search for: corstruct

...kage 'nlme' ... ** libs gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c corStruct.c -o corStruct.o In file included from matrix.h:25, from corStruct.c:25: base.h:27:28: error: S.h: No such file or directory base.h:43:20: error: nonlin.h: No such file or directory In file included from matrix.h:25, from corStruct.c:25: base.h:56: error: 'F77_...

...depend=TRUE), I get following error messages. Can someone help? I get similar messages for any package I try to compile. VR ------------- * Installing *source* package 'nlme' ... ** libs gcc -I/usr/share/R/include -I/usr/share/R/include -fvisibility=hidden -fpic -g -O2 -std=gnu99 -c corStruct.c -o corStruct.o In file included from base.h:29, from matrix.h:27, from corStruct.c:27: /usr/share/R/include/S.h:37:20: error: stdlib.h: No such file or directory /usr/share/R/include/S.h:38:19: error: stdio.h: No such file or directory In file included from /usr/...

dear list, I am wondering if one can find examples and/or more detailed descriptions of modifications needed when going beyond standard corStruct classes (i.e. those already provided for use in lme/nlme)? When I looked at pages 238-239 of Pinheiro/Bates (2000): Mixed-effects models in S and S-plus, I found that I would need a bit more explicit guidance what to do for implementing a new correlation structure than that presented there. I a...

...R-devel members, While writing a new correlation structure similar to 'corCompSymm' and intended to be used with 'gnls', I got puzzled with the 'Initialize' method. Using 'Initialize' before 'gnls' may be regarded as a mean to set an initial value for the corStruct parameter. However 'gnls' does not work properly with a 'corCompSymm' correlation structure when the data frame is not suitably ordered by group and when 'Initialize' is used for the corStruct before calling 'gnls'. Maybe the documentation could warn about this p...

...(sources) it gives 3.1-62 as Repository Version and 3.1-60 as Installed Version. When I try to update nlme, I get * Installing *source* package 'nlme' ... ** libs gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/usr/local/include -fno-common -g -O2 -c corStruct.c -o corStruct.o /var/tmp//ccOTBSDa.s:6088:** Removing '/Library/Frameworks/ R.framework/Versions/2.1.1/Resources/library/nlme' ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.1.1/ Resources/library/nlme' The downloaded packages are in /private/tmp/RtmpL1...

Hello, I would like to fit correlation structures with nlme, but R crashes. My data is similar to the "growth of orange trees" example from Pinheiro and Bates (2000), but data are not equally spaced in time, as the last observation is taken after 6 days ( and not 2 as the others). This is the code I'm using: library(nlme)

...====================== > install.packages("nlme") ((several lines removed)) * Installing *source* package 'nlme' ... ** libs i686-pc-linux-gnu-gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include -fvisibility=hidden -fPIC -O2 -mcpu=i686 -pipe -std=gnu99 -c corStruct.c -o corStruct.o cc1: error: unrecognized option `-fvisibility=hidden' make: *** [corStruct.o] Error 1 ERROR: compilation failed for package 'nlme' ============================================================== Here's my configuration: > uname -a > Linux conception.wustl.edu...

Hi, I'm fitting a relatively simple growth model to some forest plot data. Two species of trees were planted in different mixtures in 10 (nearly-adjacent) plots and measured on four occasions over 10 years. The model is constructed in terms of the diameter increments (per year; DI) in the 3 intervals, in which DI is modelled as a function of mid-interval D and DSQ. The details of the

...tion for missing values of the response variable in the model. I am trying to extract the within group correlation matrix or covariance matrix. here is my code: f = lme(y ~x0+x1+trt+tim+x1:tim +tim:trt,random=~-1|subj, data=dat,corr =corAR1()) > f$sigma [1] 2.330854 b=summary(f)$modelStruct$corStruct > b Correlation structure of class corAR1 representing Phi 0.8518711 I think 0.8518711 and f$sigma is what I need to reconstruct the variance-cavariance matrix. So, How can I extract 0.8518711 so that I can assign it to a variable? Also, I don't understand what the following parame...

...y) + 5*sin(t) + 2*g + a + r e <- round(e) df <- data.frame(x,y,g,a,t,r,e) library(nlme) # Define constructor function and methods corSPT <- function(a,b) { object <- list("time"=a,"space"=b) class(object) <- c("corSPT","corStruct") return(object) } coef.corSPT <- function(object,...) { c(coef(object[["time"]],...)[1],coef(object[["space"]],...)) } "coef<-.corSPT" <- function(object,...,value) { coef(object[["time"]]) <- value[1] coef(object[["space&quot...

...sometimes when the estimated Hessian matrix is not positive definite or something like that (i am not quite sure), the intervals function delivers an error message. Thus, i will like to ask if there is another way to access these values. I tried using the following code: hh$modelStruct$corStruct[1] hh$modelStruct$varStruct[1] Rather the output was: > hh$modelStruct$corStruct[1] [1] -1.308580 > hh$modelStruct$varStruct[1] [1] -0.03124255 I presume there is a way to calculate the correlation and variance function coefficients using these values. Could you tel...

...sometimes when the estimated Hessian matrix is not positive definite or something like that (i am not quite sure), the intervals function delivers an error message. Thus, i will like to ask if there is another way to access these values. I tried using the following code: hh$modelStruct$corStruct[1] hh$modelStruct$varStruct[1] Rather the output was: > hh$modelStruct$corStruct[1] [1] -1.308580 > hh$modelStruct$varStruct[1] [1] -0.03124255 I presume there is a way to calculate the correlation and variance function coefficients using these values. Could someone...

...l.dll building goes as follows, $ ./R CMD INSTALL --no-test-load nlme_3.1-97.tar.gz * installing to library 'C:/pfs/R/R-2.11.1/library' * installing *source* package 'nlme' ... ** libs ? making DLL ... gcc -I"C:/pfs/R/R-2.11.1/include"???????? -O3 -Wall? -std=gnu99 -c corStruct.c - o corStruct.o gcc -I"C:/pfs/R/R-2.11.1/include"???????? -O3 -Wall? -std=gnu99 -c gnls.c -o gnl s.o gcc -I"C:/pfs/R/R-2.11.1/include"???????? -O3 -Wall? -std=gnu99 -c init.c -o ini t.o gcc -I"C:/pfs/R/R-2.11.1/include"???????? -O3 -Wall? -std=gnu99 -c matrix.c -o m...

...stop("object \"phy\" is not of class \"phylo\"") attr(value, "formula") <- form attr(value, "fixed") <- TRUE attr(value, "tree") <- phy class(value) <- c("corBrownian", "corPhyl", "corStruct") value } <environment: namespace:ape> [[alternative HTML version deleted]]

Let me modify my question about user-defined covariance structures for LME models: Can somebody tell me how I can see the code for the definition of the correlation structures that come with the NLME package. Specifically I like to see the code for the functions coef, corMatrix, and intialize for any of the pre-defined correlation structures, and use this as a template to define a new correlation

A couple of questions: How to be sure that gls allowes errors to be correlated and/or have unequal variances? (is this on auto or is there a switch?) How to calculate confidence limits for a linear regresssion? -------------- next part -------------- A non-text attachment was scrubbed... Name: dthompson.vcf Type: text/x-vcard Size: 303 bytes Desc: Card for David Thompson Url :

Dear R-users, I hope you will have time to read me and I will try to be brief. I am also sorry for my poor english. I used gls function from the package nlme to correct two types of bias in my database. At first, because my replicates are spatially aggregated, I would like to fit a corStruct function like corLin, corSpher, corRatio, corExp or corGaus in my gls model, and simultaneously, because my response variable is an estimate, I would like to use weights to take into account the accuracy of the estimation. I used a varFixed object corresponding to squared standard error. Variog...

I am having trouble fitting correlation structures within nlme. I would like to fit corCAR1, corGaus and corExp correlation structures to my data. I either get the error "step halving reduced below minimum in pnls step" or alternatively R crashes. My dataset is similar to the CO2 example in the nlme package. The one major difference is that in my case the 'conc' steps are

...01 svn rev 43043 language R version.string R version 2.6.0 RC (2007-10-01 r43043) I have seen this in other versions/platforms as well. Brian Ripley informs me the segfault is in corStruct.c Code to reproduce: n <- 100 # example from Box and Jenkins p. 83 arcoefs <- c(0.8) macoefs <- c(-0.6) p <- length(arcoefs) q <- length(macoefs) require(nlme) tmp <- corARMA(value=c(arcoefs,macoefs), form=~1, p=p, q=q) Sigma <- corMatrix(tmp, covariate = 1:n) # segfault

Dear all, I am trying to define my own corStruct which is different from the classical one available in nlme. The structure of this correlation is given below. I am wondering to know how to continue with this structure by using specific functions (corMatrix, getCovariate, Initialize,...) in order to get a structure like corAR1, corSymm which...