Displaying 20 results from an estimated 1000 matches similar to: "gnls or nlme : how to obtain confidence intervals of fitted values"
2009 Jan 07
1
Extracting degrees of freedom from a gnls object
Dear all,
How can I extract the total and residual d.f. from a gnls object?
I have tried str(summary(gnls.model)) and str(gnls.model) as well as gnls(), but couldn?t find the
entry in the resulting lists.
Many thanks!
Best wishes
Christoph
--
Dr. rer.nat. Christoph Scherber
University of Goettingen
DNPW, Agroecology
Waldweg 26
D-37073 Goettingen
Germany
phone +49 (0)551 39 8807
fax +49
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())
2008 Sep 27
1
seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"}
>>>>> "VW" == Viechtbauer Wolfgang (STAT) <Wolfgang.Viechtbauer at STAT.unimaas.nl>
>>>>> on Fri, 26 Sep 2008 18:00:19 +0200 writes:
VW> Hi all, I'm trying to fit a marginal (longitudinal)
VW> model with an exponential serial correlation function to
VW> the Orange tree data set. However, R crashes frequently
VW>
2004 Feb 20
1
nlme and multiple comparisons
This is only partly a question about R, as I am not quite sure about the
underlying statistical theory either.
I have fitted a non-linear mixed-effects model with nlme. In the fixed
part of the model I have a factor with three levels as explanatory
variable. I would like to use Tukey HSD or a similar test to test for
differences between these three levels.
I have two grouping factors:
2001 Jun 01
1
nls works but not gnls
This works fine:
fit42<-nls(Vfs~SSlogis(Months,Asym.Int+Asym.Group*Groupdum,xmid,scal),
data=df,
start=c(Asym.Int=22,Asym.Group=5,xmid=2,scal=6),
na.action=na.omit)
But this, identical except using gnls, doesn't converge:
fit43<-gnls(Vfs~SSlogis(Months,Asym.Int+Asym.Group*Groupdum,xmid,scal),
data=df,
start=c(Asym.Int=22,Asym.Group=5,xmid=2,scal=6),
na.action=na.omit)
Error in gnls(Vfs
2004 Apr 05
3
2 lme questions
Greetings,
1) Is there a nice way of extracting the variance estimates from an lme fit? They don't seem to be part of the lme object.
2) In a series of simulations, I am finding that with ML fitting one of my random effect variances is sometimes being estimated as essentially zero with massive CI instead of the finite value it should have, whilst using REML I get the expected value. I guess
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,
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
2007 Oct 17
2
nmle: gnls freezes on difficult case
Hi,
I am not sure this is a bug but I can repeat it, The functions and data
are below.
I know this is nasty data, and it is very questionable whether a 4pl
model
is appropriate, but it is data fed to an automated tool and I would
have hoped for an error. Does this repeat for anyone else?
My details:
> version
_
platform i686-pc-linux-gnu
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 Aug 08
1
NLME augPred error
Could someone explain the meaming of this error message from augPred:
> augPred(area3.pen.nlme, primary=~day)
Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop =
FALSE], :
Levels 1,2,3 not allowed for block
>
predict.nlme(area3.pen.nlme) does not produce an error.
area3.pen.nlme was created with:
> area3.pen.nlme <- nlme(area ~ SSlogis(day, Asym, xmid, scal),
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
2011 Nov 17
3
Obtaining a derivative of nls() SSlogis function
Hello, I am wondering if someone can help me. I have the following function
that I derived using nls() SSlogis. I would like to find its derivative. I
thought I had done this using deriv(), but for some reason this isn't
working out for me.
Here is the function:
asym <- 84.951
xmid <- 66.90742
scal <- -6.3
x.seq <- seq(1, 153,, 153)
nls.fn <- asym/((1+exp((xmid-x.seq)/scal)))
2008 Jan 04
3
nls (with SSlogis model and upper limit) never returns (PR#10544)
Full_Name: Hendrik Weisser
Version: 2.6.1
OS: Linux
Submission from: (NULL) (139.19.102.218)
The following computation never finishes and locks R up:
> values <- list(x=10:30, y=c(23.85, 28.805, 28.195, 26.23, 25.005, 20.475,
17.33, 14.97, 11.765, 8.857, 5.3725, 5.16, 4.2105, 2.929, 2.174, 1.25, 1.0255,
0.612, 0.556, 0.4025, 0.173))
> y.max <- max(values$y)
> model <- nls(y ~
2006 Jan 09
1
trouble with extraction/interpretation of variance structure para meters from a model built using gnls and varConstPower
I have been using gnls with the weights argument (and varConstPower) to
specify a variance structure for curve fits. In attempting to extract the
parameters for the variance model I am seeing results I don't understand.
When I simply display the model (or use "summary" on the model), I get what
seem like reasonable values for both "power" and "const". When I
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
2000 Oct 14
2
Access to calculations in nls
Hi,
I would like to be able to access the calculated results from the nls package.
Using the example in R, fm3DNase1 we can reurn certain parts of the
calculations:
> coef(fm3DNase1)
Asym xmid scal
2.345179 1.483089 1.041454
> resid(fm3DNase1)
[1] -0.0136806237 -0.0126806237 0.0089488569 0.0119488569 -0.0025803222
[6] 0.0064196778 0.0026723396 -0.0003276604
2011 Aug 09
1
nls, how to determine function?
Hi R help,
I am trying to determine how nls() generates a function based on the
self-starting SSlogis and what the formula for the function would be.
I've scoured the help site, and other literature to try and figure
this out but I still am unsure if I am correct in what I am coming up
with.
**************************************************************************
dat <-
2001 Oct 07
1
Bug in Deriv? (PR#1119)
deriv seems to have problems with a minus-sign before a bracket.
Below are four examples of the same function, the top one
is wrong, all others are correct (hopefully).
Rest of expression not shown, it is the same for all versions.
_
platform i386-pc-mingw32
arch x86
os Win32
system x86, Win32
status
major 1
minor 3.0
year 2001
month 06
day 22
language R