similar to: Imports problem

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

> > 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

The coxme package has a ranef() method, as does lme4. I'm having trouble getting them to play together, as shown below. (The particular model in the example isn't defensible, but uses a standard data set.) The problem is that most of the time only one of lme4 or coxme will be loaded, so each needs to define the basic ranef function as well as a method for it. But when loaded together

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",

>>>>> Therneau, Terry M , Ph D <therneau at mayo.edu> >>>>> on Sun, 15 Feb 2015 17:31:00 -0600 writes: > 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 >

Version 2.2 of coxme has been posted to CRAN, Windows versions and mirrors should appear in due course. This is a major update with three features of note: 1. A non-upwardly compatable change: Extractor functions: beta= fixed effects, b=random effects nlme lme4 coxme <2.2 coxme 2.2 lmekin 2.2 ------------------------------------------------------ beta

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

The change has also been made to coxme. I'm in the midst of another fix (should be done by tomorrow) and will get posted to Rforge as soon as that's done. Terry On Thu, Mar 18, 2010 at 6:26 AM, Dieter Menne <dieter.menne at menne-biomed.de> wrote: > I am trying to use nlme and coxme in one Sweave document. I have read the > thread in r-devel on the subject, > >

How to set the nlme() function to return the answer without the intercept parametrization? #========================================================================================= library(nlme) Soybean[1:3, ] (fm1Soy.lis <- nlsList(weight ~ SSlogis(Time, Asym, xmid, scal),                        data = Soybean)) (fm1Soy.nlme <- nlme(fm1Soy.lis)) fm2Soy.nlme <- update(fm1Soy.nlme,

Dear expeRts, I am trying to plot a lme-object {package nlme) in such a way, that on a selected level the x-axis represents the value on a selected predictor and the y-axis represents the predicted-outcome variable. The graphs would than consist of several lines that each represent one group. I can't find such a plotting function. I could write such a function myself, based on

Dear all, This probably stems from my lack of understanding of the model, but I do not understand the variance of the random effect reported in coxme. Consider the following toy example: #------------------------------- BEGINNING OF CODE ------------------------------------------------ library(survival) library(coxme) #--- Generate toy data: d <- data.frame(id = c(1:100), #

I'm trying to use the lmeSplines package together with lme4. Below is (1) an example of lmeSplines together with nlme (2) an attempt to use lmeSplines with lme4 (3) then a comparison of the random effects from the two different methods. (1) require(lmeSplines) data(smSplineEx1) dat <- smSplineEx1 dat.lo <- loess(y~time, data=dat) plot(dat.lo) dat$all <- rep(1,nrow(dat)) times20

Hi All, I am trying to shift from running mixed models in SAS using PROC MIXED to using lme4 package in R. In trying to match the coefficients of R output to that of SAS output, I came across this problem. The dataset I am using is this one: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect034.htm If I run the following code: proc mixed data=rc

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

My question relates to problems that I'm having matching lme and lmer examples in P&B. using Matix 0.995 In the Oxide example in p167-170 I can't get the level 2 coefficient estimates to match the fm1Oxide model in lme is data(Oxide,package="nlme") lme(Thickness~1,Oxide) which I translate in Lmer syntax to fm3Oxide<-lmer(Thickness~

Hi, everyone, I have a question on using lme on a mixed effects model with nested error structure. After applying lme to the data, and put the outcome in, say TR.lme. I can extract the fixed effects by TR.lme$coef$fixed. However, when I use TR.lme$coef$random.effects, it does not give the variance components that I need, but a vector of values at each nested level. What I want are the

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

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

Hi, all. In setting up my package for post-processing regression models, I am trying to use standard notation as much as possible: thus, I use coef() to access estimated coefficients. I wrote a function called se.coef() to grab standard errors, and se.fixef() and se.ranef() to grab se's from coefficients estimated from lmer(). I also need a function to access sigma-hat (the residual sd

In a newly downloaded version (today) of R-2-4-0alpha, with all packages from CRAN also installed today, I get: > library(Matrix) Erro en loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : in 'Matrix' methods specified for export, but none defined: BIC, anova, coef, confint, deviance, fitted, fixef, formula, head, lmer, logLik, mcmcsamp, plot,