similar to: nlme: spatial autocorrelation on a sphere

Hello, I am having a problem specifying the correlation structure in lme which leads to the error: Error in getCovariate.corSpatial(object, data = data) : Cannot have zero distances in "corSpatial". I have specified a grouping variable which is the only fix I could find by searching this error on R-help. ISee the below example. When my samples (tran) - which are transects

I noticed that ?corClasses in package nlme does not list corSpatial among the standard classes. This might either be intentional because corSpatial is not "standard" , or it might be simply an oversight that needs correcting. ------------------------------------------ Robert W. Baer, Ph.D. Professor of Physiology Kirksville College of Osteopathic Medicine A. T. Still University of

Hi all, I am trying to compare two distance matrices with R. I would like to create a XY plot of these matrices and do some linear regression on it. But, I am a bit new to R, so i have a few questions (I searched in the documentation with no success). The first problem is loading a distance matrix into R. This matrix is the output of a the Phylip program Protdist and lookes like this: 5

Hi, I am trying to place my own functions in the nlme environment: The following statement works: environment(coef.corSPT) <- environment(getS3method("coef","corSpatial")) but this one returns an error: environment(get("coef<-.corSPT")) <- environment(getS3method("coef<-","corSpatial")) Error in

Dear listers, I am trying to model the distribution of fox density over years in the Doubs department. Measurements have been taken on 470 plots in March each year and georeferenced. Average density is supposed to be different each year. In a first approach, I would like to use a general model of this type, taking spatial correlation into account:

Dear list, If anyone knows how to assign dimnames to matrices or arrays I would be most grateful for help. I've tried various permutations of likely-looking code but get error messages every time. I could find no example in the documentation. Many thanks, Dan Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275000

Hello, I wonder if it is possible to change pxelinux.0's tftp prefix... I want to setup a repository like that: |-- dist1 | |-- pxelinux.cfg | | `-- default | `-- pxelinux.0 |-- dist2 | |-- pxelinux.cfg | | `-- default | `-- pxelinux.0 |-- pxelinux.cfg | |-- default | `-- menu.c32 `-- pxelinux.0 The file /pxelinux.cfg/default would contain something like that: >

Dear R community, I am analyzing plant communities with the function mvpart, using a dissimilarit matrix as input. The matrix is calculated with the funtion gdist. fit <- mvpart(gdist (ba12[,18:29], meth="maximum", full=TRUE, sq=F) ~ beers + slope_dem + elev_dem+ plc_dem + pr_curv+ +curv+max_depth+doc_rocks+ abandon+land_use+ca_old, data=ba12, xv="p") This

Is there anyway to label axes in 3D plots with mathematical expressions? In the code below, I want to replace "delta_yrsed" with what "\Delta \widehat{yrsed}" represents in TeX, but the [xyz]lab parameters of title3d appear to only accept character strings. require("rgl") fn.delta.yrsed <- function(dist, delta.dist,

Some notes on installing rgeos in R 2.14.0 on a Linux Mint 11 (x86_64-pc-linux-gnu) machine 1. rgeos 0.1-15 will not run with GEOS 3.2.0-1, which is the version currently available on Synaptic package manager 2. I installed GEOS 3.3.1 (the latest version) from http://trac.osgeo.org/geos/, but rgeos will not run with this either 3. I then install GEOS 3.2.3, and now rgeos works fine! It seems

Dear list, there are now >400 packages available on CRAN. Would it be useful to classify these packages according to what they do (e.g. classification, graphics, spatial statistics), to assist the user in finding the appropriate package for their problem? Or perhaps the search facility is enough. I would attempt such a classification, but my knowledge of statistical methods isn't good

Dear R list I have an m * n matrix P and a vector V of length n containing indices for rows in P. For each of the m columns I want to extract the value in the row specified by V, and put these values into a new vector W of length n. At present I am doing this with a for.... loop, but I imagine there is a faster way that doesn?t involve loops. If anyone knows the way I would be most grateful.

Hello, My data are numbers of trees in plots sampled in a number of forest stands. Some stands were subjected to a treatment, others not. Several plots were sampled per stand to get a better idea of what the stand means were, but replication is really at the stand level. Therefore I think this is a split-plot design. I would like to know whether the treatment affected the number of trees, so:

Hi, I'm new to R (and math ;) Would somebody please be so kind as to direct me in plotting a 3D sphere? I tried something in the lines of: #### y <- x <- seq(-pi, pi, length=pi*10) f <- function(x,y) { z <- sqrt(pi - x^2 - y^2) #z[is.na(z)] <- 0 z } z <- outer(x, y, f) persp(x, y, z, theta = 120, phi = 30) #### I've also tried: .... make.surface.grid(...) ..

Not an R question directly, but has anyone got a method for placing a moderately large number of (near) equi-spaced points on a sphere? I have a nasty feeling platonic solids are needed for exact solutions and I'm thinking of samplings involving around 200 - 1000 regularly-spaced points, Thanks, Richard Rowe Richard Rowe Senior Lecturer Department of Zoology and Tropical Ecology, James

Hello veryone, I am interested in the diffusion of particles inside a sphere, and its release through a small pore on the sphere surface. Unfortunately, I have not found the way to do this in R. Could you help me? Thank very much in advance for your help

I would like to extract predicted failure times from a coxph model in library(survival). However, none of the prediction options ("lp", "risk", "expected", "terms") seem to bear any relationship to failure time. Perhaps I am asking the wrong question, but can coxph provide predicted failure times? Thanks, Dan Bebber Department of Plant Sciences University

Hello, when I try to use the filled circle (pch = 16) in a Windows metafile, it appears highly pixelated rather than as a smooth vector. The other filled circles (pch = 19 and 20) are vector circles, filled with pixels. Results are the same whether I use windows() and save or copy as a metafile, or win.metafile() Also, some of the other symbols are misshapen, e.g. the diamond pch = 23 is not

Hello, I've just located the illuminating explanation by Douglas Bates on degrees of freedom in mixed models. The take-home message appears to be: don't trust the p-values from lme. Questions: Should I give up hypothesis testing for fixed effects terms in mixed models? Has my time spent reading Pinheiro & Bates been in vain? Is there a publication on this issue? Thanks, Dan Bebber

I am plotting subsets of my data, using ylim. This works fine, but the outer margin line widths of the plot are thin, due to clipping. If I include > trellis.par.set(clip=list(panel = "off")) then the outer margin line widths are fine, but the outlying data is visible. Is there any way of achieving both correct margin line widths and clipping of outlying data? Thanks, Dan Bebber