Displaying 20 results from an estimated 30000 matches similar to: "Error in autoloader"
2005 Aug 12
1
Problem with lme4
Hi,
I cannot seem to get lme4 to work. I have installed 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
2003 Nov 17
1
confint: which method attached?
the function
confint
uses the profiling method of the function of the package MASS
confint.glm
even after the package has been detached!
1: might this be the intenden behavior?
2. How does the function remember its 'MASS' functionality after detaching the package?
R: 1.8.0; Windows 2000
Here is a sample program
> set.seed(7882)
> x<-rep(c(0,1),c(20,20))
>
2009 Oct 02
1
confint fails in quasibinomial glm: dims do not match
I am unable to calculate confidence intervals for the slope estimate in a
quasibinomial glm using confint(). Below is the output and the package info
for MASS. Thanks in advance!
R 2.9.2
MASS 7.2-48
> confint(glm.palive.0.str)
Waiting for profiling to be done...
Error: dims [product 37] do not match the length of object [74]
> glm.palive.0.str
Call: glm(formula = cbind(alive, red) ~ str,
2004 Jul 13
2
confint.glm in a function
I can't get confint.glm to work from within a function. Consider
the following (using R 1.9.1, Windows 2000):
# FIRST: SOMETHING THAT WORKS FROM A COMMAND PROMPT
DF <- data.frame(y=.1, N=100)
(fit <- glm(y~1, family=binomial, data=DF,
weights=DF[,"N"]))
Call: glm(formula = y ~ 1, family = binomial, data = DF, weights =
DF[, "N"])
Coefficients:
2005 Dec 22
3
Windows crash in confint() with nls fit (PR#8428)
Full_Name: Ben Bolker
Version: 2.2.1
OS: Windows XP and 2000
Submission from: (NULL) (128.227.60.124)
The following code, using confint() to try
to get confidence intervals on an nls object
that has been fitted with algorithm="port"
reliably crashes R 2.2.0 and 2.2.1 with the
latest version of MASS on a Windows 2000 and
a Windows XP machine here. I *think* earlier
versions of MASS
2003 Apr 17
2
make check failure with R-1.7.0
I'm baffled. When I run make check after installing from source, I
get a Error 2. From my understanding of how these things work, it
would appear to be coming from this (as at the end of base-Ex.Rout.fail:
> has.VR <- require(MASS, quietly = TRUE)
Attaching package 'MASS':
The following object(s) are masked from package:base :
confint confint.lm nclass.FD nclass.scott
2001 Apr 09
1
Bug in help for profile; more general problem? (PR#900)
The help topic for "profile" has a link to profile.glm in MASS which
doesn't work in the HTML help. The problem is that there is no
profile.glm.html file, profile.glm is just an alias for the confint
help topic.
It would be nice if there were a general solution to this problem
(i.e. the system knew how to work with aliases), but it doesn't look
easy: profile.html is in base,
2012 Jan 18
4
confint function in MASS package for logistic regression analysis
I have the following binary data set:
Sex
Response 0 1
0 159 162
1 4 37
My commands
library(MASS)
sib.glm=glm(sib~sex,family=binomial,data=sib.data)
summary(sib.glm)
The coefficients in the output are
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.6826 0.5062 -7.274 3.48e-13
2000 Jul 21
1
confint() error
Dear all,
I have run the confint() function according to below and I get the
following error message:
> confint(stepAIC.glm.spe.var.konn2.abund, level=0.95)
Waiting for profiling to be done...
Error: missing value where logical needed
In addition: Warning message:
NaNs produced in: sqrt((fm$deviance - OriginalDeviance)/DispersionParameter)
or
> confint(stepAIC.glm.spe.var.konn2.abund,
2001 May 23
3
RE^2: New generic functions in "R base" {was `truncate'}
> From: Martin Maechler [mailto:maechler@stat.math.ethz.ch]
> Sent: Friday, May 18, 2001 11:30 AM
> To: gregory_r_warnes@groton.pfizer.com
> Subject: RE^2: [Rd] New generic functions in "R base" {was `truncate'}
>
[...]
> Apropos ci() :
>
> There's the very generally useful confint() function in MASS.
> Since MASS will become one of the
2009 Dec 07
5
confint for glm (general linear model)
Hi,
I have a glm gives summary as follows,
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.03693352 1.449574526 -1.405194 0.159963578
A 0.01093048 0.006446256 1.695633 0.089955471
N 0.41060119 0.224860819 1.826024 0.067846690
S -0.20651005 0.067698863 -3.050421 0.002285206
then I use confint(k.glm)
2005 Apr 06
2
make error in R devel
Dear list,
I just hit an error that stopped my make && make check-devel operation
on my linux box (FC3, i686 P4 2GB RAM). Just to note that I've been
building the development branch(?) for some time and this is the first
hint of a problem.
1) updated the src tree using svn update
2) ran ../configure --with-recommended-package=no from my build directory
3) got:
R is now configured
2008 Jan 07
1
xtable (PR#10553)
Full_Name: Soren Feodor Nielsen
Version: 2.5.0
OS: linux-gnu
Submission from: (NULL) (130.225.103.21)
The print-out of xtable in the following example is wrong; instead of yielding
the correct ci's for the second model it repeats the ci's from the first model.
require(xtable)
require(MASS)
data(cats)
b1<-lm(Hwt~Sex,cats)
b2<-lm(Hwt~Sex+Bwt,cats)
2006 Dec 13
1
Curious finding in MASS:::confint.glm() tied to eval()
Greetings all,
I was in the process of creating a function to generate profile
likelihood confidence intervals for a proportion using a binomial glm.
This is a component of a larger function to generate and plot confidence
intervals for proportions using the above, along with bootstrap (BCa),
Wilson and Exact to visually demonstrate the variation across the
methods to some folks.
I had initially
2013 Feb 22
1
How to do generalized linear mixed effects models
I want to analyze binary, multinomial, and count outcomes (as well as
the occasional continuous one) for clustered data.
The more I search the less I know, and so I'm hoping the list can
provide me some guidance about which of the many alternatives to choose.
The nlme package seemed the obvious place to start. However, it seems
to be using specifications from nls, which does non-linear
2006 Nov 18
1
deriv when one term is indexed
Hi,
I'm fitting a standard nonlinear model to the luminances measured
from the red, green and blue guns of a TV display, using nls.
The call is:
dd.nls <- nls(Lum ~ Blev + beta[Gun] * GL^gamm,
data = dd, start = st)
where st was initally estimated using optim()
st
$Blev
[1] -0.06551802
$beta
[1] 1.509686e-05 4.555250e-05 7.322720e-06
$gamm
[1] 2.511870
This works fine but I
2006 May 03
1
Problem in using confint method on polr model object
I fit a proportional odds model
with the polr-function of the MASS package from
Venables and Ripley
Applying the confint method to calculate confidence intervals for the
parameters I get
the following error message
Waiting for profiling to be done...
Re-fitting to get Hessian
Error in X[, -i, drop = FALSE] : incorrect number of dimensions
Can someone explain the error-message?
(The
2010 Nov 15
1
comparing levels of aggregation with negative binomial models
Dear R community,
I would like to compare the degree of aggregation (or dispersion) of
bacteria isolated from plant material. My data are discrete counts
from leaf washes. While I do have xy coordinates for each plant, it
is aggregation in the sense of the concentration of bacteria in high
density patches that I am interested in.
My attempt to analyze this was to fit negative binomial
2008 Jan 18
2
HP Autoloader
Hi,
I need to backup data to an HP autoloader, it needs to be *full* backups each time so using Amanda doesn't make sense.
Can someone point me to what utilities to use to access the autoloader, I would rather read up on this myself as my knowledge here is very weak. I am moving this unit from a windows environment running Backup Exec. I know all of those features won't be available but I
2012 Mar 09
2
How do I force confint() for glm() to be quiet?
I need confint() for glm() to supress the messages
"Waiting for profiling to be done..."
because they mess up the caching mechanism of pgfSweave (see
https://github.com/cameronbracken/pgfSweave/issues/40).
I have read the help page of confint(), but I do not know how to get
the help page for the glm() version, if any such help page exists.
Is there a general way of turning of output