Displaying 20 results from an estimated 700 matches similar to: "stepAIC() that can use new extractAIC() function implementing AICc"
2017 Aug 23
0
MASS:::dropterm.glm() and MASS:::addterm.glm() should use ... for extractAIC()
Hi,
I have sent this message to this list the July, 7th. It was about a
problem in MASS package.
Until now there is no change in the devel version.
As the problem occurs in a package and not in the R-core, I don't know
if the message should have been sent here. Anyway, I have added a copy
to Pr Ripley.
I hope it could have been fixed.
Sincerely
Marc
Le 09/07/2017 ? 16:05, Marc Girondot via
2009 May 05
0
stepAICc function (based on MASS:::stepAIC.default)
Dear all,
I have tried to modify the code of MASS:::stepAIC.default(), dropterm() and addterm() to use AICc instead of AIC for model selection.
The code is appended below. Somehow the calculations are still not correct and I would be grateful if anyone could have a look at what might be wrong
with this code...
Here is a working example:
##
require(nlme)
model1=lme(distance ~ age + Sex, data =
2002 Apr 01
0
something confusing about stepAIC
Folks, I'm using stepAIC(MASS) to do some automated, exploratory, model
selection for binomial and Poisson glm models in R 1.3. Because I wanted to
experiment with the small-sample correction AICc, I dug around in the code
for the functions
glm.fit
stepAIC
dropterm.glm
addterm.glm
extractAIC.glm
and came across something I just don't understand.
stepAIC() passes dropterm.glm() a
2006 Aug 06
1
extractAIC using surf.ls
Although the 'spatial' documentation doesn't mention that extractAIC
works, it does seem to give an output.
I may have misunderstood, but shouldn't the following give at least
the same d.f.?
> library(spatial)
> data(topo, package="MASS")
> extractAIC(surf.ls(2, topo))
[1] 46.0000 437.5059
> extractAIC(lm(z ~ x+I(x^2)+y+I(y^2)+x:y, topo))
[1]
2005 Jan 26
2
Source code for "extractAIC"?
Dear R users:
I am looking for the source code for the R function extractAIC. Type the
function name doesn't help:
> extractAIC
function (fit, scale, k = 2, ...)
UseMethod("extractAIC")
<environment: namespace:stats>
And when I search it in the R source code, the best I can find is in (R
source root)/library/stats/R/add.R:
extractAIC <- function(fit, scale, k = 2,
2011 Aug 04
0
extractAIC
Use extractAIC in frailty cox model (estimated with coxph function, gaussian
random effect) i obtaided
> extractAIC(fit.cox.f)
[1] 11.84563 8649.11736
but I don't know why I can't use the classic formulation of the AIC where
the degree of freedom are the number of the parameter (in my case 3).
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2009 Sep 22
0
AIC vs. extractAIC
Dear list,
I am confused about two functions in R: AIC(fm) and extractAIC(fm). What is
the difference between two and when do I have to use one over the other? I
have found the similar question previously and still not clear for me to
understand. I also looked at '?AIC' and '?extractAIC' in R, which is also
unclear. I pasted faked data set, fitting summary, and AICs.
Thank
2007 Dec 07
1
AIC v. extractAIC
Hello,
I am using a simple linear model and I would like to get an AIC value. I
came across both AIC() and extractAIC() and I am not sure which is best to
use. I assumed that I should use AIC for a glm and extractAIC() for lm,
but if I run my model in glm the AIC value is the same if I use AIC() on an
lm object. What might be going on? Did I interpret these functions
incorrectly?
Thanks,
2011 May 10
0
Help documentation in extractAIC
Hello.
The sentence in extractAIC's help <http://www.stat.psu.edu/~dhunter/R/html/stats/html/extractAIC.html> which discusses AIC's estimate of -2logL from RSS reads: "AIC only handles unknown scale and uses the formula n log (RSS/n) - n + n log 2pi - sum(log w) where w are the weights. Further AIC counts the scale estimation as a parameter in the edf and extractAIC does
2017 Nov 24
0
extractAIC.coxph warning
Hi,
It is not critical but in case of coxph.null model (~1)
extractAIC function generates
Warning message:
In is.na(fit$coefficients) :
is.na() applied to non-(list or vector) of type 'NULL'
As I understand it happens because of absent coefficients attribute.
Function stats:::extractAIC.coxph
Line edf <- sum(!is.na(fit$coefficients))
I think extra null-checking
2004 May 24
1
bug in extractAIC.survreg (PR#6910)
Full_Name: Dave Ramsey
Version: 1.8.0
OS: win2000
Submission from: (NULL) (202.27.240.6)
there is a bug in extractAIC.survreg in library MASS.
A survreg model object has no component called "residuals". Hence
n <- length(fit$residuals)
returns 0 resulting in errors
workaround: replace
n <- length(fit$residuals)
with
n <- length(residuals(fit))
### sorry: error
2009 Jan 23
2
R stepping through multiplie interactions
I have a lm in R in the form
model <- lm( Z ~ A*B*C*D,data=mydata)
I want to run the model and include all interactions expect the 4 way
(A:B:C:D) is there an easy way of doing this? I then want to step down the
model eliminating the non-significant terms I understand step() does this
but how would I do it by hand?
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2011 Jun 20
1
Stepwise model comparisons for mlogit
I am trying to perform a backwards stepwise variable selection with an mlogit model. The usual functions, step(), drop1(), and dropterm() do not work for mlogit models.
Update() works but I am only able to use it manually, i.e. I have to type in each variable I wish to remove by hand on a separate line.
My goal is to write some code that will systematically remove a certain set of variables
2008 Aug 01
5
drop1() seems to give unexpected results compare to anova()
Dear all,
I have been trying to investigate the behaviour of different weights in
weighted regression for a dataset with lots of missing data. As a start
I simulated some data using the following:
library(MASS)
N <- 200
sigma <- matrix(c(1, .5, .5, 1), nrow = 2)
sim.set <- as.data.frame(mvrnorm(N, c(0, 0), sigma))
colnames(sim.set) <- c('x1', 'x2') # x1 & x2 are
2003 Jun 25
2
probelem of function inside function
Hi,
I encountered a problem when I am trying to write my
own function which contains another function. To
simplify a problem, I tried the following simplified
function, hope someone can idenfity the problem for
me.
I have a simple data frame called "testdata" as
following:
>
2008 Feb 10
2
Do I need to use dropterm()??
Hello,
I'm having some difficulty understanding the useage of the "dropterm()"
function in the MASS library. What exactly does it do? I'm very new to R, so
any pointers would be very helpful. I've read many definitions of what
dropterm() does, but none seem to stick in my mind or click with me.
I've coded everything fine for an interaction that runs as follows: two sets
2005 Aug 15
2
stepAIC invalid scope argument
I am trying to replicate the first example from stepAIC from the MASS
package with my own dataset but am running into error. If someone can
point where I have gone wrong, I would appreciate it very much.
Here is an example :
set.seed(1)
df <- data.frame( x1=rnorm(1000), x2=rnorm(1000), x3=rnorm(1000) )
df$y <- 0.5*df$x1 + rnorm(1000, mean=8, sd=0.5)
# pairs(df); head(df)
lo <-
2007 Jun 27
1
stepAIC on lm() where response is a matrix..
dear R users,
I have fit the lm() on a mtrix of responses.
i.e M1 = lm(cbind(R1,R2)~ X+Y+0). When i use
summary(M1), it shows details for R1 and R2
separately. Now i want to use stepAIC on these models.
But when i use stepAIC(M1) an error message comes
saying that dropterm.mlm is not implemented. What is
the way out to use stepAIC in such cases.
regards,
2012 Oct 30
2
error in lm
Hi everybody
I am trying to run the next code but I have the next problem
Y1<-cbind(score.sol, score.com.ext, score.pur)
> vol.lm<-lm(Y1~1, data=vol14.df)
> library(MASS)
> stepAIC(vol.lm,~fsex+fjob+fage+fstudies,data=vol14.df)
Start: AIC=504.83
Y1 ~ 1
Error in addterm.mlm(fit, scope$add, scale = scale, trace = max(0, trace -
:
no addterm method implemented for
2012 Feb 08
2
dropterm in MANOVA for MLM objects
Dear R fans,
I have got a difficult sounding problem.
For fitting a linear model using continuous response and then for re-fitting the model after excluding every single variable, the following functions can be used.
library(MASS)
model = lm(perf ~ syct + mmin + mmax + cach + chmin + chmax, data = cpus)
dropterm(model, test = "F")
But I am not sure whether any similar functions is