Displaying 20 results from an estimated 6000 matches similar to: "clarification on import/depends for a method"
2015 Feb 15
2
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
2015 Feb 16
2
Imports problem
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,
2015 Feb 16
0
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
2011 Dec 30
0
New version of coxme / lmekin
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
2015 Feb 16
0
Imports problem
>>>>> 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
>
2012 Feb 03
1
coxme with frailty--variance of random effect?
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), #
2010 Mar 05
2
Defining a method in two packages
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
2011 Mar 23
1
import question
I have been struggling all day to import a particular function/method
combination (ranef(), which extracts the random effects from a mixed
model fit) from the nlme package into another package ... so far without
success.
The NAMESPACE for nlme contains the following lines:
export(..., ranef, ...)
S3method(ranef, lme)
ranef is defined as a standard S3 generic,
function (object, ...)
2006 Oct 04
1
extracting nested variances from lme4 model
I have a model:
mod1<-lmer( x ~ (1|rtr)+ trth/(1|cs) , data=dtf) #
Here, cs and rtr are crossed random effects.
cs 1-5 are of type TRUE, cs 6-10 are of type FALSE,
so cs is nested in trth, which is fixed.
So for cs I should get a fit for 1-5 and 6-10.
This appears to be the case from the random effects:
> mean( ranef(mod1)$cs[[1]][1:5] )
[1] -2.498002e-16
> var(
2010 Mar 19
0
(no subject)
The change has also been made to coxme. I'm in the midst of another fix
(should be done by tomorrow) and will get posted to Rforge as soon as
that's done.
Terry
On Thu, Mar 18, 2010 at 6:26 AM, Dieter Menne
<dieter.menne at menne-biomed.de> wrote:
> I am trying to use nlme and coxme in one Sweave document. I have read
the
> thread in r-devel on the subject,
>
>
2007 Sep 26
1
Accessing the fixed- and random-effects variance-covariance matrices of an nlme model
I would appreciate confirmation that the function vcov(model.nlme)
gives the var-cov matrix of the fixed effects in an nlme model.
Presumably the random-effects var-cov matrix is given by cov(ranef
(model.nlme)?
Rob Forsyth
2015 Mar 02
5
Import data set from another package?
I've moved nlme from Depends to Imports in my coxme package. However, a few of the
examples for lmekin use one of the data sets from nlme. This is on purpose, to show how
the results are the same and how they differ.
If I use data(nlme::ergoStool) the data is not found, data(nlme:::ergoStool) does no
better.
If I add importFrom(nlme, "ergoStool") the error message is that
2006 Sep 07
2
Matrix package in R-2.4.0alpha
In a newly downloaded version (today) of R-2-4-0alpha, with all packages
from CRAN also installed today, I get:
> library(Matrix)
Erro en loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source) :
in 'Matrix' methods specified for export, but none defined: BIC,
anova, coef, confint, deviance, fitted, fixef, formula, head, lmer, logLik,
mcmcsamp, plot,
2005 Jun 24
1
lme4 extracting individual variance components
Hi,
For further calculations I need to extract indivdual Variances of
different random effects from a fitted model.
I found out how to extract the correlations
(VarCorr(m1)@reSumry$group1) but I was not able to find a way to
extract the other components individually.
To extract the Residuals I tried: (ranef(m1)@ stdErr) which
unfortunately did not work.
Thank you very much for your help!
2010 Dec 01
1
[R-lme] Extract estimated variances from output of lme?
Hi all,
I have the output of summary() of an lme object called "lme.exp1", for
example
#############################################
> summary(lme.exp1)
Linear mixed-effects model fit by REML
Data: DATA
Log-restricted-likelihood: -430.8981
Fixed: fixed.exp1
....
Random effects:
Formula: ~-1 + mu1 + log.sig1 | animID
Structure: Diagonal
mu1 log.sig1
2006 Jul 24
3
standardized random effects with ranef.lme()
Using ranef() (package nlme, version 3.1-75) with an 'lme' object I can
obtain random effects for intercept and slope of a certain level (say:
1) - this corresponds to (say level 1) "residuals" in MLWin. Maybe I'm
mistaken here, but the results are identical.
However, if I try to get the standardized random effects adding the
paramter "standard=T" to the
2013 Sep 12
1
Importing packages in Depend
Hi,
I am currently preparing a new version of my package papeR. When I run R CMD
check using the development version of R I get the following note:
Package in Depends field not imported from: ?nlme?, ?lme4?, ?survival?
These packages needs to imported from for the case when
this namespace is loaded but not attached.
I now have problems to fix this issue. It is easy to get rid of two of the
2006 Aug 02
2
lme4 and lmeSplines
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$all <- rep(1,nrow(dat))
times20
2006 Oct 08
1
Simulate p-value in lme4
Dear r-helpers,
Spencer Graves and Manual Morales proposed the following methods to
simulate p-values in lme4:
************preliminary************
require(lme4)
require(MASS)
summary(glm(y ~ lbase*trt + lage + V4, family = poisson, data =
epil), cor = FALSE)
epil2 <- epil[epil$period == 1, ]
epil2["period"] <- rep(0, 59); epil2["y"] <- epil2["base"]
2003 May 12
1
plot.ranef.lme (PR#2986)
library(nlme)
data(Phenobarb)
na.include <- function(x)x
phe1 <- nlme(conc~phenoModel(Subject, time, dose, lCl, lV),
data = Phenobarb,
fixed = lCl+lV~1,
random= pdDiag(lCl+lV~1),
start = c(-5,0),
na.action = na.include,
naPattern = ~!is.na(conc))
phe.ranef <- ranef(phe1,augFrame=TRUE)
plot(phe.ranef, form=lCl~Wt+ApgarInd)
[Error in max(length(x0),