similar to: Importing packages in Depend

Hi, SETUP: Consider three packages PkgA, PkgB and PkgC. PkgA defines a generic function foo() and exports it; export(foo) PkgB imports PkgA::foo() and re-exports it; importFrom(PkgA, foo) export(foo) PkgC imports everything from PkgA and PkgB: imports(PkgA, PkgB) PROBLEM: Loading or attaching the namespace of PkgC will generate a warning: replacing previous import by

I'm testing out a new version of coxme and R CMD check fails with "could not find function ranef" (or random.effects or fixef, or anything from nlme). The NAMESPACE file has the line below importFrom(nlme, ranef, random.effects, fixef, fixed.effects, VarCorr) and nlme is declared in the DESCRIPTION file as an import. I feel that I must be staring at some obvious (but

On 16/02/2015 8:20 AM, Therneau, Terry M., Ph.D. wrote: > >> > I'm testing out a new version of coxme and R CMD check fails with "could not find function >> > ranef" (or random.effects or fixef, or anything from nlme). The NAMESPACE file has the >> > line below >> >> > importFrom(nlme, ranef, random.effects, fixef,

Hi all, I am currently doing a consistency analysis using an lmer model and trying to use parametric bootstrapping for the confidence intervals. My model is like this: model<-lmer(y~A+B+(1|C/D)+(1|E),binomial) where E is the individual level for consistency analysis, A-D are other fixed and random effects that I have to control for. Following Nakagawa and Scheilzeth I can work out the

If you are indeed using lme and not lmer then the needed function is VarCorr(). However, 2 recommendations. First, this is a busy list and better emails subject headers get better attention. Second, I would recommend using lmer as it is much faster. However, VarCorr seems to be incompatible with lmer and I do not know of another function to work with lmer. Hence, a better email subject header

I am having a problem extracting from "mer" objects.    I have constructed my problem using existing datasets.   Using the following commands:   require(lme4) fm1 <- lmer(Yield ~ 1 + (1 | Batch), Dyestuff) fixef(fm1) I get the following error message: "Error in UseMethod("fixef") : no applicable method for "fixef""   I know that "fixef" is in

Folks In trying to use lmer for a hierarchical model, I encountered the following message: Error in UseMethod("VarCorr") : no applicable method for 'VarCorr' applied to an object of class "mer" foo.mer <- lmer(y ~ TP + (TP|M),data=joe.q) > head(joe.q[,1:5]) TP M AB Trt y 1 1 Jan A NN 19.20002 2 1 Jan A NN 19.06378 3 1 Jan A NN

For a Monte Carlo study I need to extract from an lme model the estimated standard deviation of a random effect and store it in a vector. If I do a print() or summary() on the model, the number I need is displayed in the Console [it's the 0.1590195 in the output below] >print(fit) >Linear mixed-effects model fit by maximum likelihood > Data: datag2 > Log-likelihood:

User of the coxme library (mixed effects Cox models) are instructed to use ranef(), fixed(), VarCorr(), etc to retrieve bits out of a fitted model; it purposely uses the same methods as nlme and/or lmer. The current behavior is to "depend" on nlme. If I defined the methods myself in coxme, then someone who had both nlme and coxme loaded will suffer from "last loaded wins",

Hi all - (this is posted to r-help and R-SIG-MAC) OSX 10.3.7, R 2.0.1, lme4/Matrix/latticeExtra latest, fresh install of R. MASS loaded (or not). I am getting an error message for the print() and summary() commands with all lme models I try and run in lme4 (GLMM's work fine). Using the example from the lme help, summary and print produce the following errors, despite the model being

Dear list, I am having some problems with extracting Variance Components from a random-effects model: I am running a simple random-effects model using lme: model<-lme(y~1,random=~1|groupA/groupB) which returns the output for the StdDev of the Random effects, and model AIC etc as expected. Until yesterday I was using R v. 2.0, and had no problem in calling the variance components of the

I want to call summary on a mer object (from lme4) within my package but I can't seem to get the namespace to import the necessary method. I've simplified my package to this one function: --------------------------- ss <- function(m) { summary(m) } --------------------------- And my namespace file looks like this, where I've attempted to follow the instructions in "Writing

Hello I'm working with mixed effects models using lmer() and have some problems to get all variance components of the model's random effects. I can get the variance of the random effect out of the summary and use it for further calculations, but not the variance component of the residual term. Could somebody help me with that problem? Thanks a lot! Below an example. Aline ## EXAMPLE

I want to compute confidence intervals for the random effect estimates for each subject. From checking on postings, this is what I cobbled together using Orthodont data.frame as an example. There was some discussion of how to properly access lmer slots and bVar, but I'm not sure I understood. Is the approach shown below correct? Rick B. # Orthodont is from nlme (can't have both nlme and

HI, I would like to extract the variance components estimation in lme function like a.fit<-lme(distance~age, data=aaa, random=~day/subject) There should be three variances \sigma_day, \sigma_{day %in% subject } and \sigma_e. I can extract the \sigma_e using something like a.fit$var. However, I cannot manage to extract the first two variance components. I can only see the results in

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

Hi, I am trying to get bootstrap confidence intervals on variance components and related statistics. To calculate the variance components I use the package lme4. > off.fun <- function(data, i){ d <- data[i,] lme1<- lmer(y ~ trt + (trt-1|group), d) VarCorr(lme1)@reSumry$group[2,1] #just as an example } > off.boot <- boot(data=data.sim, statistic=off.fun, R=100) If

I have a question regarding the build of my project papeR (hosted on R-forge http://r-forge.r-project.org/R/?group_id=1574) with respect to lme4. Both, Windows and MacOS are complaining that lme4 doesn't export summary: Error : object 'summary' is not exported by 'namespace:lme4' ERROR: lazy loading failed for package 'papeR' Linux however builds the project

All, How does one extract the level-1 variance from a model fit via lmer()? In the code below the level-2 variance component may be obtained via subscripting, but what about the level-1 variance, viz., the 3.215072 term? (actually this term squared) Didn't see anything in the archives on this. Cheers, David > fm <- lmer( dv ~ time.num*drug + (1 | Patient.new), data=dat.new )

Dear all, I'm trying to store/extract the mean& standard error of the fixed effects parameter and the variance of the random effects parameter from "lmer" procedure from mlmre4 package developed by bates n pinheiro. while storing fixed effects parameter is straight forward, the same is not true for storing the variance parameter of the random effects. kindly help me ~prabhu