similar to: Problem with specifying variance-covariance matrix for random effects (nlme package)

is there any existing function for computing condition index? " analysing multivariate data" say that we can use condition index to check multicollinearity.saying that we can get it via SVD. The elements of the diagnoal matrix are the standard deviations of the uncorrelated vectors. the condition index is the ratio of the largest of these numbers to the smallest. so if i have a data

I would appreciate confirmation that the function vcov(model.nlme) gives the var-cov matrix of the fixed effects in an nlme model. Presumably the random-effects var-cov matrix is given by cov(ranef (model.nlme)? Rob Forsyth

I want to extract the variance-covariance matrix of an nlme model of a dataset. The object is to pass this to mvrnorm to create pseudo- replicates of the original data. I note the nlme package has a getVarCov method available for lme objects but not nlme objects. Is the vcov function in the base stats package suitable? If so, why is the additional getVarCov provided? thank you Rob

Hi, How extract the Variance and Covariance Matrices D of random effects and R of error in the lme object? Thanks in advance. Alexandre Galv??o

Dear R team, I would like to do a multivariate meta-analysis in R using the nlme package. In meta-analysis I fix the residuals to known sampling errors. As I do a multivariate analysis, I have a variance-covariance matrix of sampling errors. Unfortunately, via varFixed I can only fix a vector of sampling errors and no matrix. In the R package metafor using the rma.mv function I can insert the

-- Dear R users, I have data on around 2000 birds from 3 generations for which I know an individual's pedigree (i.e. the relationship it shares with other individuals e.g brother, uncle, mother) and also a pedigree based on foster-families, because half broods were removed from their nest of origin and placed in a foster parent's nest. From this I want to model two types of random

Dear all, I am estimating a mixed-model in Ubuntu Raring (13.04¸ amd64), with the code: fm0 <- lme(rt ~ run + group * stim * cond, random=list( subj=pdSymm(~ 1 + run), subj=pdSymm(~ 0 + stim)), data=mydat1) When I check the approximate variance-covariance matrix, I get: > fm0$apVar [1] "Non-positive definite

Sorry for attaching patches in emails to the mailing list, but I''m still unable to login to Devjavu for Backgroundrb (I''m able to login just fine for Merb''s Devjavu and submitted a ticket successfully). Anyway, I encountered a bug when trying to #ask_status of a worker before it''s run (or rather, before its result_hash has been set to something). Not sure why

Hello, has someone written by chance a function to extract the variance-covariance matrix from a lmer-object? I've noticed the VarCorr function, but it gives unhandy output. Regards, Roel de Jong

Hi guys! I have a problem regarding a binary logistic hierarchical model I am trying to use. The model contains various covariates that depend on the location the response was measured at but do not depend on time (year). I also have a spatial covariate that depends both on location and time. I have been trying to use the lme4 pack but the package only allows me to model variance covariance

Dear R users, I have a question about the patterned variance-covariance structure for the random effects in linear mixed effect model. I am reading section 4.2.2 of "Mixed-Effects Models in S and S-Plus" by Jose Pinheiro and Douglas Bates. There is an example of defining a compound symmetry variance-covariance structure for the random effects in a split-plot experiment on varieties of

Using lmer in the lme4 package, you can compute the conditional variance-covariance matrix of the random effects using the bVar slot: bVar: A list of the diagonal inner blocks (upper triangles only) of the positive-definite matrices on the diagonal of the inverse of ZtZ+Omega. With the appropriate scale factor (and conversion to a symmetric matrix) these are the conditional variance-covariance

Hi, does anyone know which of the scaled or unscaled version of the variance-covariance matrix of regression coefficients (as produced by ls.diag) is the correct one, or when one is better than the other? I am interested in univariate linear regression (lm). Thank you very much. Dipl.-Psych. Johannes Ullrich Philipps-Universit?t Marburg Fachbereich

Hello R list subscribers, I am trying to use the "by" command to create line-specific variance covariance matrices (where "x" is the original data matrix): by(x, x$line, function(d) { d.clean <- d[,-1]}) write.table(d.clean$line[1,1], sep = ",", file = "covariances.csv", col.names = FALSE, row.names = FALSE, append = TRUE) write.table("", sep

Dear R helpers Suppose I have a portfolio of securities with exposure to Equity, Bonds and Forex (say $ 1000000 each). Is there any fucntion in R that will help me calculate Value at Risk (VaR) using Monte carlo Simulation , Historic simulation and Variance - Covariance Simulation. With regards Maithili

Dear All, I am currently working with the coxph function within the package survival. I have the model h_ij = h_0(t) exp(b1x1 + b2x2) where the indicator variables are as follows: x1 x2 VPS 0 0 LTG 1 0 TPM 0 1 [[alternative HTML version deleted]]

Hello folks! I'm using R-Package {vars} and I'm trying to estimate an A-Model. I have serious problems regarding the restrictions. 1) My A-Matrix needs (!) to have the following form: # 1 NA NA NA # 0 1 NA NA # 0 0 1 NA # 0 0 0 1 That is done in R by: A_Matrix <- diag(4) # main diagonal = 4 restrictions A_Matrix [1, 2] <- NA # A_Matrix [1, 3] <- NA #

Hi, I am running a simple linear model with (say) 5 independent variables. Is there a simple way of getting the variance-covariance matrix of the coeffcient estimates? None of the values of the lm() seem to provide this. Thanks in advance, Ritwik Sinha rsinha@darwin.cwru.edu Grad Student Case Western Reserve University [[alternative HTML version deleted]]

Hi, How can I recover the variance-covariance matrix of the tobit model from the variance-covariance of the survreg? I first used to the survreg function and then I selected the variance matrix. However, the last parameter is log(scale) and not the variance of the standard deviation of the censored distribution as in the Tobit model. tobit<- survreg(Surv(y, y > 0, type ='left')~

Suppose I have a Variance-covariance matrix A. Is there any fast way to calculate correlation matrix from 'A' and vice-versa without emplying any 'for' loop? [[alternative HTML version deleted]]