Displaying 20 results from an estimated 10000 matches similar to: "Import data set from another package?"
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 Mar 02
1
clarification on import/depends for a method
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",
2011 Oct 06
1
multiple defines of diag
The current coxme code has functions that depend on bdsmatrix and others
that depend on Matrix, both those pacakges define S4 methods for diag.
When loaded, the message appears:
replacing previous import ?diag? when loading ?Matrix?
Questions:
1. Do I need to worry about this? If so, what can I do about it?
I suppose I could add an importFrom directive, but it will be a pain
unless there
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,
2012 May 14
1
Vignette problem
I'm having a problem rebuilding a package, new to me in R 2.15.0
(Linux) It hits all that contain the line
\usepackage[pdftex]{graphics}
and leads to the following when running R CMD check on the directory.
(I do this often; a final run on the tar.gz file will happen before
submission.)
Since I float and resize my figures, removing the line is fatal in other
ways.
2010 Apr 23
2
Deferred Default Marker
I've finally narrowed down a puzzling problem: here is the short test
case.
tmt34% R --vanilla
R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
> temp <- matrix(runif(50), ncol=2)
> t(temp) %*% temp
[,1] [,2]
[1,] 7.916016 6.049698
[2,] 6.049698 7.650694
> library(kinship)
Loading required package:
2018 Jan 09
1
resolving a names conflict
The survival package uses a generalized cholesky decompostition throughout.? If A is a
symmetric matrix A= LDL' where L is lower triangular with 1s on the diagonal, D is
diagonal, and D[i,i] =0 if column i of A is redundant.? Being able to read the rank and
dependencies directly off of D is very handy.
The bdsmatrix package uses the same, but exposes it to the user as gchol and solve
2011 Aug 02
2
Extract p value from coxme object
Dear R experts;
I am trying to extract the p values from a coxme object (package coxme). I
can see the value in the model output, but I wanted to have the result with
a higher number of decimal places.
I have searched the mailing list and followed equivalent suggestions for
nlme/lme objects, but I wasn't successful.
Thanks;
Catarina
[[alternative HTML version deleted]]
2012 Sep 14
1
Correlation between random effects in the package coxme
Hello,
Why the correlation between the random effects is negative?
library(coxme)
rats1 <- coxme(Surv(time, status) ~ (1|litter), rats)
random.effects(rats1)[[1]] #one value for each of the 50 litters
print(rats1)
rats2 <- lmekin(time ~ (1|litter), rats)
fixed.effects(rats2)
random.effects(rats2)[[1]] #one value for each of the 50 litters
print(rats2)
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
2006 Mar 23
2
lme plot
Hi all,
I have a questions regarding mixed effects models:
I'm trying to plot e.g. fitted vs residuals for each level of the
random effects, and i'm getting the same error.
I guess this might be a problem of the graphic capabilities of R.
Is there any way to obtain those plots?
library(nlme)
attach(ergoStool)
names(ergoStool)
[1] "effort" "Type"
2012 Sep 06
1
How to extract p value from the lmekin object obtained by fitting mixed model with function lmekin() in package coxme?
Hi, R experts
I am currently using lmekin() function in coxme package to fit a
mixed effect model for family based genetic data. How can I extract the p
value from a lmekin object? When I print the object in R console, I can
see the p value and Z value are just over there. But I can not extract them
by the coef() function. kinfit$coefficient$fixed (kinfit is the name of the
lmekin object)
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 Apr 15
1
no solution yet, please help: extract p-value from mixed model in kinship package
I am making the question clear. Please help.
> Dear R experts
>
> I was using kinship package to fit mixed model with kinship matrix.
> The package looks like lme4, but I could find a way to extract p-value
> out of it. I need to extract is as I need to analyse large number of
> variables (> 10000).
>
> Please help me:
>
> require(kinship)
>
> #Generating
2009 Aug 13
2
CMD check error (bug?)
R version 2.9.0 running on Centos (Red Hat linux).
I have a pair of packages coxme and bdsmatrix. The latter is installed
in my local library (I don't have permission for global install at
work.) That is, it is in the location pointed to in R_LIBS_USER. In R,
the command library(bdsmatrix) works fine.
Coxme depends on bdsmatrix, in fact uses some cross-calls to it's C
routines, which
2008 Aug 05
4
literate programming
I'm working on the next iteration of coxme. (Rather slowly during the summer).
This is the most subtle code I've done in S, both mathematically and
technically, and seems a perfect vehicle for the "literate programming" paradym
of Knuth. The Sweave project is pointed at S output however, not source code.
I would appreciate any pointers to an noweb type client that was
2017 Dec 29
3
winbuilder warning message wrt function pointers
I've recently updated the coxme package, which calls internal routines from the bdsmatrix
package.? (It is in fact mentioned as an example of this in the Extensions manual.)
The call connections are a blocks like this, one for each of the 9 called C routines.
void bdsmatrix_prod4(int nrow,??? int nblock,?? int *bsize,
??????????????????? double *bmat, double *rmat,
??????????????????? int
2008 Apr 16
2
Post hoc tests with lme
Using the "ergoStool" data cited in Mixed-Effects Models in S and
S-PLUS by Pinheiro and Bates as an example, we have
========
> library(nlme)
> fm <- lme(effort~Type-1, data=ergoStool, random=~1|Subject)
> summary(fm)
Linear mixed-effects model fit by REML
Data: ergoStool
AIC BIC logLik
133.1308 141.9252 -60.5654
Random effects:
Formula: ~1 | Subject
2017 Feb 09
2
R CMD check error
Martyn,
No, that didn't work.
One other thing in the mix (which I don't think is the issue) is that I call one of the
C-entry points of expm. So the DESCRIPTION file imports expm, the NAMESPACE file imports
expm, and the init.c file is
#include "R.h"
#include "R_ext/Rdynload.h"
/* Interface to expm package. */
typedef enum {Ward_2, Ward_1, Ward_buggy_octave}
2012 Jan 24
1
Sweave driver extension
Almost all of the coxme package and an increasing amount of the survival
package are now written in noweb, i.e., .Rnw files. It would be nice to
process these using the Sweave function + a special driver, which I can
do using a modified version of Sweave. The primary change is to allow
the following type of construction
<<coxme>>
coxme <- function(formula, data, subset, blah blah