Displaying 20 results from an estimated 900 matches similar to: "bootstrapping nonlinear mixed effects models"
1999 Nov 25
1
gnls
Doug,
I have been attempting to learn a little bit about nlme without too
much documentation except the online help. The Latex file in the nlme
directory looks interesting but uses packages that I do not have so
that I have not been able to read it.
I have run the example from gnls to compare it with the results I
get from my libraries (code below - I have not included output as it
is rather
2001 Jan 17
1
Pinheiro/Bates Soybean nlme failure
Dear Mixed Effect Friends,
Somehow, R(1021, Windows) seem to run differently from S Plus:
The soybean example from Pinheiro/Bates on page 290 fails
in R. (Soybean1 is Soybean with the NA and "critical" case
removed. Same procedure with full Soybean).
> fm1Soy.lis<-nlsList(weight~SSlogis(Time,Asym,xmid,scal),data=Soybean1)
> fm1Soy.nlme<-nlme(fm1Soy.lis)
Error: Singularity
2000 Feb 11
1
R CMD check [nlme|MASS] fails (PR#431)
Mmmh, seems as if I really should change my options as I seem to keep
sending off empty bug-reports ;-/ Sorry guys. Here is the content
that should have been in the last e-mail:
`R CMD check nlme' fails on my machine. The final output in
nlme-Ex.Rout is:
> library(nlme)
> data(Soybean)
> fm1 <- nlme(weight ~ SSlogis(Time, Asym, xmid, scal), data = Soybean,
+ fixed =
2001 May 31
1
nlme and memory
I am trying to follow an example in Pineiro & Bates's book
library(nlme)
data(Soybean)
soy.lis<-nlsList(weight~SSlogis(Time,Asym,xmid,scal),data=Soybean)
soy.nlme<-nlme(soy.lis)
Error: Calloc could not allocate (151974496 of 8) memory
This is not a large problem-- only 412 observations. I am using R-1.2.3
with automatic memory allocation. Does this message mean that I need to
run
2009 May 04
1
how to change nlme() contrast parametrization?
How to set the nlme() function to return the answer without the intercept parametrization?
#=========================================================================================
library(nlme)
Soybean[1:3, ]
(fm1Soy.lis <- nlsList(weight ~ SSlogis(Time, Asym, xmid, scal),
data = Soybean))
(fm1Soy.nlme <- nlme(fm1Soy.lis))
fm2Soy.nlme <- update(fm1Soy.nlme,
2006 May 17
1
nlme model specification
Hi folks,
I am tearing my hair out on this one.
I am using an example from Pinheiro and Bates.
### this works
data(Orange)
mod.lis <- nlsList(circumference ~ SSlogis(age, Asymp, xmid, scal),
data=Orange )
### This works
mod <- nlme(circumference ~ SSlogis(age, Asymp, xmid, scal),
data=Orange,
fixed = Asymp + xmid + scal ~ 1,
start =
2005 Jul 26
1
evaluating variance functions in nlme
Hi,
I guess this is a final plea, and maybe this should go to R-help but
here goes.
I am writing a set of functions for calibration and prediction, and to
calculate standard
errors and intervals I need the variance function to be evaluated at new
prediction points.
So for instance
fit<-gnls(Y~SSlogis(foo,Asym,xmid,scal),weights=varPower())
2003 Apr 03
0
debugging question
Dear R-devel,
A user reported a strange problem with predict.randomForest in the
randomForest package yesterday, and I'm baffled by it. The code at the end
of the message produces the error. The problem is that, in
predict.randomForest, there's a .Fortran call to "runforest". One of the
arguments passed in is "countts", which is a vector of doubles. The error
2011 Feb 08
4
Interactions in a nls model
I am interested in testing two similar nls models to determine if the
lines are statistically different when fitted with two different data
sets; one corn, another soybean. I know I can do this in linear models
by testing for interactions. See Introductory Statistics with R by
Dallgaard p212-218 for an example. I have two different data sets I am
comparing to lai. ci.re should have very
2004 Aug 02
3
Title with substitute and paste
Hello All,
I am generating some plots where the title is generated with substitute
and paste. An example:
nval <- 20
plot(0,0)
title(substitute(paste("n = ", n), list(n = nval)))
But when compared to:
plot(0,0)
title("n = 20")
the title in the first plot looks slightly different (it is not in
bold). How can I get the two titles to look exactly the same?
Also, how can I
2006 Feb 09
0
bootstrapping lambda values from projections matrices
Dear all,
I'm working with a population projections matrix model from demographic
data. The dominant eigenvalue of the matrix is the growth rate of the
population (lambda). I would like to estimate confidence intervals for the
lambda values with bootstrap.
The function for calculating the eigenvalue I wrote like this:
mat.fun <- function(d,i){
mat<-matrix(c(0,
2004 Sep 01
1
[R/S] strange
Dear R and S People:
I have run across something very strange. Here is a function that I wrote
for R:
boot1 <- function(y,method="f",p=1) {
n1 <- length(y)
n2 <- n1*p
n3 <- n2 - 1
a <- 0.5*(outer(1:n3,1:n3,function(x,y){n2 - pmax(x,y)}))
return(a)
}
and here is the R output:
> y1
[1] 9 8 7 3 6
> source("boot1.R")
> boot1(y=y1,p=4)
[,1] [,2]
2004 Sep 01
0
Re: [S] [R/S] strange solution
Hi, Erin:
A cleaner way is to pass "n2" to "outer" as a "..." argument, as
in the following modification of your code:
boot1 <- function(y,method="f",p=1) {
n1 <- length(y)
n2 <- n1*p
n3 <- n2 - 1
a <- 0.5*(outer(1:n3,1:n3,function(x,y, n2.){n2. - pmax(x,y)}, n2.=n2))
return(a)
}
y1 <- c( 9, 8, 7, 3, 6)
boot1(y=y1,p=4)
2003 Apr 02
4
randomForests predict problem
Hello everybody,
I'm testing the randomForest package in order to do some simulations and I
get some trouble with the prediction of new values. The random forest
computation is fine but each time I try to predict values with the newly
created object, I get an error message. I thought I was because NA values
in the dataframe, but I cleaned them and still got the same error. What am
I
2006 May 24
0
the computation of exact p-value for the nonparametric cor-test with ties
Hello,
I wuold like to propose my modifications of the original cor.test to you : I
tried to calcolate the correct p-value for Spearman and Kendall's test with
ties.
Let me know what you think.
Thanks you for your time.
Antonietta di Salvatore
test <- function(x, ...) UseMethod("test")
test.default <-
function(x, y, alternative = c("two.sided",
2010 May 11
1
merge two data frames
Dear group,
I have these 2 following data frame:
allcon <-
structure(list(DESCRIPTION = structure(1:17, .Label = c("COFFEE C Jul/10",
"COPPER May/10", "CORN Jul/10", "CORN May/10", "COTTON NO.2 Jul/10",
"CRUDE OIL miNY May/10", "GOLD Jun/10", "HENRY HUB NATURAL GAS May/10",
"ROBUSTA COFFEE (10)
2002 Jan 07
0
rsync-2.5.1 / zlib patches
The following zlib files need patches in order to compile using Compaq C
on OpenVMS. These patches should also be needed on a Tru64 or LINUX on
ALPHA using Compaq C. These should work on any ANSI compliant compiler.
Operating System: OpenVMS ALPHA V7.3
Compiler: Compaq C T6.5
Compiler switches: /WARN=ENABLE=(LEVEL4, QUESTCODE)
The module adler32.c is testing the unsigned value len to see if
2005 Mar 02
1
Using varPower in gnls, an answer of sorts.
Back on January 16, a message on R-help from Ravi Varadhan described a
problem with gnls using weights=varPower(). The problem was that the
fit failed with error
Error in eval(expr, envir, enclos) : Object "." not found
I can reliably get this error in version 2.0.1-patched 2004-12-09 on
Windows XP and 2.0.1-Patched 2005-01-26 on Linux.
The key feature of that example is that the
2005 Jun 27
0
SSlogis problem with min(y)==0
Hi, I think this is a problem solved but I would be interested to know
if there is some good reason why SSlogis() behaves like this (apologies
if this has been noticed before- I'm not confident my archive searches
were effective):
I have been fitting large numbers of regressions using nls with a
self-starting 3 parameter logistic model (SSlogis()). I got a series of
unexpected errors of the
2020 Apr 28
0
[PATCH v3 2/3] device: detect if changing endianness failed
v2: relax the checks a little
Signed-off-by: Karol Herbst <kherbst at redhat.com>
---
drm/nouveau/nvkm/engine/device/base.c | 26 +++++++++++++++++++++-----
1 file changed, 21 insertions(+), 5 deletions(-)
diff --git a/drm/nouveau/nvkm/engine/device/base.c b/drm/nouveau/nvkm/engine/device/base.c
index 37589f365..c732074bf 100644
--- a/drm/nouveau/nvkm/engine/device/base.c
+++