last<-' assignment methods



Modified: pkg/gdata/NAMESPACE
===================================================================
--- pkg/gdata/NAMESPACE	2016-02-03 20:15:02 UTC (rev 2074)
+++ pkg/gdata/NAMESPACE	2016-02-03 20:17:21 UTC (rev 2075)
@@ -14,12 +14,14 @@
        elem,
        env,
        first,
+       'first<-',
        frameApply,
        installXLSXsupport,
        interleave,
        is.what,
        keep,
        last,
+       'last<-',
        left,
        ll,
        ls.funs,
@@ -40,6 +42,8 @@
        trim,
        trimSum,
        unmatrix,
+       update.list,
+       update.data.frame,
        upperTriangle,
        "upperTriangle<-",
        wideByFactor,
@@ -164,4 +168,6 @@
 S3method(right, data.frame)
 S3method(right, matrix)
 
-
+# update methods for list, data.frame
+S3method(update, list)
+S3method(update, data.frame)


From noreply at r-forge.r-project.org  Fri Feb  5 18:30:08 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  5 Feb 2016 18:30:08 +0100 (CET)
Subject: [R-gregmisc-commits] r2076 - in pkg/gdata: R man
Message-ID: <20160205173008.BD623187D4D@r-forge.r-project.org>

Author: warnes
Date: 2016-02-05 18:30:08 +0100 (Fri, 05 Feb 2016)
New Revision: 2076

Added:
   pkg/gdata/R/mv.R
   pkg/gdata/man/mv.Rd
Log:
Add mv() function to rename an object.

Added: pkg/gdata/R/mv.R
===================================================================
--- pkg/gdata/R/mv.R	                        (rev 0)
+++ pkg/gdata/R/mv.R	2016-02-05 17:30:08 UTC (rev 2076)
@@ -0,0 +1,10 @@
+mv <- function(from, to, envir=parent.frame())
+{
+  if( !is.character(from) || !exists(from, envir=envir, inherits = TRUE) )
+    stop("`from` must be a character string specifying the name of an object.") 
+  if( !is.character(to)   ) 
+    stop("`to` must be a characater string.")
+  value <- get(from, envir=envir) 
+  assign(x=to, value=value, envir=envir)
+  rm(list=from, envir=envir)
+}
\ No newline at end of file

Added: pkg/gdata/man/mv.Rd
===================================================================
--- pkg/gdata/man/mv.Rd	                        (rev 0)
+++ pkg/gdata/man/mv.Rd	2016-02-05 17:30:08 UTC (rev 2076)
@@ -0,0 +1,37 @@
+\name{mv}
+\alias{mv}
+\title{
+  Rename an Object
+}
+\description{
+  Rename an object.
+}
+\usage{
+mv(from, to, envir = parent.frame())
+}
+\arguments{
+  \item{from}{Character scalar giving the source object name}
+  \item{to}{Character scalar giving the desination object name}
+  \item{envir}{Environment in which to do the rename} 
+}
+\details{
+  This function renames an object by the value of object \code{a} to the name \code{b}, and removing \code{a}.
+}
+\value{
+  Invisibly returns the value of the object.
+}
+\author{
+  Gregory R. Warnes \email{greg at warnes.net}
+}
+\seealso{
+  \code{\link[base]{rm}}, \code{\link[base]{assign}}  
+}
+\examples{
+  a <- 1:10
+  a
+  mv("a", "b")
+  b
+  exists("a")
+}
+\keyword{environment}
+\keyword{data}


From noreply at r-forge.r-project.org  Fri Feb  5 18:30:41 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  5 Feb 2016 18:30:41 +0100 (CET)
Subject: [R-gregmisc-commits] r2077 - pkg/gdata/man
Message-ID: <20160205173041.BD98F187D4D@r-forge.r-project.org>

Author: warnes
Date: 2016-02-05 18:30:41 +0100 (Fri, 05 Feb 2016)
New Revision: 2077

Modified:
   pkg/gdata/man/update.list.Rd
Log:
Add documentation for update() data.frame method.

Modified: pkg/gdata/man/update.list.Rd
===================================================================
--- pkg/gdata/man/update.list.Rd	2016-02-05 17:30:08 UTC (rev 2076)
+++ pkg/gdata/man/update.list.Rd	2016-02-05 17:30:41 UTC (rev 2077)
@@ -1,5 +1,6 @@
 \name{update.list}
 \alias{update.list}
+\alias{update.data.frame}
 \title{
   Update the elements of a list
 }
@@ -11,11 +12,13 @@
 \usage{
 update.list(object, new, unnamed=FALSE, ...)
 \method{update}{list}(object, new, unnamed=FALSE, ...)
+\method{update}{data.frame}(object, new, unnamed=FALSE, ...)
 }
 \arguments{
   \item{object}{List to be updated.}
   \item{new}{List containing new elements.}
   \item{unnamed}{Logical. If \code{TRUE}, unnamed elements of \code{new} will be appended to \code{object}}
+  \item{...}{optional method arguments (ignored)}
 }
 \note{
   This method can be called directly, or as via the S3 base method for \code{update}.


From noreply at r-forge.r-project.org  Fri Feb 26 20:58:25 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 26 Feb 2016 20:58:25 +0100 (CET)
Subject: [R-gregmisc-commits] r2078 - pkg/gplots/R
Message-ID: <20160226195825.1A985187331@r-forge.r-project.org>

Author: warnes
Date: 2016-02-26 20:58:24 +0100 (Fri, 26 Feb 2016)
New Revision: 2078

Modified:
   pkg/gplots/R/heatmap.2.R
Log:
- heatmap.2() can now be used to plot subsets of a previous heatmap.
- Remove stray 'browser()' debuggint statement from heatmap.2() code.
- Decrease the granularity of the carpet in heatmap.2()'s color key to
  avoid visual artifacts.


Modified: pkg/gplots/R/heatmap.2.R
===================================================================
--- pkg/gplots/R/heatmap.2.R	2016-02-05 17:30:41 UTC (rev 2077)
+++ pkg/gplots/R/heatmap.2.R	2016-02-26 19:58:24 UTC (rev 2078)
@@ -225,6 +225,7 @@
         stop("row dendrogram ordering gave index of wrong length")
     } else {
       rowInd <- nr:1
+      ddr <- as.dendrogram(Rowv)
     }
 
   ## if( dendrogram %in% c("both","column") )
@@ -273,6 +274,7 @@
   else
     {
       colInd <- 1:nc
+      ddc <- as.dendrogram(Colv)
     }
 
   retval$rowInd <- rowInd
@@ -627,7 +629,6 @@
   if(!is.null(main)) title(main, cex.main = 1.5*op[["cex.main"]])
 
   ## Add the color-key
-  browser()
   if(key)
     {
       mar <- c(5, 4, 2, 1)
@@ -655,7 +656,7 @@
           max.raw <- max.breaks
         }
 
-      z <- seq(min.raw, max.raw, by=min(diff(breaks)/4))
+      z <- seq(min.raw, max.raw, by=min(diff(breaks)/100))
       image(z=matrix(z, ncol=1),
             col=col, breaks=tmpbreaks,
             xaxt="n", yaxt="n")


From noreply at r-forge.r-project.org  Fri Feb 26 20:59:52 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 26 Feb 2016 20:59:52 +0100 (CET)
Subject: [R-gregmisc-commits] r2079 - in pkg/gplots: R man
Message-ID: <20160226195952.7D951187361@r-forge.r-project.org>

Author: warnes
Date: 2016-02-26 20:59:52 +0100 (Fri, 26 Feb 2016)
New Revision: 2079

Added:
   pkg/gplots/R/angleAxis.R
   pkg/gplots/man/angleAxis.Rd
Log:
New angleAxis() function to create axis labels with rotated text.

Added: pkg/gplots/R/angleAxis.R
===================================================================
--- pkg/gplots/R/angleAxis.R	                        (rev 0)
+++ pkg/gplots/R/angleAxis.R	2016-02-26 19:59:52 UTC (rev 2079)
@@ -0,0 +1,22 @@
+angleAxis <- function(side, labels, at=1:length(labels), srt=45, adj, xpd=TRUE, ...)
+{
+  usr <- par("usr")
+  emH <- strheight("M")
+  emW <- strwidth("M")
+  
+  if(missing(adj))
+    adj <- switch(side, 1, 1, 0, 0)
+  
+  switch(side,
+         #1 - below
+         text(x=at,           y=usr[3]-emH/2, labels=labels, srt=srt, adj=adj, xpd=xpd, ...), 
+         #2 - left
+         text(x=usr[1]-emW/2, y=at,           labels=labels, srt=srt, adj=adj, xpd=xpd, ...), 
+         #3 - above
+         text(x=at,           y=usr[4]+emH/2, labels=labels, srt=srt, adj=adj, xpd=xpd, ...), 
+         #4 - right
+         text(x=usr[2]+emW/2, y=at,           labels=labels, srt=srt, adj=adj, xpd=xpd, ...)
+  )       
+  
+  invisible(NULL)
+}
\ No newline at end of file

Added: pkg/gplots/man/angleAxis.Rd
===================================================================
--- pkg/gplots/man/angleAxis.Rd	                        (rev 0)
+++ pkg/gplots/man/angleAxis.Rd	2016-02-26 19:59:52 UTC (rev 2079)
@@ -0,0 +1,90 @@
+\name{angleAxis}
+\alias{angleAxis}
+\title{Add a Axis to a Plot with Rotated Labels}
+\description{
+Add a labeled axis to the current plot with rotated text
+}
+\usage{
+angleAxis(side, labels, at = 1:length(labels), srt = 45, adj, xpd = TRUE, ...)
+}
+\arguments{
+  \item{side}{
+    an integer specifying which side of the plot the axis is to be
+    drawn on. The axis is placed as follows: 1=below, 2=left, 3=above and 
+    4=right.
+    }
+  \item{labels}{character or expression vector of labels to be placed at the
+    tickpoints.
+    }
+  \item{at}{the points at which tick-marks are to be drawn. Non-finite
+    (infinite, NaN or NA) values are omitted.
+    }
+  \item{srt}{
+    The string rotation in degrees. Defaults to 45 degrees (clockwise).
+    }
+  \item{adj}{Text justification.  
+    A value of 0 produces left-justified text, 0.5 centered text and 1 
+    right-justified text. For \code{side=1} and \code{side=2}, the 
+    default value is \code{adj=1}.  For \code{side=3} and \code{side=4} 
+    the default value is \code{adj=0}.
+    }
+  \item{xpd}{A logical value or NA. If FALSE, labels are clipped to the 
+    plot region, if TRUE, labels are clipped to the figure region, and
+    if NA, labels are clipped to the device region.
+    }
+  \item{\dots}{optional arguments passed to \code{text}.  Common examples are \code{col}, \code{cex}.}
+}
+\details{
+This function augments the feature of the \code{axis} functon by allowing the axis labels to be rotated.
+}
+\author{Gregory R. Warnes \email{greg at warnes.net} }
+\seealso{
+\code{\link{axis}}
+}
+\examples{
+\dontshow{set.seed(42)}
+# create a vector with some values and long labels
+values <- sample(1:10)
+names(values) <- sapply(letters[1:10], 
+                        function(x) paste(rep(x, 10), sep="",collapse="") 
+                        ) 
+
+# barplot labels are too long for the available space, hence some are not plotted
+barplot(values)
+
+# to add angled labels, tell barplot not to label the x axis, and store the bar location
+at <- barplot(values, xaxt="n")
+# then use angleAxs
+angleAxis(1, at=at, labels = names(values))
+
+# angle counter-clockwise instead
+at <- barplot(values, xaxt="n")
+angleAxis(1, at=at, labels = names(values), srt=-45, adj=0)
+
+# put labels at the top
+oldpar <- par()$mar
+par(mar=c(1,4,5,2)+0.1)
+at <- barplot(values, xaxt="n")
+angleAxis(3, at=at, labels = names(values))
+par(oldpar)
+
+# put labels on the left
+oldpar <- par()$mar
+par(mar=c(5,5,3,2)+0.1)
+at <- barplot(values, yaxt="n", horiz=TRUE)
+angleAxis(2, at=at, labels = names(values))
+par(oldpar)
+
+# put labels on the right
+oldpar <- par()$mar
+par(mar=c(2,5,3,5)+0.1)
+at <- barplot(values, yaxt="n", horiz=TRUE)
+angleAxis(4, at=at, labels = names(values))
+par(oldpar)
+
+# specify colors for bars and labels
+at <- barplot(values, xaxt="n", col=1:10)
+angleAxis(1, at=at, labels = names(values), col=1:10)
+}
+\keyword{aplot}
+


From noreply at r-forge.r-project.org  Fri Feb 26 21:00:37 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 26 Feb 2016 21:00:37 +0100 (CET)
Subject: [R-gregmisc-commits] r2080 - pkg/gplots/R
Message-ID: <20160226200037.3AE9B187361@r-forge.r-project.org>

Author: warnes
Date: 2016-02-26 21:00:36 +0100 (Fri, 26 Feb 2016)
New Revision: 2080

Modified:
   pkg/gplots/R/venn.R
Log:
venn() now support matrix arguments.

Modified: pkg/gplots/R/venn.R
===================================================================
--- pkg/gplots/R/venn.R	2016-02-26 19:59:52 UTC (rev 2079)
+++ pkg/gplots/R/venn.R	2016-02-26 20:00:36 UTC (rev 2080)
@@ -26,6 +26,11 @@
     getVennCounts.list(l, universe=universe, verbose=verbose)
   }
 
+getVennCounts.matrix <- function(l, universe=NA, verbose=F, ...)
+{
+  getVennCounts.data.frame(as.data.frame(l), universe=NA, verbose=F, ...)
+}
+
 # l offers a list of arrays, their values are to
 # be tested for the size of their intersects.
 getVennCounts.list<-function(l, universe=NA, verbose=F, intersections=TRUE) {