Displaying 20 results from an estimated 1000 matches similar to: "nlsList problems: control option does not effect output and strange environment search"
2008 Feb 18
2
skip non-converging nls() in a list
Howdee,
My question appears at #6 below:
1. I want to model the growth of each of a large number of individuals using
a 4-parameter logistic growth curve.
2. nlme does not converge with the random structure that I want to use.
3. nlsList does not converge for some individuals.
4. I decided to go around nlsList using:
t(sapply(split(data, list(data$id)),
function(subd){coef(nls(mass ~
2008 Feb 19
0
nlsList - Error in !unlist(lapply(coefs, is.null))
Howdee,
I am able to fit a 4-parameter logistic growth curve to a dataset which
comprise many individuals (using R v. 2.3.1). Yet, if I want to obtain the
parameters for each individual (i.e., for each 'id') using nlsList, then I
obtain an Error message which I have trouble interpreting. Any advice as to
how I can solve this problem?
Thanks for your time,
Marc
> reg <-nls(mass ~
2005 Apr 23
1
start values for nls() that don't yield singular gradients?
I'm trying to fit a Gompertz sigmoid as follows:
x <- c(15, 16, 17, 18, 19) # arbitrary example data here;
y <- c(0.1, 1.8, 2.2, 2.6, 2.9) # actual data is similar
gm <- nls(y ~ a+b*exp(-exp(-c*(x-d))), start=c(a=?, b=?, c=?, d=?))
I have been unable to properly set the starting value '?'s. All of
my guesses yield either a "singular gradient" error if they
2001 May 01
0
SSfpl self-start sometimes fails... workaround proposed
Hello,
nls library provides 6 self-starting models, among them: SSfp, a four
parameters logistic function. Its self-starting procedure involves several
steps. One of these steps is:
pars <- as.vector(coef(nls(y ~ cbind(1, 1/(1 + exp((xmid - x)/exp(lscal)))),
data = xydata, start = list(lscal = 0), algorithm = "plinear")))
which assumes an initial value of lscal equal to 0. If lscal
2009 Jun 29
0
nlsList {nlme} - control arguments problem
Hi All.
I'd like to send some control arguments to the nls function when
performing a nlsList analysis.
I'm fitting a power model to some grouped data and would like to
impose lower bounds on the estimates using the "port" algorithm.
Obtaining the lower bound constraint works fine with a direct call to
nls for a single level of the grouping variable. ?However, the bounds
2010 Apr 15
0
nlsList {nlme} - control arguments problem
Hi Rick
Thanks to Dieter Menne I did manage to solve the problem of imposing bounds on
the parameter space duirng an nlsList fit. He suggested using optim to optimize
the parameters prior to each fit. This worked well for me as I had a customized
selfStart function that then optimized the parameters for each individual
separately.
if you rewrote your selfStart function as:
powrDpltInit <-
2004 May 27
0
specifying starting values in nlsList/conversion problems
Hi
I am using nlsList from the nlme package to estimate group specific
coefficient sets to get a first impression of the structure of coefficients
in relation to potential predictor variables. In some cases I got
coefficients in other there are conversion problems due to bad start values
I guess, resulting in typical error messages as known from nls:
Error in nls(formula = formula, data = data,
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
2005 Jun 02
1
nls.control: increasing number of iterations
Hello,
I'm using the nls function and would like to increase the number of
iterations. According to the documentation as well as other postings on
R-help, I've tried to do this using the "control" argument:
nls(y ~ SSfpl(x, A, B, xmid, scal), data=my.data,
control=nls.control(maxiter=200))
but no matter how much I increase "maxiter", I get the following error
2001 Aug 03
0
step factor below minimum
I am trying to fit the 4-parameter logistic model with SSfpl. The
estimation is terminated with a message "step factor 0.000488281 reduced
below 'minFactor' of 0.000976562". I tried to change the minFactor with
nls.control(minFactor=yy) with no apparent success. A call of
nls.control() without arguments always shows the value of 0.000976562.
Also the estimation terminates as
2006 Feb 12
1
lme, nlsList, nlsList.selfStart
Dear listers,
I am trying to fit a model using nlsList() using alternately a SSfol()
selfstart function or its developped equivalent formulae.
This preliminary trial works well
mydata<-groupedData(Conc~Tps|Organ,data=mydata)
mymod1<-nls(Conc~SSfol(Dose,Tps,lKe,lKa,lCl),data=mydata)
as well as a developped form:
mymod2<-nls(Conc~Dose * exp(lKe+lKa-lCl) *
2010 Mar 31
1
nlsList{nlme} control of min and max parameter bounds?
Hi All
I'm analysing growth rates using a gompertz (logistic) curve and am attempting
to fit parameters for all of my study birds using nlsList.
I've been looking for an option in nlsList to set min and max limits for
parameter values during estimation, although I have failed to find any under
'control'. Other users seem to have reported that using control in the port
algorithm
2008 Jan 25
1
nlsList (nlme) error
Hi All.
I'm trying to run nlsList an getting an error that makes no sense to
me. I have accuracy and reaction time data over many trials for each
person (id)
When I use nlsList code that is virtually identical to the example in
the doc file I get the following error. I've tried everything I could
think of and can't get around it. Any ideas what I'm doing wrong?
**************
2017 Oct 20
1
Error messages using nonlinear regression function (nls)
Thank you Martin.
If I understand correctly, OP could do
wheat.list <- nlsList(Prop ~ SSfpl(end, A, B, xmid, scal), data=wlg)
or add some small value to all zeroes
wlg$prop < -wlg$Prop+1e-7
wheat.list <- nlsList(prop ~ SSlogis(end,Asym, xmid, scal), data=wlg)
which gives fairly reasonable results.
plot(augPred(wheat.list))
Am I correct?
Cheers
Petr
> -----Original Message-----
2007 Aug 23
0
Lost in substitute: nlsList and nlme with dynamic formula
DeaR
I am trying to use a dynamically create formula with nlsList and nlme, but I
cannot get the environment of the string-generated formal to work similarly
to the manually entered one.
Any idea?
Dieter
#-----
library(nlme)
# Pinheiro/Bates p 280
fm1Indom.lis = nlsList(conc~SSbiexp(time,A1,lrc1,A2,lrc2),
data=Indometh)
nlme(fm1Indom.lis,random=pdDiag(A1+lrc1+A2~1))
# works...
# Simulating
2004 Feb 23
0
Question concerning functions nlsList and nlme from nlme R library.
I hope that the mailing list is the correct forum for the question below. I
have trouble calling functions nlsList and nlme from
another function. Any help would be greatly appreciated.
Jens Praestgaard
Human Genome Sciences
Rockville MD.
I have a data set v with two components, v$mixeddat and v$init. They are
listed below:
> v$mixeddat
conc result rep sample z
11 20.00000000
2008 Mar 26
1
Compare parameter estimates of a nlsList object
Hello together,
Is there a tool to test the statistical differences between parameter estimates of a nlsList fit?
I fitted degradation data using the nlsList method and want to find out whether derived rate constants are significantly different from each other at the grouping factors soil and temperature.
Regards
Frank Scherr
2009 Jan 26
0
why two diff. se in nlsList?
Hi list,
In the object returned by summary.nlsList, what's the difference between "coefficients" and "parameters"? The have the same "Estimate", different se (therefore t value), but same p values.
R.2.8.0 on winxp with nlme_3.1-89
Thanks,
...Tao
+++++++++++++++++++++++++++++++++++++++++++++++++
> library(nlme)
> fm1 <- nlsList(uptake ~
2017 Oct 20
0
Error messages using nonlinear regression function (nls)
>>>>> PIKAL Petr <petr.pikal at precheza.cz>
>>>>> on Fri, 20 Oct 2017 06:33:36 +0000 writes:
> Hi
> Keep your messages in the list, you increase your chance to get some answer.
> I changed your data to groupedData object (see below), but I did not find any problem in it.
> plot(wlg)
> gives reasonable picture and I am
2006 Feb 01
1
Passing additional paramaters to nlsList(nlme) fit function
Hello, nls-users,
is it possible to pass additional parameters to the model function that are
known and groupwise constant with nlsList? I could not find something like a
"keep this fixed" option in the documentation and the code (my fault...?)
The current workaround is to break the problem down into groups and use
globals to pass the constant parameters, but it is ugly code and