Displaying 20 results from an estimated 4000 matches similar to: "nlme trouble"
2009 Sep 21
1
How to use nls when [selfStart] function returns NA or Inf??
Hi Everyone,
I posted this a couple of weeks ago with no responses. My interface (via
gmane) seemed a bit flakey at the time, so I'm venturing to repost with some
additional information.
I'm trying to write selfStart non-linear models for use with nls. In these
models some combinations of parameter values are illegal; the function value
is undefined.
That's OK when calling the
2008 Aug 18
1
"nested" getInitial calls; variable scoping problems
Hi All,
Another nls related problem (for background, I'm migrating a complicated
modelling package from S-plus to R).
Below I've reduced this to the minimum necessary to demonstrate my problem
(I think); the real situation is more complicated.
Two similar selfStart functions, ssA and ssB.
The 'initial' function for ssB modifies its arguments a little and then
calls getInital
2006 May 24
1
problem-nlme
Hi,
I have great problems with my work in R.
I look for to model the growth of fish.
I have "Longitudinal data", a serie of repeated
measures for each individual.
Using the corresponding packages "nlme" in R.
I treat to fit to the data different growth functions,
wich were entered by me.
Unfortunately for no it was arrived at the
convergence, several error messages appeared.
I
2009 Oct 17
1
custom selfStart model works with getInitial but not nls
Hello,
I'm having problems creating and using a selfStart model with nlme. Briefly,
I've defined the model, a selfStart object, and then combined them to make a
selfStart.default model.
If I apply getInitial to the selfStart model, I get results. However, if I try
usint it with nls or nlsList, these routines complain about a lack of initial
conditions.
If someone could point out
2005 Sep 07
1
summary of problem with mCall function.
Last week I posted a question concerning the mCall function, which is
used to create self-starting functions and is described in the book by
Pinheiro, J.C. and Bates, D.M. (Mixed-effects models in S and S-PLUS).
On page 345 one finds the following call:
xy<-sortedXyData(mCall[["x"]], LHS,data)
It is necessary to replace the "x" in the call to mCall by the actual
2005 Sep 01
1
making self-starting function for nls
Hello. Following pages 342-347 of Pinheiro & Bates, I am trying to
write a self-starting nonlinear function (a non-rectagular hyperbola) to
be used in nonlinear least squares regression (and eventually for a
mixed model). When I use the getInitial function for my self-starting
function I get the following error message:
> getInitial(photo~NRhyperbola(Irr,theta,Am,alpha,Rd),dat)
Error
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 <-
2008 Aug 29
1
nls() fails on a simple exponential fit, when lm() gets it right?
Dear R-help,
Here's a simple example of nonlinear curve fitting where nls seems to get
the answer wrong on a very simple exponential fit (my R version 2.7.2).
Look at this code below for a very basic curve fit using nls to fit to (a)
a logarithmic and (b) an exponential curve. I did the fits using
self-start functions and I compared the results with a more simple fit
using a straight lm()
2002 Jul 19
1
selfStart function problem
Hello, list,
I am making a self-starting nonlinear function to model the relation of tree height (H)
and diameter (D) in a forest stand. The function I am trying is
H=a*exp[b*(D+5.8)^(-c)].
To calculate the initial estimates of the parameters, I linearized the formula by taking
logarithms and fixing the parameter c=1. Then I calculated the initial estimates of a
and b using lm() on the
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
2009 Sep 04
1
How should a SelfStart function handle illegal parameter values?
Hi Everyone,
I'm trying to write selfStart non-linear models for use with nls. In these
models some combinations of parameter values are illegal; the function value
is undefined.
That's OK when calling the function directly [e.g. SSmodel(x, pars...)]; I
return an appropriate non-value such as NA or Inf.
However, when called from nls [e.g. nls(y~SSmodel(x, pars...), ...)] those
2013 Jun 26
2
Error on executing functions from installed package
Hi,
I am currently building an R package and I am facing a peculiar problem
where some of the functions does not work within the package. However, if I
source the script the function works.
For example, in a method for parallelization of analysis on each chromosome
simultaneously I am receiving error at the following position of the code:
# this profile the information chromosome wise and
2004 Oct 30
1
Destructive str(...)?
I have encountered a strange behavior of the str function - it seems to
modify the object that is displayed. Probably I'm using something
unsupported (objects consisting just of an external reference), but
still I'm curious as of why this happens. I create (in C code)
EXTPTRSXP and associate a class to it via SET_CLASS. Such objects works
fine until it's passed to str as the
2005 Oct 26
0
self starting function for nonlinear least squares.
Following on my posting of this morning, concerning a problem that I am
having constructing a self-starting function for use with nls (and
eventually with nlsList and nlme), the following is the self-starting
function called NRhyperbola:
> NRhyperbola
function (Irr,theta,Am,alpha,Rd)
{
# Am is the maximum gross photosynthetic rate
# Rd is the dark resiration rate (positive value)
#
2006 Mar 24
1
predict.glmmPQL Problem
Dear all,
for a cross-validation I have to use predict.glmmPQL() , where the
formula of
the corresponding glmmPQL call is not given explicitly, but constructed
using as.formula.
However, this does not work as expected:
x1<-rnorm(100); x2<-rbinom(100,3,0.5); y<-rpois(100,2)
mydata<-data.frame(x1,x2,y)
library(MASS)
# works as expected
model1<-glmmPQL(y~x1, ~1 | factor(x2),
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
2013 Dec 03
2
[PATCH 1/2] ppc64: Add ppc64le support
Add PowerPC 64bit little endian support.
Signed-off-by: Anton Blanchard <anton at samba.org>
---
Makefile | 7 +++++--
usr/klibc/arch/ppc64/MCONFIG | 4 ++--
usr/klibc/arch/ppc64/crt0.S | 34 ++++++++++++++++++++-----------
usr/klibc/arch/ppc64/setjmp.S | 40 ++++++++++++++++++++++++++----------
usr/klibc/arch/ppc64/sysstub.ph | 45
2009 Jun 09
1
Non-linear regression/Quantile regression
Hi,
I'm relatively new to R and need to do a quantile regression. Linear
quantile regression works, but for my data I need some quadratic function.
So I guess, I have to use a nonlinear quantile regression. I tried the
example on the help page for nlrq with my data and it worked. But the
example there was with a SSlogis model. Trying to write
dat.nlrq <- nlrq(BM ~ I(Regen100^2),
2000 Jul 24
1
How to use groupedData() within a function?
Dear Group:
I have been trying to write an R function within which the function
groupedData() would be used.
The following is a sample program:
#######################
sid<-rep(1:6,times=2)
time<-c(1:12)
trt<-rep(letters[1:3],times=4)
tem<-data.frame(sid,time,trt)
test1.fun<- function(dat=dat)
{
groupedData(time ~ trt|sid, data=dat)
}
test1.fun(dat=tem)
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