similar to: analyzing suvival data using splines (a.k.a., piecewise log-hazard-ratio models)

I'd like to generate on a single device multiple plots, each of which contains two plots. Essentially, I've got sub-plots which consist of two tracks, the upper one displaying gene expression data, and the lower one mapping position. I'd like to display four of these two-track sub-plots on one device, but I can't seem to invoke the par(mfrow=...) or layout(matrix(...)) functions at

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

Hello, I am interested in using nlme to model repeated measurements, but I don't seem to get good CIs. With the code below I tried to generate data sets according to the model given by equations (1.4) and (1.5) on pages 7 and 8 of Pinheiro and Bates 2000 (having chosen values for beta, sigma.b and sigma similar to those estimated in the text). For each data set I used lme() to fit a model,

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

Hi, I was reading a paper published in JCO "Prediction of risk of distant recurrence using 21-gene recurrence score in node-negative and node-positive postmenopausal patients with breast cancer treated with anastrozole or tamoxifen: a TransATAC study" (ICO 2010 28: 1829). The author uses a method to estimate the 9-year risk of distant recurrence as a function of continuous recurrence

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

Tom, Bingo! 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 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

Hi All, I'm using the party package to grow conditional inference trees for survival analysis. When I used party version party_0.9-9991 everything worked well, but when I update to party_1.0-2 (due to using 64bit R), I get an error. For simplicity I will show the error I get for the example in the party documentation: ### survival analysis if (require("ipred")) {

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 with the same R and rgl versions on CentOS 5.3 (see details below). The maintainer of rgl, Duncan Murdoch, responded (see below) that

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 }

I had to move my RedHat 5 box acting as a PDC to a new IP address. It is running samba 3.5.10. After the move, none of my windows or linux samba clients worked anymore. I tried rejoining some to the domain, but would get error Unable to find a suitable server Join to domain 'MRIRESEARCH' is not valid The old PDC IP address is 132.183.202.95 and nothing is at that IP anymore (for 4

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

Full_Name: Marek Ancukiewicz Version: 1.8.1 OS: Linux Submission from: (NULL) (132.183.12.87) Function cor() incorrectly handles missing observation with method="spearman": > x <- c(1,2,3,NA,5,6) > y <- c(4,NA,2,5,1,3) > cor(x,y,use="complete.obs",method="s") [1] -0.1428571 >

Dear all, I'd like to change a point pattern to a grid of cells and use one of the variables as the output. e.g. The point pattern is of a window of (500*500) and several features such as pH, SoilType etc. I like to divide it into a grid with cell size 5*5, and use the mean of the point values falling inside the cell as the output. Is there any package in R working with this? Thanks in

Right now we do a lot of hard to hard disk backup by using rsync to weekly "mirror" the source filesystem to a backup filesystem. This works fairly well for most sources. However, one issue with rsync is that simple things like changing the file name or directory name cause the whole file or directory structure to get recopied over a previous sync. Also, like for mail spools, large

Hi, I'm new to R and using it for Cox survival analysis. Thanks to this great forum I learned how to compute the HR with its confidence interval. My question would be: Is there any way to get the p-value for a hazard ratio in addition to the confidence interval? Thanks, Thierry -- Thierry Panje Visiting Student Researcher Department of Psychology Stanford

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

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