[R] customizing color key with plot3D

Hi, I am doing composite plots with the package plot3D. One of my variables is qualitative and indexed to integers, and I would like the legend for it to have labels located at the integer values (midpoints), and not at the breaks between classes. In the example below, the Elev Classes legend

Re: [R] customizing color key with plot3D

gton, USA > -Original Message----- > From: Karline Soetaert [mailto:karline.soeta...@nioz.nl] > Sent: Wednesday, June 21, 2017 4:16 AM > To: Waichler, Scott R > Subject: RE: customizing color key with plot3D > > There is an example in the colkey help file: > > exa

[R] plot3D color ramp not working as expected

Hi, I want to use a discrete color ramp with plot3D, and show NA values as white (default). I get unexpected results per the following. # as in help(slice3D) example: par(mfrow = c(2,2)) x <- y <- z <- seq(-1, 1, by = 0.1) grid <- mesh(x, y, z) colvar <- with(grid, x*exp(-x^2 - y^2 - z^2)) slice

[R] ggplot's aes_ doesn't work as expected for x=factor()

I'm learning how to use ggplot in a programming approach where I supply variable names on the fly. Using aes_ doesn't work as I expected when x = factor(x). Is this a bug or am I not understanding something? # toy dataset df <- data.frame(LogicalVar = c(FALSE, TRUE, FALSE, TRUE, FALSE, TRUE),

[R] write.table with append=T after using cat on same file

Hi, For years I've been writing text to the beginning of files with cat(append=F) , then following that text with data written by write.table(append=T). It is now giving me an error message. I'm using R-3.1.2. What gives? df <- data.frame(x = 1, y = 1:10, z = 10:1) cat(file="junk.txt", sep=

[R] Can't install rgl: installed package can't be loaded; 'memory not mapped'

Hi, I can't install package rgl. The last lines from the install process talking about the error are: ** testing if installed package can be loaded sh: line 1: 11949 Segmentation fault '/files3/R/R-3.2.1_install/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpQCpp6N/file2b115f4f8e1d'

Re: [R] Can't install rgl: installed package can't be loaded; 'memory not mapped'

> > Hi, I can't install package rgl. The last lines from the install process > > talking > about the error are: > > I'd guess you have an OpenGL problem. Does glxgears run? Yes, it does. I wasn't aware of the program before you mentioned it, but a display opens with 3 gears and here is some

[R] How to 2d cross sections from a 3d finite element mesh

Hi, I have a 3D finite element mesh where each element (cell) is defined by 8 vertices. Each element is a regular polyhedron. The overall domain is a block in shape, but its horizontal principal axes are not coincident with x and y (i.e. the domain is rotated about the z-axis). I want to pl

[R] seq() problem with chron

Hi, I encountered the problem below where the last value in the chron vector created with seq() should have a time of 15:30, but instead has 15:15. What causes this and how can I make sure that the last value in the chron vector is the same as the "to" value in seq()? library(chron) dt1 <- c

[R] plot one levelplot over another

Hi, I am using levelplot() to plot a primary response surface, z1. I wish to write a custom panel function that will let me plot another surface z2 = f(x,y) over z1. The second surface z2 is either NA or 1, and at locations where z2 = 1, I will use a color with low alpha to let the the z1 surf

[R] Using axis limits with plot3D

I would like to use the functions in the plot3D package but I am having trouble getting the axis limits to work correctly. The slices plotted by the code below go beyond the bounds of the persp box and obscure the axis information. How can I show just the part of the domain within x.limits and

[R] Reading chunks of data from a file more efficiently

Hi, I have some very large (~1.1 GB) output files from a groundwater model called STOMP that I want to read as efficiently as possible. For each variable there are over 1 million values to read. Variables are not organized in columns; instead they are written out in sections in the file, like

[R] how apply.monthly() in package xts works

Hi, I found that apply.monthly() in xts does not work as I expected in the case of a sparse timeseries: my.dates <- as.Date(c("1992-06-01", "1992-06-24", "1992-06-30", "1993-06-22", "1994-06-07", "1995-06-08")) my.xts <- xts(1:6, my.dates) start(my.xts) # "1992-06-24" end(my.xts) # "1995-06

[R] Output from as.windrose() in oce package baffles me

I'm having trouble understanding the output from as.windrose(). For one thing, data on a boundary between sectors seem to be left out of the counts. I assume that explains the missing point in the output below (angle 45). Shouldn't one side of each sector interval be open, to include values such

Re: [R] Output from as.windrose() in oce package baffles me

Dan, > May I ask you to report this as an issue on the oce webpage, > so that others can see the discussion? (The "R help" is > perhaps not the right place to report bugs ... and, yes, this > is a bug.) > http://code.google.com/p/r-oce/issues/list Yes, I will. > A possible solu

[R] Using contour3d: axes, plotting to file, with lattice

I am looking for examples of how to plot with contour3d() to a PNG or PDF file, add axes and other elements to the isosurface plot, and use contour3d in conjunction with lattice. Regarding lattice, I'm not necessarily looking for conditioning on the data shown in the isosurface plots, just a wa

Re: [R] Using contour3d: axes, plotting to file, with lattice

ection 4.4 will be very helpful to me. Scott Waichler Pacific Northwest National Laboratory P.O. Box 999, Richland, WA 99352 scott.waich...@pnl.gov 509-372-4423, 509-341-4051 (cell) > > luke > > On Thu, 11 Feb 2010, Waichler, Scott R wrote: > > > I am looking for e

[R] Screen settings for point of view in lattice and misc3d

I'm making some 3D plots with contour3d from misc3d and wireframe from lattice. I want to view them from below; i.e. the negative z-axis. I can't figure out how to do so. I would like my point of view looking up from below, with the z, y, and x axes positive going away. Can anyone tell me th

[R] Eliminate border in wireframe plot

How can I eliminate the border drawn by default around a wireframe plot? I've tried using border=NA and box=FALSE to no avail. Scott Waichler Pacific Northwest National Laboratory scott.waich...@pnl.gov __ R-help@r-project.org mailing list https://s

[R] Cut-aways with contour3d

Luke, Thanks for your previous advice on using misc3d; I've been able to get a good start with it. Most of my colleagues use Tecplot for graphing and are wondering if I can make "cut-aways" using R. An example is attached. The idea is show a 3D isosurface of one property together with a 2D c

[R] RPMs for R on the Redhat EPEL site

Martyn, > The maintainer of the RHEL RPMs no longer has an i386 machine > running EL4, and cross-building on an x86_64 machine did not > work, so I did not distribute them. > > As noted in a previous thread, there is a project to port the > Fedora R RPMs to Enterprise Linux: > > On Thursday 2

Re: [R] 3-D response surface using wireframe()

Regarding the screen argument in wireframe(), here is what I understand about how it works after much trial-and-error: After each rotation, new axes are in effect defined for the next rotation as at the start: x is to the right of the 2D view, y is towards the top, and z is positive out of the

[R] Binaries no longer compiled for RH EL4, i386?

I see that R 2.9.0 *.rpms have been compiled for RH EL5, i386 and x86_64, and also for EL4 x86_64, but not for EL4 i386. Is this an oversight or will that version no longer be compiled? Scott Waichler Pacific Northwest National Laboratory scott.waich...@pnl.gov __

[R] how to get xmlToList() to retry if http fails

Hi, I am using xmlToList() in a loop with a call to a webservice, per the code below. # Loop thru target locs for(i in 1:num.target.locs) { url <- paste(sep="/", "http://www.earthtools.org/timezone";, lat[i], lon[i]) tmp <- xmlToList(url) df$time.offset[i] <- tmp$offset sys

[R] vector field from a 3D scalar field

I have a 3D field of a scalar variable (x, y, z, value). Is there a way to generate a vector field from this data--gradient at defined points? I found the rasterVis package for 2D data, but as yet nothing for 3D data. Thanks, Scott Waichler Pacific Northwest National Laboratory Richland, WA sc

[R] problem with pip2d() from ptinpoly

Hi, pip2d() doesn't seem to work correctly for me. I have a plot of a triangle that a query point fits inside, but the point is defined as outside the polygon by pip2d. library(ptinpoly) verts <- matrix(c(594891,115309,59,117201,594891,117201), ncol=2, byrow=T) query <- matrix(c(594885.0

Re: [R] problem with pip2d() from ptinpoly

v2, Queries = query) > [1] 1 > > Cheers, > B. > > On 2014-04-18, at 6:00 PM, Waichler, Scott R wrote: > > > Hi, > > > > pip2d() doesn't seem to work correctly for me. I have a plot of a > triangle that a query po

[R] Using apply with more than one matrix

Hi, I want to apply a custom function to all the elements of one matrix. The function uses the value in the same i,j in a second matrix. How can I use apply() or similar function to avoid nested loops in i and j? Thanks, Scott Waichler Pacific Northwest National Laboratory Richland, WA, USA

Re: [R] Using apply with more than one matrix

n1[i,j] && length(ind.not.na) > 0) { ans[i,j] <- a1[i,j,ind.not.na[1]] + m2[i,j] } } } Scott Waichler > -Original Message- > From: Bert Gunter [mailto:gunter.ber...@gene.com] > Sent: Wednesday, April 30, 2014 12:18 PM > To: Waichler, Scott R > Cc: r-he

Re: [R] Using apply with more than one matrix

Here is a working example with no random parts. Thanks for your patience and if I'm still off the mark with my presentation I'll drop the matter. v <- c(NA, 1.5, NA, NA, NA, 1.1, 0.5, NA, NA, 1.3, 0.4, 0.9) a1 <- array(v, dim=c(2,2,3)) m1 <- matrix(c(NA, 1.5, 2.1, NA), ncol=2, by

Re: [R] Using apply with more than one matrix

if(length(ind.not.na) > 0) { return(condition1*(a1[idx,ind.not.na[1]] + m2[idx])) # doesn't work; improper indexing for a1 } } vec <- sapply(seq(length(m2)), evaluate) Scott Waichler > -Original Message- > From: David Winsemius [mailto:dwinsem...@comcast.net] >

Re: [R] Using apply with more than one matrix

> > Sapply or mapply may work, I haven't used these much and will try to > learn better how to use them. Your use of sapply looks good; but I'm > trying to understand if and how I can bring in the operation on a1. This > doesn't work: > > > > evaluate <- function(idx) { > > ind.not.na <- which(!

Re: [R] Using apply with more than one matrix

ow my computing will be more efficient. Thanks also to David and the others who responded to my question. It all helped. --Scott Waichler > -Original Message- > From: arun [mailto:smartpink...@yahoo.com] > Sent: Thursday, May 01, 2014 6:24 AM > To: R. Help > Cc: Waich

[R] How to find regions enclosed by edges within a TIF image

I am processing grayscale TIF images that represent X-rays of a sand- and gravel-filled tube. Each image represents a plane through the porous medium, and I need to classify each pixel in the image as void or solid. For the most part, voids are dark and solids are bright, but there are many gr

Re: [R] Alternative to interp.surface() offered

This is a correction to a post from 3/10/09. I just wanted to get this in the archive. It is the same thread as http://www.mail-archive.com/r-help@r-project.org/msg48762.html Thanks to Matt Oliver for bringing this to my attention. The correct code for my.interp.surface() follows. # A fun

[R] Can't get R to recognize Java for rJava installation

Hi, I am unable to install the package rJava. I tried doing what the output suggests, but it doesn't help. How can I get R to find/recognize my Java installation? I am running R-2.15.0. waichler@snow> sudo R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_22 Java home

Re: [R] Can't get R to recognize Java for rJava installation

Milan, Merci. I did find the javah file and put it in /usr/bin, where R can now find it. However, I still get a similar error message when trying to install rJava, i.e. configure: error: One or more Java configuration variables are not set. The only field that doesn't have a value now are t

[R] Can't read a binary file

Hi, I've read up on readBin() and chapter 6 in the R Data Import/Export manual, but I still can't read a binary file. Here is how the creator of the file described the code that would be needed in Fortran: "Every record has a return in fortran. The length of each record is nx*ny*4. To read y

[R] Parallel computing with rgenoud and snow: external file I/O possible?

I am trying to use rgenoud and snow with an external model and file I/O. Unlike the typical application of rgenoud and snow, I need to run an external executable and do pre- and post-processing of input and output files for each parameter set generated by genoud(). I'm hoping that someone can sugg

[R] Range of circular data

I want to get the minimum arc (in degrees) needed to include a set of compass directions. I would like to use the range.circular() function of the package circular, because that package understands a compass-type of angle convention, but it gives results I don't understand. Howver, I can get the

[R] Using aggregate() and apply() on circular data

I would like to use aggregate.ts() and apply() on circular data, but I can't figure out how to get the circular data components to pass through: library(circular) x <- circular(c(20, 30, 355, 5, 345, 25), units = "degrees") % I want to get the mean angle for each successive pair; answer should be

Re: [R] Creating smooth color regions with panel.contourplot()

Thank you very much, Deepayan. There is just one more feature I'd like to get, the ability to add the contour lines. My revision to your code below prints too many lines. What needs to be changed? --Thanks, Scott Waichler [EMAIL PROTECTED] library(gridBase) library(lattice) data(volcano) pa

Re: [R] Creating smooth color regions with panel.contourplot()

> > Thank you very much, Deepayan. There is just one more feature I'd > > like to get, the ability to add the contour lines. My revision to > > your code below prints too many lines. What needs to be changed? > You need to name arguments here. as.double(at) is being > matched to 'nlevels', b

Re: [R] Creating smooth color regions with panel.contourplot()

> Does the contour() solution work? If not, there's not really > much that can be done. Yes, I figured out how to add the naming of arguments. This works great: library(gridBase) library(lattice) data(volcano) panel.filledcontour <- function(x, y, z, subscripts, at, col.regions = cm.colors,

[R] Still no R-2.7.2 rpms for Redhat Enterprise Linux

There's already an announcement about R 2.8.0, and yet there are still no R-2.7.2 binaries (rpms) for Redhat Enterprise Linux 4 and 5. Can the usual responsible party get on it? Can the system be improved to get more timely builds out on CRAN? Thanks, Scott Waichler Pacific Northwest National La

[R] error installing lattice package

I just updated my Redhat EL systems to R-2.7.2, and tried to update my packages as well. Lattice is one that failed. What do I need to do? R version 2.7.2 (2008-08-25) > install.packages("lattice", repos = "http://cran.fhcrc.org/";) Warning in install.packages("lattice", repos = "http://cran.fh

Re: [R] error installing lattice package

> > I just updated my Redhat EL systems to R-2.7.2, and tried > to update my > > packages as well. Lattice is one that failed. What do I > need to do? > > Install the R-devel RPM? (Assuming you installed R from an RPM.) Yes, I installed R from an RPM. Installing the R-devel RPM worked on o

[R] Using an image background with graphics

I would like to use a map or aerial photo as a background to plotting solid lines and text, and semi-transparent color contours, in base and lattice graphics. Plot coordinates need to be consistent with the georeferenced background. For example, a color contour plot would have an gray-toned aeri

Re: [R] Using an image background with graphics

Greg, > The rimage package has functions for reading in and plotting > jpeg files that you could use for displaying the photograph. > If you then can find 2 points in the image (not on the same > horizontal or vertical line) for which you know the > coordinates in the coordinate system that y

Re: [R] Using an image background with graphics

Dr. Ripley, Thank you, yes, it's the anti-aliasing thing again. I'm using Redhat EL4, R-2.8.0, and pdf(). I had the problem with images displayed in xpdf, even with xpdf -aa no. I do not get the problem in Adobe Reader 7.0 for Linux. I'll try harder to remember this point. Scott Waichler Pac

[R] Alternative to interp.surface() offered

I wanted a simple function for bilinear interpolation on a 2-D grid, and interp.surface() in the fields package didn't quite suit my needs. In particular, it requires uniform spacing between grid points. It also didn't have the "visual" reference frame I was looking for. Here is an alternative f

[R] Using a background photo in lattice--title and axes missing

I am trying to use a background photo in a lattice plot. I am using the rimage and TeachingDemos packages to plot the photo and translate from the photo coordinates in pixels to geographic coordinates, which is what I want to use for plotting contours, lines, etc. The (unrunable) code below does

Re: [R] Using a background photo in lattice--title and axes missing

> I am trying to use a background photo in a lattice plot. I > am using the rimage and TeachingDemos packages to plot the > photo and translate from the photo coordinates in pixels to > geographic coordinates, which is what I want to use for > plotting contours, lines, etc. The (unrunable) co

[R] rimage doesn't install on Mac OS X 10.4

Hi, I'm trying to install rimage on a Mac OS X 10.4 machine. I followed the advice in previous R-help threads and got over the hurdles of having the header files in the right places, among other things. But I can't figure out what to do with this error. ice.pnl.gov:/home/waichler<949>system_pro

[R] plotting sf with lattice

Hi, I want to plot 2d cross sections from physical model output in a 3d domain, where the same cross section is represented at different times in the lattice panels. The cross section is a set of sf polygons, where one attribute is being plotted, with a color ramp. Can anyone point me to an