Displaying 13 results from an estimated 13 matches for "getcovariateformula".
2005 Mar 01
3
packages masking other objects
hello all,
I am trying to use the function getCovariateFormula(nlme) in conjunction with the library lme4. When I load both packages I get the following message and the getCovariateFormula function no longer works:
library(nlme)
library(lme4)
Attaching package 'lme4':
The following object(s) are masked from package:nlme :
contr.SA...
2001 Jul 31
4
nlme: bug in getCovariateFormula (PR#1038)
...age about a
non-numeric argument to a binary vector in one of three nearly identical
uses.
Error in Inh/Ki : non-numeric argument to binary operator
(Inh and Ki are arguments to the function used in the formula for the
object whose predictions were requested).
It turns out that the problem is in getCovariateFormula().
The final line in getCovariateFormula() in the nlme package (version
3.1-16) is:
eval(parse(text = paste("~", deparse(form))))
however, if deparse(form) exceeds 'width.cutoff (which defaults to 60)',
this results in inappropriately placed "~" signs:
For example,...
2005 Jul 26
1
evaluating variance functions in nlme
...evaluated at new
prediction points.
So for instance
fit<-gnls(Y~SSlogis(foo,Asym,xmid,scal),weights=varPower())
fit2<-gnls(Y~SSlogis(foo,Asym,xmid,scal),weights=varPower(form=~foo))
Now using fit or fit2 I would like to get the variance function
evaluated at new points.
I have played with getCovariateFormula, and looked at Initialize.gnls,
summary etc.
but it is not clear to me how to evaluate the form component, especially
in the case of fit
above where form=~fitted(.), in any safe way.
I can grep for "fitted" in the formula eg.
grep("fitted",deparse(getCovariateFormula(fit$modelS...
2005 Aug 12
1
Problem with lme4
...led the lme4 and Matrix
package with apt-get. and both can be found in /usr/lib/R/site-library.
When I tried an example for lmer, R could not find the function lmer(),
> library(lme4)
Attaching package: 'lme4'
The following object(s) are masked from package:nlme :
getCovariateFormula getResponseFormula groupedData
Error in autoloader(name = "confint", package = "MASS") :
autoloader did not find 'confint' in 'MASS'
> (fm1 <- lmer(decrease ~ treatment + (1|rowpos) + (1|colpos),
+ OrchardSprays))
Error: couldn't...
2006 Jul 25
1
Follow Up To: Splitting the left and right hand terms of a formula
...t;))[-1])
Is there a better or cleaner way to do this?
I got one reply to try this (thanks Gabor!):
> all.vars(update(a.formula, .~0))
[1] "x"
> all.vars(update(a.formula, 0~.))
[1] "y" "z"
This works, but seems a bit of a hack.
There are two methods, "getCovariateFormula", and "getCovariate,"
which return, respectively, objects of class "formula" for the left
and right hand sides of the formula. To get the right hand side or
left hand side I wrap one of these method calls in a call to
"all.vars". Is there a better way to get the...
2002 Feb 12
1
problem plotting nls objects: couldn't find function "..."
...s(data))))) {
stop(paste(allV[naV], "not found in data"))
}
}
}
else data <- NULL
if (inherits(data, "groupedData")) {
ff <- formula(data)
rF <- deparse(getResponseFormula(ff)[[2]])
cF <- deparse(getCovariateFormula(ff)[[2]])
lbs <- attr(data, "labels")
unts <- attr(data, "units")
if (!is.null(lbs$x))
cL <- paste(lbs$x, unts$x)
else cF <- NULL
if (!is.null(lbs$y))
rL <- paste(lbs$y, unts$y)
else rF <...
2010 Jul 28
0
nlme: augPred.lme for factor covariates
...}
if (is.null(primary)) {
if (!inherits(data, "groupedData")) {
stop(paste(sys.call()[[1]], "without \"primary\" can only be
used with fits of groupedData objects"))
}
primary <- getCovariate(data)
prName <- deparse(getCovariateFormula(data)[[2]])
}
else {
primary <- asOneSidedFormula(primary)[[2]]
prName <- deparse(primary)
primary <- eval(primary, data)
}
# allow for non numeric covariates #
if (!is.null(newprim)) {
newprimary <- newprim
} else if (is.numeric(p...
2004 Dec 19
1
PBIB datataset
I'm looking at Pinheiro & Bates "Mixed-Effects Models in
S and S-PLUS" at the moment. Several datasets are used,
one of which is called "PBIB" (a partially balanced
incomplete block design).
All the other datasets can be found somewhere or other in R.
However, I cannot locate PBIB, and it does not seem to
be mentioned in the latest edition of the R Full Reference
2002 Jun 07
1
Bug list summary (automatic post)
...perpose with ordered factor groups
From: John Maindonald <john.maindonald@anu.edu.au>
Date: Sat, 9 Jun 2001 11:08:51 +1000 (EST)
--The warning is standard S and R behaviour.
--Probably xyplot needs to avoid it (by unclassing?)
--Still there in lattice 0.3-0.
* PR# 1038 *
Subject: nlme: bug in getCovariateFormula
From: Setzer.Woodrow@epamail.epa.gov
Date: Tue, 31 Jul 2001 11:24:09 -0400
--change needed in package nlme
* PR# 1044 *
Subject: Polymarsall.c
From: pleu@hotmail.com
Date: Tue, 7 Aug 2001 22:42:07 +0200 (MET DST)
* PR# 1116 *
Subject: get.hist.quote does not work
From: arto.luoma@uta.fi
Date: Thu,...
2001 Sep 24
1
R-devel Digest V1 #314
...R behaviour.
- --Probably xyplot needs to avoid it (by unclassing?)
* PR# 981 *
Subject: read.xport() bug
From: abroman@jhu.edu
Date: Fri, 15 Jun 2001 00:25:54 +0200 (MET DST)
- --confirmed on Windows and Solaris.
- --Seems that file is not in the expected format
* PR# 1038 *
Subject: nlme: bug in getCovariateFormula
From: Setzer.Woodrow@epamail.epa.gov
Date: Tue, 31 Jul 2001 11:24:09 -0400
- --change needed in package nlme
* PR# 1044 *
Subject: Polymarsall.c
From: pleu@hotmail.com
Date: Tue, 7 Aug 2001 22:42:07 +0200 (MET DST)
Directory: Analyses
none
Directory: Documentation
* PR# 988 *
Subject: input f...
2002 Jul 07
1
Bug list summary (automatic post)
...perpose with ordered factor groups
From: John Maindonald <john.maindonald@anu.edu.au>
Date: Sat, 9 Jun 2001 11:08:51 +1000 (EST)
--The warning is standard S and R behaviour.
--Probably xyplot needs to avoid it (by unclassing?)
--Still there in lattice 0.3-0.
* PR# 1038 *
Subject: nlme: bug in getCovariateFormula
From: Setzer.Woodrow@epamail.epa.gov
Date: Tue, 31 Jul 2001 11:24:09 -0400
--change needed in package nlme
* PR# 1044 *
Subject: Polymarsall.c
From: pleu@hotmail.com
Date: Tue, 7 Aug 2001 22:42:07 +0200 (MET DST)
* PR# 1178 *
Subject: segfault using svm from e1071
From: Jan Rychter <jan@rychter....
2002 Aug 21
1
Bug list summary (automatic post)
...perpose with ordered factor groups
From: John Maindonald <john.maindonald@anu.edu.au>
Date: Sat, 9 Jun 2001 11:08:51 +1000 (EST)
--The warning is standard S and R behaviour.
--Probably xyplot needs to avoid it (by unclassing?)
--Still there in lattice 0.3-0.
* PR# 1038 *
Subject: nlme: bug in getCovariateFormula
From: Setzer.Woodrow@epamail.epa.gov
Date: Tue, 31 Jul 2001 11:24:09 -0400
--change needed in package nlme
* PR# 1044 *
Subject: Polymarsall.c
From: pleu@hotmail.com
Date: Tue, 7 Aug 2001 22:42:07 +0200 (MET DST)
* PR# 1178 *
Subject: segfault using svm from e1071
From: Jan Rychter <jan@rychter....
2002 Sep 21
1
Bug list summary (automatic post)
...perpose with ordered factor groups
From: John Maindonald <john.maindonald@anu.edu.au>
Date: Sat, 9 Jun 2001 11:08:51 +1000 (EST)
--The warning is standard S and R behaviour.
--Probably xyplot needs to avoid it (by unclassing?)
--Still there in lattice 0.3-0.
* PR# 1038 *
Subject: nlme: bug in getCovariateFormula
From: Setzer.Woodrow@epamail.epa.gov
Date: Tue, 31 Jul 2001 11:24:09 -0400
--change needed in package nlme
* PR# 1044 *
Subject: Polymarsall.c
From: pleu@hotmail.com
Date: Tue, 7 Aug 2001 22:42:07 +0200 (MET DST)
* PR# 1178 *
Subject: segfault using svm from e1071
From: Jan Rychter <jan@rychter....