Displaying 20 results from an estimated 40000 matches similar to: "RE^2: New generic functions in "R base" {was `truncate'}"
2002 Oct 31
1
Re: gregmisc version 0.7.3 now available
Dear Greg,
Thanks for the new release. The decomposition of the SSQ is just what I need!
Regards,
Martin.
Martin Hoyle,
School of Life and Environmental Sciences,
University of Nottingham,
University Park,
Nottingham,
NG7 2RD,
UK
Webpage: http://myprofile.cos.com/martinhoyle
>>> gregory_r_warnes at groton.pfizer.com 10/30/02 07:16PM >>>
Version 0.7.3 of the gregmisc package
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
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 Aug 11
1
Error in autoloader
Hi,
After installing the latest versions of lme4, Matrix, VR on a Debian
Box, I have run into a problem. When I use library(lme4) on R Version
2.1.0 (2005-04-18) I get the following error message:
> library(lme4)
Loading required package: Matrix
Error in autoloader(name = "confint", package = "MASS") :
autoloader did not find 'confint' in 'MASS'
2002 Feb 20
1
Bug in "[<-.matrix"? (Was: Feature Request: "matrix[1:10,1:10, block=F] <- 1:10")
Thanks to David Meyer [david.meyer@ci.tuwien.ac.at] and David Brahm
[brahm@alum.mit.edu] who suggested:
m[ cbind(index.i, index.j) ] <- vals
This works fine for the example I gave.
Unfortunately, this approach doesn't extend to using the row and column
names to make assignments:
> m <- matrix("",ncol=3,nrow=3)
> dimnames(m) <-
Could generic functions check different S3 methods for an object when one of them produces an error?
2019 Jun 17
1
Could generic functions check different S3 methods for an object when one of them produces an error?
Hi,
Let's say one has an object with multiple classes, and a generic function to apply to it has associated S3 methods for more than one of those classes. Further, the method it chooses (I do not know how; some order in the class vector?) is not the suitable one and it produces an error. Would there be some way to make the generic function to choice the correct method, or in case that for
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 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)
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
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,
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
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
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)
2001 May 23
3
New generic functions in "R base" {was `truncate'}
This message is in MIME format. The first part should be readable text,
while the remaining parts are likely unreadable without MIME-aware tools.
Send mail to mime@docserver.cac.washington.edu for more info.
---2088752589-1867062326-990643072=:2129
Content-Type: TEXT/PLAIN; charset=US-ASCII
1) What are the issues with making _existing_ functions in base into
generics?
EG, I've recently
2003 May 22
4
grep, gsub, sub have problems with NA values (PR#3078)
In a string context, grep, gsub, sub are improperly treating NA (missing) as
the string "NA", and returning unexpected results
> grep("A", c(NA,"NA"))
[1] 1 2
# expected:
# [1] 2
> gsub("A", "X", c(NA,"NA"))
[1] "NX" "NX"
# expected
# [1] NA "NX"
> sub("A", "X",
2001 Nov 14
3
rpart:plotcp doesn't allow ylim argument (PR#1171)
Full_Name: Gregory R. Warnes
Version: R 1.3.1
OS: Solaris 2.8
Submission from: (NULL) (192.77.198.200)
rpart library version 3.1-2
Error message:
> plotcp(fit.thirds.1,ylim=c(0.7,1.5));
Error in plot.default(ns, xerror, axes = FALSE, xlab = "cp", ylab = "X-val
Relative Error", :
formal argument "ylim" matched by multiple actual arguments
>
This can be
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,
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
2002 Sep 23
3
New version of gregmisc package
Version 0.6.0 of the gregmisc package has just been released on CRAN.
Description:
===========
Package: gregmisc
Description: Misc Functions written/maintained by Gregory R. Warnes
Title: Greg's Miscellaneous Functions
Version: 0.6.0
Date: 2002/09/23
Maintainer: Gregory R. Warnes <Gregory_R_Warnes at groton.pfizer.com>
Author: Gregory R. Warnes. Includes code provided by Ben
2002 Sep 23
3
New version of gregmisc package
Version 0.6.0 of the gregmisc package has just been released on CRAN.
Description:
===========
Package: gregmisc
Description: Misc Functions written/maintained by Gregory R. Warnes
Title: Greg's Miscellaneous Functions
Version: 0.6.0
Date: 2002/09/23
Maintainer: Gregory R. Warnes <Gregory_R_Warnes at groton.pfizer.com>
Author: Gregory R. Warnes. Includes code provided by Ben