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...for that curve. A plot of this nature can also be found as figure 4 in Paik, et al., "A Multigene Assay to Predict Recurrence of Tamoxifen-Treated, Node-Negative Breast Cancer," 2004, New England Journal of Medicine, pp 2817-26. Any help would be greatly appreciated. Thanks. -Ben Ben Wittner Research fellow, MGH & Harvard Medical School wittner.ben at mgh.harvard.edu

Is there some fast (built-in?) way to get the OR of all the elements in a logical vector? In other words, is there some fast (built-in) version of the function vor below? Thanks. -Ben vor <- function(v) { ans <- v[1] if (length(v) > 1) for (i in 2:length(v)) ans <- ans | v[i] ans }

Hi, In the code below, the labels I put on the x-axis are too high (they cross the axis). Can anyone tell me how to move them down? I've tried adj=, padj=, mar=, and various other things, but cannot move them down. Thanks. -Ben labs <- paste('sample', 1:10) plot(1:10, xaxt='n', xlab='') axis(1, at=1:10, labels=labs, padj=1, las=2) # las is a par() parameter

Hello, As an example, I ran the following code: library("rgl") example(plot3d) rgl.snapshot("test.png") The full plot is visible in the window titled RGL device 1 [Focus], but only a small

Hello, As an example, I ran the following code: library("rgl") example(plot3d) rgl.snapshot("test.png") The full plot is visible in the window titled RGL device 1 [Focus], but only a small

...so that the nouveau driver might get fixed. I'll also post to R-help so someone with the same problem who only searches R-help and not this SIG will see the solution. -Ben -----Original Message----- From: Tom Callaway [mailto:tcallawa at redhat.com] Sent: Monday, January 11, 2016 4:10 PM To: Wittner, Ben, Ph.D.; r-sig-fedora at r-project.org Cc: Duncan Murdoch Subject: Re: [R-sig-Fedora] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7 I have not tried it personally, but these instructions seem correct: http://www.dedoimedo.com/computers/cent...

I would like to plot points in 3D and then be able to rotate the plot in real time in order to understand the distribution of the points using the visual parallax that results from the rotation. The R-package scatterplot3d will plot in 3D, but I've not found a way to rotate the results in real time. (It also does not seem to get the projection from 3D to a viewing plane right.) The R-package

...nd compare Gaussian linear and nonlinear mixed-effects models. Depends: graphics, stats, R (>= 2.4.0) Imports: lattice LazyLoad: yes LazyData: yes License: GPL (>=2) Packaged: Thu Oct 4 23:25:21 2007; hornik Built: R 2.6.0; i686-pc-linux-gnu; 2007-12-26 15:48:00; unix -- File: /home/bwittner/R-2.6.0/library/nlme/DESCRIPTION > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 6.0 year 2007 month 10 day 03 svn rev 43063 languag...

R-packages leaps and subselect implement various methods of selecting best or good subsets of predictor variables for linear regression models, but they do not seem to be applicable to logistic regression models. Does anyone know of software for finding good subsets of predictor variables for linear regression models? Thanks. -Ben p.s., The leaps package references "Subset Selection

..., and glReadPixels, which seem to be functions in the OpenGL library. Can anyone take a look at this or advise me on how to proceed? Thanks very much in advance. -Ben -----Original Message----- From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] Sent: Friday, January 08, 2016 8:13 PM To: Wittner, Ben, Ph.D.; r-help at r-project.org Subject: Re: [R] rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7 On 08/01/2016 4:13 PM, Wittner, Ben, Ph.D. wrote: > Hello, > > As an example, I ran the following code: > > library("rgl&quot...

Short form: How do I transform the output of grid.locator() (or grid.locator(unit='npc')) to the native (or npc) coordinates of a viewport other than the top-level viewport? Thanks in advance. -Ben Long form: I would like the user to be able to click anywhere on the R graphics window. I would then like to figure out which leaf viewport the user clicked in and compute the native

Some time ago I tried to find out how to compute remainders in R. I now know that it is done with %%, which is documented in help('+'), but before someone told me that I tried: help('remainder'), help.search('remainder'), apropos('remainder') help('modulo'), help.search('modulo'), and apropos('modulo') all of which yielded nothing. I then

Tom, > Okay. I do "official" package builds of R for RHEL/CentOS as part of the EPEL repository: > https://fedoraproject.org/wiki/EPEL > If its not painful for you to do so, testing my packages vs yours just to rule out misconfiguration in R would be > helpful. I don't think this is likely, but I'm being thorough. I've now tried the EPEL version of R and it

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value

I recently upgraded my OS to Fedora 8 from Red Hat Enterprise Work Station 3. Before I upgraded certain operations would produce a warning to the effect that a desired font was not available so one had been substituted, which was okay. After the upgrade to Fedora 8, the plotting operation halts midway through and I get the following error message: "X11 font at size 6 could not be loaded"

On 01/11/2016 10:55 AM, Wittner, Ben, Ph.D. wrote: > Dear R-SIG-Fedora, > > I'm finding that on CentOS 7, rgl.snapshot (a function in the R package rgl, which provides an R interface to the OpenGL 3-d graphics library) only captures a small portion what's visible in the RGL device window. This does not happen wi...

On 01/11/2016 01:24 PM, Wittner, Ben, Ph.D. wrote: > Dear Tom, Thank you very much for thinking about this. Please see my replies below. -Ben > >> Are you using the EPEL R 3.2.3 builds? > > I'm not sure what the question means, but I'm pretty sure the answer is no. I know I built the versions of R I us...

On 01/11/2016 03:52 PM, Wittner, Ben, Ph.D. wrote: > I started trying to do this, but I'm stuck. > I started with http://us.download.nvidia.com/XFree86/Linux-x86_64/340.96/README/installdriver.html , which led me to http://us.download.nvidia.com/XFree86/Linux-x86_64/340.96/README/commonproblems.html#nouveau . I created...

On 01/11/2016 05:13 PM, Wittner, Ben, Ph.D. wrote: > I followed the instructions in the link below, which allowed me to install the nvidia driver, which fixed the original problem with rgl.snapshot. > > Thanks very much for all your help. > > I guess I'll file a bug in the CentOS Bug Tracker so that the nouve...

Does anyone know how to make a plot like Fig. 4 of Paik, et al., New England Journal of Medicine, Dec. 30, 2004? Given survival data and a covariate, they plot a curve giving "Rate of Distant Recurrence at 10 Yr (% of patients)" on the y-axis versus the covariate on the x-axis. They also plot curves giving a 95% confidence interval. Thanks very much. -Ben The information in this