Displaying 20 results from an estimated 4000 matches similar to: "no convergence using lme"
2006 Aug 04
1
gnlsControl
When I run gnls I get the error:
Error in nls(y ~ cbind(1, 1/(1 + exp((xmid - x)/exp(lscal)))), data = xy, :
step factor 0.000488281 reduced below 'minFactor' of 0.000976563
My first thought was to decrease minFactor but gnlsControl does not contain
minFactor nor nlsMinFactor (see below). It does however contain nlsMaxIter
and nlsTol which I assume are the analogs of
2012 Jan 22
1
How to construct a formula
Hi,
I need to construct a formula programaticly, and pass it to a function
such as the linear mixed model lme. The help says it requires "a
two-sided linear formula object describing the fixed-effects part of the
model" but I do not know how to create this formula. I have tried
various things using formula(x, ...), as.formula(object, env =
parent.frame()) and as.Formula(x, ...)
2009 Mar 07
2
ttest in R
Dear list,
i am a biologist who needs to do some ttest between disease and non disease,
sex, genotype and the serum levels of proteins on a large number of
individuals. i have been using excel for a long time but it is very tedious
and time consuming. i am posting the data below and ask your help in
generating a code to get this analysis done in R. thanks
gender disease genotype data
M N CC
2006 Jan 31
1
lme in R (WinXP) vs. Splus (HP UNIX)
R2.2 for WinXP, Splus 6.2.1 for HP 9000 Series, HP-UX 11.0.
I am trying to get a handle on why the same lme( ) code gives
such different answers. My output makes me wonder if the
fact that the UNIX box is 64 bits is the reason. The estimated
random effects are identical, but the fixed effects are very
different. Here is my R code and output, with some columns
and rows deleted for space
2011 Mar 08
1
NaNs in Nested Mixed Model
Dear R users,
I have a problem with something called "NaNs" in a nested mixed model.
The background is that I have studied the number of insect nymphs
emerging from replicated Willow genotypes in the field. I have 15
replicates each of 4 Willow genotypes belonging two 2 Willow species.
Now I want to elucidate the effect of Willow genotype on the number of
emerging nymphs. Previously I
2004 Jul 23
1
nlme parameters in nlmeControl
Hello all.
I'm doing a simulation study where I will be making use of the 'nlme' package. I want to
loosen up the convergence criteria so that I increase the likelihood of convergence
(potentially at the cost of obtaining slightly less than ideal results). The parameters in
the function nlmeControl() control the convergence criteria. These default values can be
modified to make
2009 Jan 22
1
convergence problem gamm / lme
Hope one of you could help with the following question/problem:
We would like to explain the spatial
distribution of juvenile fish. We have 2135 records, from 75 vessels
(code_tripnr) and 7 to 39 observations for each vessel, hence the random effect
for code_tripnr. The offset (‘offsetter’) accounts for the haul duration and
sub sampling factor. There are no extreme outliers in lat/lon. The model
2007 Oct 02
1
Trouble obtaining results from a loop
#Hello,
#I have a question about obtaining results from a loop I have written.
#Below is a sample of individual genotypes from a genetic question I am
working on called "P.genotype.sample ".
P.genotype.sample<-matrix(10,10,10)
P.genotype.sample[,1]<-c(2,2,1,5,1,1,5,6,1,3)
P.genotype.sample[,2]<-c(6,3,3,6,8,1,6,7,2,3)
P.genotype.sample[,3]<-c(2,2,2,3,3,2,2,2,3,3)
2007 Sep 26
1
Paste a matrix column in pairwise fashion with other columns?
#Hello,
#I have would like to paste a single column of a matrix
# in pair wise fashion with other columns based upon
# even and odd column numbers.
# I can do it in a very clunky fashion and I know there
# must be a better way. below is a sample matrix and my extremely
# clunky code that gets the job done for a small matrix, but i plan to
# do this on a much grander scale. any help would be very
2006 May 26
2
lme, best model without convergence
Dear R-help list readers,
I am fitting mixed models with the lme function of the nlme package.
If I get convergence depends on how the method (ML/REM) and which (and
how much) parameters will depend randomly on the cluster-variable.
How get the bist fit without convergence?
I set the parameters msVerbose and returnObject to TRUE:
lmeControl(maxIter=50000, msMaxIter=200, tolerance=1e-4,
2010 Oct 09
1
question related to multiple regression
Hi,
I am conducting an association analysis of genotype and a phenotype such as
cholesterol level as an outcome and the genotype as a regressor using
multiple linear regression. There are 3 possibilities for the genotype AA,
AG, GG. There are 5 people with the AA genotype, 100 with the AG genotype
and 900 with the GG genotype. I coded GG genotype as 1, AG as 2 and AA as 3
and the p-value for the
2008 Aug 20
4
Looping over groups
Hello,
My R skills are somewhere between novice and intermediary, and I am hoping that some of you very helpful forum members, whom I've seen work your magic on other peoples' problems/questions, can help me here.
I have a matrix with the following format:
(i) individual plants comprising many different genotype groups (i.e., a plant is genotype 1 or genotype 2 or genotype 3, etc). The
2005 Apr 21
2
ANOVA model
Hi,
Could someone tell me if this is the correct model syntax for the
following dataset:
lme(height~treatment+genotype+treatment*genotype,drought,random=~genotyp
e)
The dataset has two factors: one fixed - treatment, and one random -
genotype. I need to test the effect of both factors to identify their
significance. There are multiple (but not equal) replicates at each
level of genotype (the
2005 Jun 30
1
FW: plot legend outside the grid
-----Original Message-----
From: Ghosh, Sandeep
Sent: Thursday, June 30, 2005 5:43 PM
To: 'Berton Gunter'
Subject: plot legend outside the grid
Thanks for the pointers... I managed to get everything to look and feel the way I want except for the legend to plot outside the grid... Thanks for the note on the par, but I'm not able to it to plot outside the plot grid..
dataFrame <-
2003 Apr 08
2
Basic LME
Hello R Users,
I am investigating the basic use of the LME function, using the following example;
Response is Weight, covariate is Age, random factor is Genotype
model.lme <- lme (Weight~Age, random=~ 1|Genotype)
After summary(model.lme), I find that the estimate of Age is 0.098 with p=0.758.
I am comparing the above model with the AOV function;
model.aov <- aov (Weight~Age + Genotype)
2004 Nov 21
1
Two factor ANOVA in lme
I want to specify a two-factor model in lme, which should be easy?
Here's what I have:
factor 1 - treatment FIXED (two levels)
factor 2 - genotype RANDOM (160 genotypes in total)
I need a model that tells me whether the treatment, genotype and
interaction terms are significant. I have been reading 'Mixed effects
models in S' but in all examples the random factor is not in the main
2003 May 22
3
How to avoid function masking
Hi All,
I've been working on updating the 'genetics' package. As a consequence of
the upgrade, .First.lib() looks like:
.First.lib <- function(libname, pkgname)
{
if (!require(combinat))
warning("Unable to load 'combinat' library. Function
`diseq.ci' will fail.")
require(gregmisc)
genotype <-
2013 Oct 14
1
R Help-how to use sapply w/tapply
Hi,
(Please use ?dput() to share the example dataset. Avoid using images to show dataset. Also, please read the posting guide esp. regarding home work, assignments etc.)
res <- sapply(Gene[,-1],function(x) tapply(x,list(Gene$Genotype),mean))
#or
res2 <-? aggregate(.~Genotype, data=Gene,mean)
#or
library(plyr)
?res3 <- ddply(Gene,.(Genotype),numcolwise(mean))
identical(res2,res3)
2012 Nov 03
2
reorder() in the latticeExtra library
Hello all, thanks for your time and help. Below are my commands, and it
generates a really nice plot, however I am not happy with the reorder()
function. I would like the order to be the same as they appear in the
genotype variable "genotype <- c("CJ1450 NW 4/25/12","CJ1450 BAL
4/25/12","CJ1450 NW 4/27/12","CJ1450 BAL 4/27/12","CJ1721 NW
2010 Sep 03
3
define colors for groups in lattice xyplot
Dear all,
Lattice provides automatic coloring for subgroups on each panel by the
simple use of a groups statement. For an application I want to change
these colors to a predifined set. This works well using a panel function
in stead of the default as long as there are only points in the graphs.
When I set type="b" things get messed up. Any idea why? I include sample
code for