Displaying 20 results from an estimated 800 matches similar to: "singular variance-covariance warning in lmer"
2005 Dec 29
1
'last.warning' problem at startup; package Matrix (PR#8453)
On starting an R session, I get the messages:
Fatal errir: unable to restore save data in .RData
Error in fun(...): couldn't find function "assignInNamespace"
Error: .onLoad failed in 'loadNamespace' for 'Matrix'
The only object in my .RData is last.warning, thus:
> last.warning
$"optim or nlminb returned message false convergence (8)"
2006 Mar 16
1
lme4/Matrix: Call to .Call("mer_update_y"...) and LMEoptimize gives unexpected side effect...
Dear all
I want to compute Monte Carlo p-values in lmer-models based on sampled data sets. To speed up calculations, I've tried to use internal functions from the Matrix package (as suggested ealier on the list by Doug Bates).
So I did:
fm2 <- lmer(resistance ~ ET + position + (1|Grp), Semiconductor,method='ML')
simdata<-simulate(fm2,nsim=1)
ynew <- simdata[,1]
mer
2005 Aug 13
2
monte carlo simulations/lmer
Hi - I am doing some monte carlo simulations comparing bayesian (using
Plummer's jags) and maximum likelihood (using lmer from package lme4
by Bates et al).
I would like to know if there is a way I can flag nonconvergence and
exceptions. Currently the simulations just stop and the output reads
things like:
Error in optim(.Call("lmer_coef", x, 2, PACKAGE = "Matrix"), fn,
2011 Dec 12
2
i can't read large NETCDF file like CRU
i use library(ncdf) to read this file as follow
library(ncdf)
sst.nc = open.ncdf(title)
lonall = get.var.ncdf(sst.nc,'lon')
latall = get.var.ncdf(sst.nc,'lat')
precip = get.var.ncdf(sst.nc,'pre')
close(sst.nc)
if i use this method my pc freeze and not respond until i restart it is
there
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2012 Nov 16
2
R-Square in WLS
Hi,
I am fitting a weighted least square regression and trying to compute
SSE,SST and SSReg but I am not getting SST = SSReg + SSE and I dont know
what I am coding wrong. Can you help please?
xnam <-colnames(X) # colnames Design Matrix
fmla1 <- as.formula(paste("Y ~",paste(xnam, collapse=
2009 Feb 20
3
mean over previous cells
Dear RUsers,
I guess this is an easy question for someone a little familiar with
programming...(which I am not)...
I've got 2 colummns, one shows just dates(SST_date, Class 'Date' num), the
other one shows the SeaSurfaceTemperature (SST, num) at that certain date.
SST_date SST
2008-01-01 22.2
2008-01-02 21.8
2008-01-03 22.8
2008-01-04 22.9
2008-01-05 23.1
2008-01-06 23.2
...
2011 May 06
1
read a netcdf file _Fill_value=-32768
Hello
I am a new user of R .
and I ve problem with R and netcdf .
I succed installation , I could use all examples .
But when I take my netcf it is different .
I want to do statistic on this kind of file .
1)
first calculate mean .
my data is like that
through ncdump -h test.nc
netcdf test {
dimensions:
lat = 301 ;
lon = 401 ;
time = UNLIMITED ; // (80 currently)
2009 Nov 20
1
problem selecting 330 to 30 longitude
Hello,
This is probably very simple but I am trying to select a region from the
OIv2 SST dataset that crosses 0 longitude. The longitude variable is
arranged from 0 to 360 and I get an error message when trying to go from 330
to 30 for example. The data are from a NOAA netCDF file.
*temp = open.ncdf("c:/documents and settings/theoni/desktop/sstoi_v2.nc")
print(temp)
y1 = get.var.ncdf(
2006 Nov 26
1
GLM and LM singularities
Hi-
I'm wrestling with some of my data apparently not being called into a GLM or
an LM. I'm looking at factors affecting fish annual catch rates (ie. CPUE)
over 30 years. Two of the factors I'm using are sea surface temperature and
sea surface temperature anomaly. A small sample of my data is below:
CPUE
Year
Vessel_ID
Base_Port
Boat_Lgth
Planing
SST
Anomaly
0.127
2006 Aug 03
2
fitting a model with the nlme package
Dear all,
I am analyzing some data that requires a mixed model. I have been
reading Pinheiro and Bates' book,
but cannot find the notation to fit the following model:
Suppose I have the dataset below. Here I am fitting variable p as a
fixed effect, variable h
as a random effect and variable t as nested within h. I would like to
include the variable j as well
as an independent (non-nested)
2013 Jan 16
1
setting the legend scale in contour plots
Hi,
I'd like to compare SST data for year 2000 with SST for year 2001. I managed
to get filled contour plots showing monthly SST for both years (12 plots for
each year, 24 plots in total). In order to compare year 2000 and year 2001,
however, I'd need to have the same legend scale (same color bar) in both
years plots.
Thus, my question is: is there a way to set the legend scale in
2009 May 11
1
R and McAfee 8.5
Hi,
I have been working with R for the last year and using the UKFSST package to look at satellite tag track data and SST information. Fpr those not familiar, the package uses the positions estimated by the satellite tags themselves and the associated SST data from servers (in this case, from the University of Hawaii and the NOAA Coastwatch website) for the time preiod to estimate a reasonable
2008 Aug 14
1
autocorrelation in gams
Hi,
I am looking at the effects of two explanatory variables on chlorophyll.
The data are an annual time-series (so are autocorrelated) and the
relationships are non-linear. I want to account for autocorrelation in
my model.
The model I am trying to use is this:
Library(mgcv)
gam1 <-gam(Chl~s(wintersecchi)+s(SST),family=gaussian,
na.action=na.omit, correlation=corAR1(form =~
2010 Nov 05
1
prob with legend in my plots!
Hi,
I have a problem with the appearance of legend in my plots. If I specify the legend positions in characters like "topright"..etc, it appears, if i specify it in terms of coordinates like "-1, 1" .. etc, it does not appear. Can anyone help me with this?
script -
x.date <- as.Date(paste(year, month, day, sep="-"))
ts1.n.e3 <- ts(data.nemr.e3[,3])
z1.n.e3
2005 Jun 13
1
Warning messages in lmer function (package lme4)
Hi:
I'm using function lmer from package lme4, and I get this message:
" There were 12 warnings (use warnings() to see them)"
So I checked them:
Warnings 1 to 11 said:
1: optim returned message ERROR: ABNORMAL_TERMINATION_IN_LNSRCH
in: "LMEoptimize<-"(`*tmp*`, value = structure(list(maxIter = 50, ...
and Warning 12 said:
12: IRLS iterations for glmm did
2006 Jan 06
1
lmer p-vales are sometimes too small
This concerns whether p-values from lmer can be trusted. From
simulations, it seems that lmer can produce very small, and probably
spurious, p-values. I realize that lmer is not yet a finished product.
Is it likely that the problem will be fixed in a future release of the
lme4 package?
Using simulated data for a quite standard mixed-model anova (a balanced
two-way design; see code for the
2007 Jan 26
1
Form of the equation produced by a GLM with Poisson family and log link function
Hi everyone,
My background is not math and I am trying to figure out exactly what equation to use to map a response variable in GIS based on the coefficients obtained from the GLM and the values of the independent variables in each grid cell of my study area. Most specifically, I want to know how to incorporate the Poisson family and log link function in the equation. I would really appreciate if
2002 May 11
2
Bug on Mac version of lm()?
Dear Mac users,
Hi, as you might have probably read the thread of
"[R] Rsquared in summary(lm)" on May 10, it seems that Mac version of
lm() seem to be working incorrectly.
I enclose the script to produce the result both for lm() and manual
calculation for a simple regression. Could you run the script and
report with the version of R, so I don't have to go through every
builds
2018 May 24
2
Problem with adding a raster and a brick
Hi,
I seem to be having a problem adding the following two raster objects
together - one is a rasterLayer, the other is a rasterBrick. The extent,
resolution, and origin are the same, so according to my understand it
should work. The objects look like so:
> obs.clim
class : RasterLayer
dimensions : 60, 200, 12000 (nrow, ncol, ncell)
resolution : 0.5, 0.5 (x, y)
extent : -70,
2007 Jan 04
0
A question on REML in R
Hello, everyone, I'm using R to deal with a REML problem. I found "lmer" is
the right function for this. But I got stuck because I couldn't interpret
the result. I'm attaching a short example of my executing log. Please have a
look and give me some advice on it. Thanks a lot!
Plot Block Treatment Data
1 1 2 7.8
2 1 1