Displaying 20 results from an estimated 1000 matches similar to: "mgcv out of memory"
2012 Nov 29
1
[mgcv][gam] Manually defining my own knots?
Dear List,
I'm using GAMs in a multiple imputation project, and I want to be able
to combine the parameter estimates and covariance matrices from each
completed dataset's fitted model in the end. In order to do this, I
need the knots to be uniform for each model with partially-imputed
data. I want to specify these knots based on the quantiles of the
unique values of the non-missing
2012 Jan 30
1
mgcv bam() with grouped binomial data
Hello,
I'm trying to use the bam() function in the R mgcv package for a large set of grouped binary data. However, I have found that this function does not take data in the format of cbind(numerator, denominator) on the left hand side of the formula. As an example, consider the following
dat1 <- data.frame(id=rep(1:6, each=3), num=rbinom(18, size=10, prob=0.8), den=rbinom(18, size=5,
2012 Jul 23
1
mgcv: Extract random effects from gam model
Hi everyone,
I can't figure out how to extract by-factor random effect adjustments from a
gam model (mgcv package).
Example (from ?gam.vcomp):
library(mgcv)
set.seed(3)
dat <- gamSim(1,n=400,dist="normal",scale=2)
a <- factor(sample(1:10,400,replace=TRUE))
b <- factor(sample(1:7,400,replace=TRUE))
Xa <- model.matrix(~a-1) ## random main effects
Xb <-
2016 Apr 27
1
Random effects in package mgcv
Hello R users,
I have a quick question I was hoping to get your input on. I am new to R
and the smooth statistical regression world, and am trying to wrap my mind
around the issues concerning using splines for mixed effect modeling.
My question is the following: in the ?gamm? function, generalized additive
mixed models can be estimated by including random components. These can be
explicitly
2010 Mar 04
2
which coefficients for a gam(mgcv) model equation?
Dear users,
I am trying to show the equation (including coefficients from the model
estimates) for a gam model but do not understand how to.
Slide 7 from one of the authors presentations (gam-theory.pdf URL:
http://people.bath.ac.uk/sw283/mgcv/) shows a general equation
log{E(yi )} = ?+ ?xi + f (zi ) .
What I would like to do is put my model coefficients and present the
equation used. I am an
2011 Nov 09
2
Problem with simple random slope in gam and bam (mgcv package)
Dear useRs,
This is the first time I post to this list and I would appreciate any
help available. I've used the excellent mgcv package for a while now
to investigate geographical patterns of language variation, and it has
has always worked without any problems for me. The problem below
occurs using R 2.14.0 (both 32 and 64 bit versions in Windows and the
64 bit version in Unix) and mgcv (both
2012 Jun 02
2
mgcv (bam) very large standard error difference between versions 1.7-11 and 1.7-17, bug?
Dear useRs,
I reran an analysis with bam (mgcv, version 1.7-17) originally
conducted using an older version of bam (mgcv, version 1.7-11) and
this resulted in the same estimates, but much lower standard errors
(in some cases 20 times as low) and lower p-values. This obviously
results in a larger set of significant predictors. Is this result
expected given the improvements in the new version? Or
2011 Dec 14
0
mgcv 'bam' : prediction levels for random effects
Hi R users,
I'm using the 'bam' function in mgcv to examine trends in a remotely sensed
vegetation index. I have one random effect variable, 'cons' (with six
levels) which identifies different subjects within this analysis.
My model is specified as follows:
rm4<-bam(trend~factor(zone)+s(cons,bs="re")+s(year,
2005 Mar 14
2
Problem updating mgcv package
Hi All:
I tried to update the package mgcv from my current version 1.1-8 to mgcv version 1.2. Using the command update.packages("mgcv") to update mgcv failed in my computer and the returning message was:
"Error in old.packages(lib.loc=lib.loc, contriburl=contriburl, method=method, :no installed.packages for (?invalid) lib.loc=mgcv"
When I typed installed.packages(), I got
2003 Sep 30
2
cluster & mgcv update
Hello,
After reinstalling the whole OS and R as well, I tried to update.packages()
and get the follwing error message:
concerning the mgcv update: atlas2-base is installed and blas as well (on
debian). I haven't found lf77blas, I assume it's a library or something
similar associated with blas.
any suggestion how to solve that, thanks Martin
* Installing *source* package
2013 Jun 07
1
gamm in mgcv random effect significance
Dear R-helpers,
I'd like to understand how to test the statistical significance of a
random effect in gamm. I am using gamm because I want to test a model
with an AR(1) error structure, and it is my understanding neither gam
nor gamm4 will do the latter.
The data set includes nine short interrupted time series (single case
designs in education, sometimes called N-of-1 trials in medicine)
2005 Mar 11
0
mgcv 1.2-0
mgcv version 1.2 is on CRAN now. mgcv provides generalized additive models
and generalized additive mixed models with automatic estimation of the
smoothness of model components.
Changes in this version are:
* A new gam fitting method is implemented for the generalized case. It
provides more reliable convergence than the previous default, but can be
a little slower. See ?gam.method,
2005 Mar 11
0
mgcv 1.2-0
mgcv version 1.2 is on CRAN now. mgcv provides generalized additive models
and generalized additive mixed models with automatic estimation of the
smoothness of model components.
Changes in this version are:
* A new gam fitting method is implemented for the generalized case. It
provides more reliable convergence than the previous default, but can be
a little slower. See ?gam.method,
2004 Jun 03
3
Problem with mgcv PACKAGES file format?
Hello All,
I'm getting this error (Version: 1.9.0-1 on a debian system)
> update.packages("mgcv")
trying URL `ftp://mirror.aarnet.edu.au/pub/cran/src/contrib/PACKAGES'
ftp data connection made, file length 169516 bytes
opened URL
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... ..........
2012 May 08
2
mgcv: inclusion of random intercept in model - based on p-value of smooth or anova?
Dear useRs,
I am using mgcv version 1.7-16. When I create a model with a few
non-linear terms and a random intercept for (in my case) country using
s(Country,bs="re"), the representative line in my model (i.e.
approximate significance of smooth terms) for the random intercept
reads:
edf Ref.df F p-value
s(Country) 36.127 58.551 0.644
2012 Apr 23
2
Problem extracting enough coefs from gam (mgcv package)
Dear useRs,
I have used using the excellent mgcv package (version 1.7-12) to
create a generalized additive model (gam) including random effects -
represented with s(...,bs="re") - on the basis of dialect data.
My model contains two random-effect factors (Word and Key - the latter
representing a speaker) and I have added both random intercepts and
various random slopes for these
2013 Apr 20
0
Calculate confidence intervals in mgcv for unconditional on the, smoothing parameters
Dear R-Help members,
I am using Simon Wood`s mgcv package version1.7-22and R version 3.0.0
(2013-04-03) for fitting a GAM-Model to the LIDAR Data contained in the
"SemiPar" package. Here is the code for fitting the model and for
plotting the result:
data("lidar")
attach(lidar)
###
# mgcv fitting
###
gam_fit <- gam(logratio ~ s(range, k = 40, bs = "cr"), gamma
2013 Dec 05
0
mgcv gam modeling trend variation over cases
Dear R-Helpers,
I posted two days ago on testing significance of random effects in mgcv,
but realize I did not make my overall purpose clear. I have a series of
N short time series, where N might range from 3-10 and short means a
median of 20 time points. The sample data below (PCP) has N = 4 cases
with 9, 13, 16 and 16 observations over time respectively. The data set
contains four
2013 Jan 10
0
mgcv: Plotting probabilities for binomial GAM with crossed random intercepts and factor by variable
mgcv: Constructing probabilities for binomial GAM with crossed random
intercepts and factor by variable
Hello,
(I'm sorry if this has been discussed elsewhere; I may not have been
looking in the right places.)
I ran a binomial GAM in which "Correct" is modelled in terms of the
participant's age and the modality in which the stimulus is presented
(written vs spoken).
2004 Dec 01
2
step.gam
Dear R-users:
Im trying (using gam package) to develop a stepwise analysis. My gam
object contains five pedictor variables (a,b,c,d,e,f). I define the
step.gam:
step.gam(gamobject, scope=list("a"= ~s(a,4), "b"= ~s(b,4), "c"= ~s(c,4),
"d"= ~s(d,4), "e"= ~s(e,4), "f"= ~s(f,4)))
However, the result shows a formula containing the whole