filled.contour in R 3.0.x throws error - r

Question

I have a customized function for plotting filled contours which is heavily based on Carey McGilliard and Bridget Ferris work (http://wiki.cbr.washington.edu/qerm/sites/qerm/images/1/16/Filled.contour3.R) and http://wiki.cbr.washington.edu/qerm/index.php/R/Contour_Plots .
the filled.contour3 function runs perfectly in R 2.15.3 but throws an error in R 3.0.x
Error in .Internal(filledcontour(as.double(x), as.double(y), z, as.double(levels), :
there is no .Internal function 'filledcontour'
Could you please help me with a solution or a workarround so that I can use the filled.contour3() function in R 3.0.x . *A great deal of my work depends on this function and I am on LInux so changing R versions is not that easy on production machines. Will be happy to offer bounty.*
To reproduce the error please source first the following
filled.contour3 <-
function (x = seq(0, 1, length.out = nrow(z)),
y = seq(0, 1, length.out = ncol(z)), z, xlim = range(x, finite = TRUE),
ylim = range(y, finite = TRUE), zlim = range(z, finite = TRUE),
levels = pretty(zlim, nlevels), nlevels = 20, color.palette = cm.colors,
col = color.palette(length(levels) - 1), plot.title, plot.axes,
key.title, key.axes, asp = NA, xaxs = "i", yaxs = "i", las = 1,
axes = TRUE, frame.plot = axes,mar, ...)
{
# modification by Ian Taylor of the filled.contour function
# to remove the key and facilitate overplotting with contour()
# further modified by Carey McGilliard and Bridget Ferris
# to allow multiple plots on one page
if (missing(z)) {
if (!missing(x)) {
if (is.list(x)) {
z <- x$z
y <- x$y
x <- x$x
}
else {
z <- x
x <- seq.int(0, 1, length.out = nrow(z))
}
}
else stop("no 'z' matrix specified")
}
else if (is.list(x)) {
y <- x$y
x <- x$x
}
if (any(diff(x) <= 0) || any(diff(y) <= 0))
stop("increasing 'x' and 'y' values expected")
# mar.orig <- (par.orig <- par(c("mar", "las", "mfrow")))$mar
# on.exit(par(par.orig))
# w <- (3 + mar.orig[2]) * par("csi") * 2.54
# par(las = las)
# mar <- mar.orig
plot.new()
# par(mar=mar)
plot.window(xlim, ylim, "", xaxs = xaxs, yaxs = yaxs, asp = asp)
if (!is.matrix(z) || nrow(z) <= 1 || ncol(z) <= 1)
stop("no proper 'z' matrix specified")
if (!is.double(z))
storage.mode(z) <- "double"
.Internal(filledcontour(as.double(x), as.double(y), z, as.double(levels),
col = col))
if (missing(plot.axes)) {
if (axes) {
title(main = "", xlab = "", ylab = "")
Axis(x, side = 1)
Axis(y, side = 2)
}
}
else plot.axes
if (frame.plot)
box()
if (missing(plot.title))
title(...)
else plot.title
invisible()
}
filled.legend <-
function (x = seq(0, 1, length.out = nrow(z)), y = seq(0, 1,
length.out = ncol(z)), z, xlim = range(x, finite = TRUE),
ylim = range(y, finite = TRUE), zlim = range(z, finite = TRUE),
levels = pretty(zlim, nlevels), nlevels = 20, color.palette = cm.colors,
col = color.palette(length(levels) - 1), plot.title, plot.axes,
key.title, key.axes, asp = NA, xaxs = "i", yaxs = "i", las = 1,
axes = TRUE, frame.plot = axes, ...)
{
# modification of filled.contour by Carey McGilliard and Bridget Ferris
# designed to just plot the legend
if (missing(z)) {
if (!missing(x)) {
if (is.list(x)) {
z <- x$z
y <- x$y
x <- x$x
}
else {
z <- x
x <- seq.int(0, 1, length.out = nrow(z))
}
}
else stop("no 'z' matrix specified")
}
else if (is.list(x)) {
y <- x$y
x <- x$x
}
if (any(diff(x) <= 0) || any(diff(y) <= 0))
stop("increasing 'x' and 'y' values expected")
# mar.orig <- (par.orig <- par(c("mar", "las", "mfrow")))$mar
# on.exit(par(par.orig))
# w <- (3 + mar.orig[2L]) * par("csi") * 2.54
#layout(matrix(c(2, 1), ncol = 2L), widths = c(1, lcm(w)))
# par(las = las)
# mar <- mar.orig
# mar[4L] <- mar[2L]
# mar[2L] <- 1
# par(mar = mar)
# plot.new()
plot.window(xlim = c(0, 1), ylim = range(levels), xaxs = "i",
yaxs = "i")
rect(0, levels[-length(levels)], 1, levels[-1L], col = col)
if (missing(key.axes)) {
if (axes)
axis(4)
}
else key.axes
box()
}
#
# if (!missing(key.title))
# key.title
# mar <- mar.orig
# mar[4L] <- 1
# par(mar = mar)
# plot.new()
# plot.window(xlim, ylim, "", xaxs = xaxs, yaxs = yaxs, asp = asp)
# if (!is.matrix(z) || nrow(z) <= 1L || ncol(z) <= 1L)
# stop("no proper 'z' matrix specified")
# if (!is.double(z))
# storage.mode(z) <- "double"
# .Internal(filledcontour(as.double(x), as.double(y), z, as.double(levels),
# col = col))
# if (missing(plot.axes)) {
# if (axes) {
# title(main = "", xlab = "", ylab = "")
# Axis(x, side = 1)
# Axis(y, side = 2)
# }
# }
# else plot.axes
# if (frame.plot)
# box()
# if (missing(plot.title))
# title(...)
# else plot.title
# invisible()
#}
and then run
#Example Four Panel Contour Plot with One Legend
#Author: Carey R McGilliard
#September 2010
#This code uses a modified version of filled.contour called filled.contour3 (created by Carey McGilliard, Ian Taylor, and Bridget Ferris)
#to make an example figure of four contour plots sharing a legend (to the right).
#The example demonstrates how to use various color schemes for the contour plots and legend, but the user will want to
#pick one color scheme for all four plots such that the legend matches the plots.
#Changing the x- and y-axis values will change the placement of text added to the figure using the text() function and adjustments will be necessary
#Source the following functions (change the paths as necessary)
#source("./print.letterTrevor.R")
#gplots has the function colorpanel, which is handy for making gray-scale contour plots
library(gplots)
#------------------------------------------------------
#Generate some fake data
x = rep(c(10,11,12),length = 9)
y = rep(c(1,2,3),each = 3)
z = rnorm(n=9,mean = 0,sd = 1)
xcoords = unique(x)
ycoords = unique(y)
surface.matrix = matrix(z,nrow=length(xcoords),ncol=length(ycoords),byrow=T)
#------------------------------------------------------
#plot.new() is necessary if using the modified versions of filled.contour
plot.new()
#I am organizing where the plots appear on the page using the "plt" argument in "par()"
par(new = "TRUE",
plt = c(0.1,0.4,0.60,0.95), # using plt instead of mfcol (compare
# coordinates in other plots)
las = 1, # orientation of axis labels
cex.axis = 1, # size of axis annotation
tck = -0.02 ) # major tick size and direction, < 0 means outside
#Top left plot:
#
# the filled contour - coloured areas
filled.contour3(xcoords,
ycoords,
surface.matrix,
color=terrain.colors,
xlab = "", # suppress x-axis annotation
ylab = "", # suppress y-axis annotation
xlim = c(min(xcoords),max(xcoords)),
ylim = c(min(ycoords),max(ycoords)),
zlim = c(min(surface.matrix),max(surface.matrix))
)
# the contour part - draw iso-lines
contour(xcoords,
ycoords,
surface.matrix,
color=terrain.colors,
xlab = "",
ylab = "",
xlim = c(min(xcoords),max(xcoords)),
ylim = c(min(ycoords),max(ycoords)),
zlim = c(min(surface.matrix),max(surface.matrix)),
add=TRUE, # add the contour plot to filled-contour,
#thus making an overlay
col = grey(0.4) # color of overlay-lines
)
#
# An annotation inside first plot
#The xpd=NA allows for writing outside the plot limits, but still using the the x and y axes to place the text
par(xpd = NA)
text(x=11,y=1.5,"x",cex = 1.5,font = 2)
print.letter(text = "(a)")
######################################################################
#
#
#Top right plot:
par(new = "TRUE",
plt = c(0.5,0.8,0.60,0.95), # defining window for second plot
las = 1,
cex.axis = 1)
#
filled.contour3(
xcoords,
ycoords,
surface.matrix,
color=heat.colors,
xlab = "",
ylab = "",
xlim = c(min(xcoords),max(xcoords)),
ylim = c(min(ycoords),max(ycoords)),
zlim = c(-1,1)
)
#
contour(
xcoords,
ycoords,
surface.matrix,
xlab = "",
ylab = "",
xlim = c(min(xcoords),max(xcoords)),
ylim = c(min(ycoords),max(ycoords)),
zlim = c(-1,1),
add=TRUE
)
#
#Alternatively, you could set z axis limits to depend
#on the min and max values in surface.matrix.
#filled.contour3(xcoords,ycoords,surface.matrix,color=heat.colors,xlab = "",ylab = "",xlim = c(min(xcoords),max(xcoords)),ylim = c(min(ycoords),max(ycoords)),zlim = c(min(surface.matrix),max(surface.matrix)))
#
# Add annotation
text(x=11,
y=1.5,
"x",
cex = 1.5,
font = 2)
######################################################################
#
#Bottom left plot:
par(new = "TRUE",
plt = c(0.1,0.4,0.15,0.5),
las = 1,
cex.axis = 1)
#
filled.contour3(xcoords,
ycoords,
surface.matrix,
col=colorpanel(11, "white", "grey10"),
nlevels=11,
xlab = "",
ylab = "",
xlim = c(min(xcoords),max(xcoords)),
ylim = c(min(ycoords),max(ycoords)),
zlim = c(-1,1))
#
contour(xcoords,
ycoords,
surface.matrix,
xlab = "",
ylab = "",
xlim = c(min(xcoords),max(xcoords)),
ylim = c(min(ycoords),max(ycoords)),
zlim = c(-1,1),
add = TRUE)
#
text(x=11,
y=1.5,
"x",
cex = 1.5,
font = 2,
col = "white")
######################################################################
#
#Bottom right plot:
par(new = "TRUE",
plt = c(0.5,0.8,0.15,0.5),
las = 1,
cex.axis = 1)
#
filled.contour3(
xcoords,
ycoords,
surface.matrix,
color = terrain.colors,
xlab = "",
ylab = "",
xlim = c(min(xcoords),max(xcoords)),
ylim = c(min(ycoords),max(ycoords)),
zlim = c(-1,1)
)
#
contour(
xcoords,
ycoords,
surface.matrix,
xlab = "",
ylab = "",
xlim = c(min(xcoords),max(xcoords)),
ylim = c(min(ycoords),max(ycoords)),
zlim = c(-1,1),
add=TRUE
)
text(x=11,
y=1.5,
"hello",
cex = 1.5,
font = 2)
#
######################################################################
#Add a legend:
par(new = "TRUE",
plt = c(0.85,0.9,0.25,0.85), # define plot region for legend
las = 1,
cex.axis = 1)
#
filled.legend(
xcoords,
ycoords,
surface.matrix,
color = terrain.colors,
xlab = "",
ylab = "",
xlim = c(min(xintercepts),max(xintercepts)),
ylim = c(min(slopes),max(slopes)),
zlim = c(-1,1))
#Add some figure labels
par(xpd=NA,cex = 1.3)
text(x = -16.7,y = 0,"slope",srt = 90,cex = 1.3)
text(x = -8,y = -1.62,expression(paste(italic(x),"-intercept",sep = "")),cex = 1.3)

Answer 1

This happens if you use a non-standard API. You are allowed to do that, but cannot expect that it is maintained.
Change
.Internal(filledcontour(as.double(x), as.double(y), z, as.double(levels),
col = col))
to
.filled.contour(as.double(x), as.double(y), z, as.double(levels),
col = col)
The change was announced with the release notes:
The C code underlying base graphics has been migrated to the graphics
package (and hence no longer uses .Internal() calls).
Have you ever heard of a "minimal reproducible example" (emphasis on "minimal")?