similar to: Linear Mixed Model set-up

Hi, I'm still having problems putting the variance components of my model in to a data frame, it is a continuation of this discussion, http://r.789695.n4.nabble.com/ANOVA-problem-td4609062.html, but now focussed on the problem of extracting variance components. I have got my mixed effects model now /narrow$line<-as.factor(narrow$line) rg.lmer <- lapply(split(narrow,

Hello, I am trying to use varcomp to decompose the variance across multiple nested levels on a lme object. I am able to successfully do this and when I view the varcomp object I can see the individual values / estimates for the variance at different levels. However, I want to be able to extract each of them separately, as I need to build a confidence interval using bootstrapping on the sample

Hi try str(varcompobject) to see structure of this object. You can extract parts by standard R means. Cheers Petr > -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Sharada > Ramadass > Sent: Tuesday, August 8, 2017 3:33 PM > To: r-help at r-project.org > Subject: [R] how to extract individual values from varcomp? > >

I am trying to use varcomp to obtain the variance partitioning across different nested levels of random effects (say x,y and z). I get the three variance components (for each of my along with an additional one called 'within' from varcomp output. I am using the 'scale total variance to 1' option and though the within component is small, it does form a part of what explains the

Hello everyone, I have a plot showing chloride concentrations for various point over time. I also have a dotted line that show the Secondary Maximum Contaminant Level (my screening limit) on the graphs at 250 mg/L. But I can not figure out how to include the dotted line / Secondary Maximum Contaminant Level in the legend. Any thoughts? My code is as following and is linked to my data on the

Dear all, I?m analyzing this dataset containing biodiversity indices, measured over time (Week), and at various contaminant concentrations (Treatment). We have two replicates (Replicate) per treatment. I?m looking for the effects of time (Week) and contaminant concentration (Treatment) on diversity indices (e.g. richness). Initial analysis with GAM models showed temporal autocorrelation of

Hi, I'm trying to fit a model using variance components in R, but if very new on it, so I'm asking for your help. I have imported the SPSS database onto R, but I don't know how to convert the commands... the SPSS commands I'm trying to convert are: VARCOMP RATING BY CHAIN SECTOR RESP ASPECT ITEM /RANDOM = CHAIN SECTOR RESP ASPECT ITEM /METHOD = MINQUE (1) /DESIGN

Hi! I'm comparing the differences in contaminant concentration between 2 different groups of people ( N=36, N=37). When using a simple linear regression model I found no differences between groups, but when evaluating the diagnostic plots of the residuals I found my independent variable to have deviations from normality (even after log transformation). Therefore I have used bootstrap on

Dear all, I'm using zeroinfl() from the pscl-package for zero inflated Poisson regression. I would like to calculate (aproximate) prediction intervals for the fitted values. The package itself does not provide them. Can this be calculated analyticaly? Or do I have to use bootstrap? What I tried until now is to use bootstrap to estimate these intervals. Any comments on the code are welcome.

Hi Everyone, I am using ASReml to fit a spatial model. I do not have all the components of ASReml when I call; names(summary()) e.g. names(summary(fcov.asr2)) [1] "call" "loglik" "nedf" "sigma" "varcomp" I am trying to get the coefs but I get "NULL". Does anybody know the reason? Any help would be much appreciated. Regards

I'm running simulation using lme and sometimes the estimated variance-covariance matrix is not positive definite so that the intervals function won't work for the random effect coefficients. I've tried varcomp from the ape package but this does not return all the coefficients. How can I extract the random effect coefficients without using intervals? Rick B.

Dear all, I'd like to remove the space between the x-axis and the 0 of the y-axis in the hist function. I saw the previous post https://stat.ethz.ch/pipermail/r-help/2012-September/324177.html suggesting adding the x-axis at position 0 (or the lowest value of y) after making the histogram. Unfortunately, it doesn't work in my case as I want to use it with a histogram with a ylim starting

Dear All, I need to calculate the variance components in a mixed effect model (one fixed and one random effect) with REML (maximizing the proportion of the likelihood that does not depend on the fixed effects). In S+ there is the varcomp function, but I would like to do it in R. Is there a way to do that? Thanks! Katalin ___ Katalin Csillery Division of Biological Sciences University of

Hi all, I have written a script in R that simulates genetically informative data - it is posted on my website and available to the public. This is my first time to write a script for use by others and am learning that it isn't as easy as it seems. To the issue. My script runs fine on my machine and on a server I have access to, but a user has written me saying that it crashes the first time

I am trying to understand better an analysis mean RT in various conditions in a within subjects design with the overall mean RT / subject as one of the factors. LME seems to be the right way to do this. using something like m<- lme(rt~ a *b *subjectRT, random= ~1|subject) and then anova(m,type = "marginal"). My understanding is that lme is an easy interface for dummy coding

Hi all I am trying to generate a normal unbalanced data to estimate the coefficients of LM, LMM, GLM, and GLMM and their standard errors. Also, I am trying to estimate the variance components and their standard errors. Further, I am trying to use the likelihood ratio test to test H0: sigma^2_b = 0 (random effects variance component), and the t-test to test H0:mu=0 (intercept of the model Yij = mu

On Tue, 2018-06-05 at 10:05 -0700, Nick Desaulniers wrote: > Functions marked extern inline do not emit an externally visible > function when the gnu89 C standard is used. Some KBUILD Makefiles > overwrite KBUILD_CFLAGS. This is an issue for GCC 5.1+ users as without > an explicit C standard specified, the default is gnu11. Since c99, the > semantics of extern inline have changed

On Tue, 2018-06-05 at 10:05 -0700, Nick Desaulniers wrote: > Functions marked extern inline do not emit an externally visible > function when the gnu89 C standard is used. Some KBUILD Makefiles > overwrite KBUILD_CFLAGS. This is an issue for GCC 5.1+ users as without > an explicit C standard specified, the default is gnu11. Since c99, the > semantics of extern inline have changed

>What happens if you make SPEEX_PREPROCESS_SET_ECHO_SUPPRESS_ACTIVE less >aggressive. Does it end up with too much echo or it just doesn't realise >that it's in double-talk conditions? My impression is that it does not make much difference on the timing to set this parameter less aggressive. Depending on the how loud the near end is talking it may detect double talk but most

Hi Jean-Marc > Can you explain what you mean here by "speech switching" By speech switching I mean the adaption of "gain2" when near-end or far-end is talking. What is important is that the timing is good and that the gain is low/high while far/near-end is talking. By timing I mean that the "gain2" should remain low until all far-end talk is final and that the