Displaying 20 results from an estimated 1000 matches similar to: "start values for nls() that don't yield singular gradients?"
2002 May 02
2
a question
Hi,
I have a program written in R which is good on the version 1.2, but for
the fallowing versions of R, an error always is at the same place.
That is at the level of the fallowing line:
Sur<-
getInitial(res2[m:M,2]~SSasymp(res2[m:M,1],Asymp,resp0,lrc),data=res2)
Error in eval(expr,envir,enclos):numeric envir arg not of length one
I don't know at all this langage for the instant.
2013 Oct 03
2
SSweibull() : problems with step factor and singular gradient
SSweibull() : problems with step factor and singular gradient
Hello
I am working with growth data of ~4000 tree seedlings and trying to fit non-linear Weibull growth curves through the data of each plant. Since they differ a lot in their shape, initial parameters cannot be set for all plants. That’s why I use the self-starting function SSweibull().
However, I often got two error messages:
2011 Jun 17
2
Non-linear Regression best-fit line
I am trying to fit a curve to a cumulative mortality curve (logistic) where y is the cumulative proportion of mortalities, and t is the time in hours (see below). Asym. at 0 and 1
> y
[1] 0.00000000 0.04853859 0.08303777 0.15201970 0.40995074 0.46444992 0.62862069 0.95885057 1.00000000
[10] 1.00000000 1.00000000
> t
[1] 0 13 20 24 37 42 48 61 72 86 90
I tried to find starting values for
2006 Aug 24
2
my error with augPred
Dear all
I try to refine my nlme models and with partial success. The model is
refined and fitted (using Pinheiro/Bates book as a tutorial) but when
I try to plot
plot(augPred(fit4))
I obtain
Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop =
FALSE], :
Levels (0,3.5],(3.5,5],(5,7],(7,Inf] not allowed for
vykon.fac
>
Is it due to the fact that I have unbalanced
2010 Apr 12
0
How to derive function for parameters in Self start model in nls
Dear all
i want to fit the self start model in nls. i have two question. i have a
function,
(asfr ~ I(((a*b)/c))+ ((c/age)^3/2)+ exp((-b^2)*(c/age)+(age/c)-2)
i am wondering how to build the selfstart model. there is lost of example,
(i.e. SSgompertz, SSmicman, SSweibull, etc). my question is, how to derive
the function of parameters. and also which model to use for get
the initials values. In the
2013 Jan 04
2
(no subject)
Hi,
I am using the nls function and it stops because the number of iterations
exceeded 50, but i used the nls.control argument to allow for 500
iterations. Do you have any idea why it's not working?
fm1 <- nls(npe ~ SSgompertz(npo, Asym, b2, b3),
data=f,control=nls.control(maxiter=500))
Error in nls(y ~ exp(-b2 * b3^x), data = xy, algorithm = "plinear", start =
c(b2 =
2010 Jul 19
1
nls with some coefficients fixed
I'm using nls to fit a variety of different models. Here I use SSgompertz as
an example.
I want the ability to fix one (or more) of the coefficients that would
normally be optimised (e.g. fix b3=0.8).
Examples; based on and using data from example(SSgompertz)
#---------------------
# vanilla call to nls, no coefficients fixed, works fine
nls(density ~ SSgompertz(log(conc), Asym, b2, b3),
2004 Aug 10
0
Check failed after compilation (PR#7159)
Full_Name: Madeleine Yeh
Version: 1.9.1
OS: AIX 5.2
Submission from: (NULL) (151.121.225.1)
After compiling R-1.9.1 on AIX 5.2 using the IBM cc compiler, I ran the
checks. One of them failed. Here is the output from running the check solo.
root@svweb:/fsapps/test/build/R/1.9.1/R-1.9.1/tests/Examples:
># ../../bin/R --vanilla < stats-Ex.R
R : Copyright 2004, The R
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 ~
2009 Jun 11
1
formula for degrees of freedom for nonlinear mixed model in nlme
Dear forum members,
What is the formula to calculate denominator degrees of freedom (den df) for nonlinear mixed-effect models with covariates? My model is similar to a CO2 uptake example from Pinheiro and Bates (2000, page 376). In this CO2 dataset, there are two treatments and two types (84 observations in total), but den df for each parameter of the model is 64. Isn’t it too high?
Your
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
2003 Mar 28
1
winbind with ADS error
RedHat AS 2.1 kernel 2.4.9-e.16 with kbr5-1.2.7
I've been playing with ADS features of samba-3.0alpha21 and am having
problems getting winbind to work.
I can join the domain:
[root@asecl etc]# net ads join
Joined 'ASECL' to realm 'ASE-LRC-AD.AE.UTEXAS.EDU'
After joining the domain, I can use the other 'net ads' options of user,
group, status and info.
2012 Feb 18
3
foreach %do% and %dopar%
Hi everyone,
I'm working on a script trying to use foreach %dopar% but without success,
so I manage to run the code with foreach %do% and looks like this:
The code is part of a MCMC model for projects valuation, returning the most
important results (VPN, TIR, EVA, etc.) of the simulation.
foreach (simx = NsimT, .combine=cbind, .inorder=FALSE, .verbose=TRUE) %do% {
MCPVMPA = MCVAMPA[simx]
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
2017 Aug 23
2
strange nlme augpred behaviour
Dear all
I encountered strange behaviour of augPred with virtually the same data
First I made groupedData object.
> mar.g<-groupedData(rutilizace~doba|int, data=mar)
When I perform nlme on complete dataset I get an error with augPred
> fit<-nlsList(rutilizace~SSasymp(doba, Asym, R0, lrc), data=mar.g)
Warning message:
c("1 error caught in nls(y ~ cbind(1 - exp(-exp(lrc) * x),
2017 Aug 23
0
strange nlme augpred behaviour
Better posted on r-sig-mixed-models , no?
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Wed, Aug 23, 2017 at 5:17 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote:
> Dear all
>
> I encountered strange
2012 Aug 14
1
bootstrapped CI for nonlinear models using nlsBoot from nlstools
Hi all
I?m trying to get confidence intervals for parameters from nls modeling. I fitted a nls
model to the following variables:
> x
[1] 2 1 1 5 4 6 13 11 13 101 101 101
> y
[1] 1.281055090 1.563609934 0.001570796 2.291579783 0.841891853
[6] 6.553951324 14.243274230 14.519899320 15.066473610 21.728809880
[11] 18.553054450 23.722637370
The model fitted was:
2002 Sep 27
2
How to apply SSfpl with binary data
Dear R-help subscribers
Would you tell me how to apply SSfpl with binary data as below?
Unfortunately, there is not the EXAMPLE in help(SSfpl) for binary data but for quantitative data(Chick).
V1: dose
V2: log-transformed dose
V3: response (rate)
V1 V2 V3
1 0.775 -0.2548922 0.1666667
2 5.000 1.6094379 0.8148148
3 10.000 2.3025851 0.5000000
4 20.000 2.9957323
2017 Aug 23
2
strange nlme augpred behaviour
Hi
Well, yes I tried it about two weeks ago but my post did not get through as it still awaits moderator approval. I could check which column is offending but actually it is only minor nuisance, I can live with selection of columns before fitting a model. What seems to me strange is that both full dataset and only selected colums gave me identical fit results but only one works within augPred.
2009 Oct 19
2
How to get slope estimates from a four parameter logistic with SSfpl?
Hi,
I was hoping to get some advice on how to derive estimates of slopes from four parameter logistic models fit with SSfpl.
I fit the model using:
model<-nls(temp~SSfpl(time,a,b,c,d))
summary(model)
I am interested in the values of the lower and upper asymptotes (parameters a and b), but also in the gradient of the line at the inflection point (c) which I assume tells me my rate of