[R] Extract Coeff, Std Error, etc from gnls output

2005-06-22 Thread Christian Mora
Dear list members;

Is there any trick to extract the coefficients along with std errors,
t-values and p-values for each beta from a gnls fit model (similar to the
results obtained using summary(lm)$coeff for linear models)?

Thanks for any hint

cm

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[R] error in gnls

2005-07-25 Thread Christian Mora




Dear R users;

I'm trying to fit nonlinear model (asymptotic regression model) with gnls
from library nlme in R 2.1.0 with no big issues so far. However after
installed the version R 2.1.1, when I tried to update the initial model
including a var-cov model I've got the error: "Error: Object "convIter" not
found". This error occurs only with R 2.1.1. Any ideas?

Thanks

Christian Mora

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[R] nlme questions

2005-11-03 Thread Christian Mora




Dear R users;

Ive got two questions concerning nlme library 3.1-65 (running on R 2.2.0 /
Win XP Pro). The first one is related to augPred function. Ive been working
with a nonlinear mixed model with no problems so far. However, when the
parameters of the model are specified in terms of some other covariates,
say treatment (i.e. phi1~trt1+trt2, etc) the augPred function give me the
following error: "Error in predict.nlme(object,
value[1:(nrow(value)/nL),,drop=FALSE], : Levels 0,1 not allowed for trt1,
trt2". The same model specification as well as the augPred function under
SPlus 2000 run without problems. The second question has to deal with the
time needed for the model to converge. It really takes a lot of time to fit
the model on R in relation to the time required to fit the same model on
SPlus. I can imagine this is related to the optimization algorithm or
something like that, but I would like to have a different opinion on these
two issues.

Thanks in advance

Christian Mora

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Re: [R] nlme questions

2005-11-18 Thread Christian Mora





Spencer;

Thanks for your suggestions. I found the problem is in the library nlme. If
you define phi1~factor(trt1)+factor(trt2) instead of phi1~trt1+trt2 the
augPred function works. A bug? I don't know.

Christian






Spencer Graves <[EMAIL PROTECTED]> on 17-11-2005 20:19:32

To:    Christian Mora <[EMAIL PROTECTED]>
cc:r-help@stat.math.ethz.ch

Subject:Re: [R] nlme questions


   Both your questions seem too vague to me.  You might get more useful
replies if you provide a simple example in a few lines of R code that a
reader could copy from your email into R and see the result (as
suggested in the posting guide! "www.R-project.org/posting-guide.html").
  The process of preparing such a simple example might by itself provide
the insight you desire.  Alternatively, you might work line by line
through the code for the R function you are using.  Also, if you don't
have Pinheiro and Bates (2000) Mixed-Effects Models in S and S-PLUS
(Springer), I suggest you get it;  it is excellent for things like this.

   I'm sorry I couldn't help more.
   spencer graves

Christian Mora wrote:

>
>
>
> Dear R users;
>
> Ive got two questions concerning nlme library 3.1-65 (running on R 2.2.0
/
> Win XP Pro). The first one is related to augPred function. Ive been
working
> with a nonlinear mixed model with no problems so far. However, when the
> parameters of the model are specified in terms of some other covariates,
> say treatment (i.e. phi1~trt1+trt2, etc) the augPred function give me the
> following error: "Error in predict.nlme(object,
> value[1:(nrow(value)/nL),,drop=FALSE], : Levels 0,1 not allowed for trt1,
> trt2". The same model specification as well as the augPred function under
> SPlus 2000 run without problems. The second question has to deal with the
> time needed for the model to converge. It really takes a lot of time to
fit
> the model on R in relation to the time required to fit the same model on
> SPlus. I can imagine this is related to the optimization algorithm or
> something like that, but I would like to have a different opinion on
these
> two issues.
>
> Thanks in advance
>
> Christian Mora
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

--
Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
333 West San Carlos Street Suite 700
San Jose, CA 95110, USA

[EMAIL PROTECTED]
www.pdf.com <http://www.pdf.com>
Tel:  408-938-4420
 Fax: 408-280-7915

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Re: [R] nlme questions

2005-11-18 Thread Christian Mora





Yes, I agree. But if you define at the beginning of the code:

data$trt1<-as.factor(data$trt1)
data$trt2<-as.factor(data$trt2)

being trt1 and trt2 dummy variables with values 0 or 1, and then run the
model, for instance:

fit_1<-nlme(Y~b0/(1+exp((b1-X)/b2)),fixed=b0+b1+b2~trt1+trt2,
random=b0+b1+b2~1,data=data,start=fixef(fit_0))

the augPred function doesn't work and return the error

"Error in predict.nlme(object, value[1:(nrow(value)/nL),,drop=FALSE], : Levels 
0,1 not allowed for trt1,
trt2"

but, if you modify the code as

fit_2<-nlme(Y~b0/(1+exp((b1-X)/b2)),fixed=b0+b1+b2~factor(trt1)+factor(trt2),
random=b0+b1+b2~1,data=data,start=fixef(fit_0))

i.e. indicating again that trt1 and trt2 are factors, even when they were
previouslly defined as factors through the function "as.factors", then
augPred works








"Austin, Matt" <[EMAIL PROTECTED]> on 18-11-2005 07:19:24

To:"'Christian Mora'" <[EMAIL PROTECTED]>, Spencer Graves
   <[EMAIL PROTECTED]>
cc:r-help@stat.math.ethz.ch

Subject:RE: [R] nlme questions


Warning:  non-expert thoughts to follow.

When passing an object to a predict method, the method looks at (a copy) of
the original information from the dataframe that was used in the fit.  Your
original data contains information on trt1 and trt2, but factor(trt1) and
factor(trt2) cannot be found in the original data.  If you did the factor
conversion in the original data

myDat <- factor(myDat$trt1)
myDat <- factor(myDat$trt2)

then used myDat as the dataframe in the nlme call, all information would be
available for the augPred method.  That's why it works when you use trt1
and
trt2 instead of factor(trt1) and factor(trt2).  There is actually an
implicit factor conversion happening in the nlme call if trt1 and trt2 are
character variables, however if trt1 and trt2 are defined as numeric (ie 0
1) then it will fit as a numeric.

--Matt

> -----Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] Behalf Of Christian Mora
> Sent: Friday, November 18, 2005 4:01 AM
> To: Spencer Graves
> Cc: r-help@stat.math.ethz.ch
> Subject: Re: [R] nlme questions
>
>
>
>
>
>
>
> Spencer;
>
> Thanks for your suggestions. I found the problem is in the
> library nlme. If
> you define phi1~factor(trt1)+factor(trt2) instead of
> phi1~trt1+trt2 the
> augPred function works. A bug? I don't know.
>
> Christian
>
>
>
>
>
>
> Spencer Graves <[EMAIL PROTECTED]> on 17-11-2005 20:19:32
>
> To:Christian Mora <[EMAIL PROTECTED]>
> cc:r-help@stat.math.ethz.ch
>
> Subject:Re: [R] nlme questions
>
>
>Both your questions seem too vague to me.  You might get
> more useful
> replies if you provide a simple example in a few lines of R
> code that a
> reader could copy from your email into R and see the result (as
> suggested in the posting guide!
> "www.R-project.org/posting-guide.html").
>   The process of preparing such a simple example might by
> itself provide
> the insight you desire.  Alternatively, you might work line by line
> through the code for the R function you are using.  Also, if you don't
> have Pinheiro and Bates (2000) Mixed-Effects Models in S and S-PLUS
> (Springer), I suggest you get it;  it is excellent for things
> like this.
>
>I'm sorry I couldn't help more.
>spencer graves
>
> Christian Mora wrote:
>
> >
> >
> >
> > Dear R users;
> >
> > Ive got two questions concerning nlme library 3.1-65
> (running on R 2.2.0
> /
> > Win XP Pro). The first one is related to augPred function. Ive been
> working
> > with a nonlinear mixed model with no problems so far.
> However, when the
> > parameters of the model are specified in terms of some
> other covariates,
> > say treatment (i.e. phi1~trt1+trt2, etc) the augPred
> function give me the
> > following error: "Error in predict.nlme(object,
> > value[1:(nrow(value)/nL),,drop=FALSE], : Levels 0,1 not
> allowed for trt1,
> > trt2". The same model specification as well as the augPred
> function under
> > SPlus 2000 run without problems. The second question has to
> deal with the
> > time needed for the model to converge. It really takes a
> lot of time to
> fit
> > the model on R in relation to the time required to fit the
> same model on
> > SPlus. I can imagine this is related to the optimization
> algorithm or
> > something like that, but I would like to have a different opinion on
> these
> > two issues.
> >
> > Thanks in advance
> >
> > Christian Mora
> >
> > _

RE: [R] Tutorial for graphics

2004-06-16 Thread Christian Mora
A fairly good tutorial is “Gráficos Estadísticos con R” by Juan Carlos
Correa and Nelfi González (PDF [2110kB]) that you can find in
Documentation/Contributed (in Spanish though). 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Phil
Sent: Wednesday, June 16, 2004 10:13 PM
To: [EMAIL PROTECTED]
Subject: [R] Tutorial for graphics


Hi all,

I'm coming to R from Matlab and I'm finding it difficult to find a good
introduction to graphics in R.  (The best I've found so far is Ch. 4 of
Emmanuel Paradis "R for Beginners".  Still, I have been unable to
discover simple things like how to resize the axes on an existing plot,
how to add (or change) axis labels on an existing plot, etc.  Can anyone
point me to a suitable tutorial, or even tell me how to perform those
tasks?

Also, Matlab's graphical widget has the ability to zoom (and unzoom) by
drawing a rectangle on the graph with the mouse.  Is there anything
similar in R?

Thanks in advance,

Phil Morenz

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[R] intersect two files

2004-08-10 Thread Christian Mora
Hi all;
Im working with two datasets in R, say data1 and data2. Both datasets
are composed of several rows and columns (dataframe) and some of the
rows are identical in both datasets. Im wondering if there is any way to
remove from one set, say data1, the rows that are identical in the other
set, say data2, using R?
Thanks for any hint in advance
Christian

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RE: [R] covariate selection?

2004-10-12 Thread Christian Mora
Hi Ian
Have you tried help.search("pca")?
Christian

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Martínez Ovando
Juan Carlos
Sent: Tuesday, October 12, 2004 7:56 PM
To: Ian Fiske
Cc: [EMAIL PROTECTED]
Subject: RE: [R] covariate selection?


Hello Ian,

Sorry. I don't really understand your problem, which is of model
selection. That's right? 

You could use some criteria based in likelihood. For instante Akaike
(AIC) or Schwarz criteria (BIC), see: 

?AIC

?mle.aic

(The best model is determined minimizing AIC or BIC).

I hope this help you.

Greetings,
 
Juan Carlos 

-Mensaje original-
De: Ian Fiske [mailto:[EMAIL PROTECTED] 
Enviado el: Martes, 12 de Octubre de 2004 05:17 PM
Para: Martínez Ovando Juan Carlos
CC: [EMAIL PROTECTED]
Asunto: Re: [R] covariate selection?

Thanks Juan.  I thought that was what I was looking for, but really, I 
want to know which of the original covariates could best be used to take

advantage of their colinearity without creating new variables.  I think 
PCA creates new variables.  SAS and SPSS can do what I'm talking about, 
but I would like to use R for this.

Thanks,
Ian



Martínez Ovando Juan Carlos wrote:

>Hello Ian,
>
>?princomp
>
>If your covariates are scalars, and the following documents:
>
>http://www.jstatsoft.org/v07/i01/drdoc.pdf
>
>http://www.bioconductor.org/workshops/Milan/PDF/Lab12.pdf
>
>
>Best wishes.
>
>Saludos,
> 
>Juan Carlos Martínez Ovando
>Banco de México
>Av. 5 de Mayo No. 18
>Piso 5 Sección D
>Col. Centro
>06059  México, D. F.
>Tel. +52 55 52.37.20.00 ext. 3594
>Fax. +52 55 52.37.27.03
>e-mail: [EMAIL PROTECTED]
> 
>
>-Mensaje original-
>De: Ian Fiske [mailto:[EMAIL PROTECTED]
>Enviado el: Martes, 12 de Octubre de 2004 04:08 PM
>Para: [EMAIL PROTECTED]
>Asunto: [R] covariate selection?
>
>Hello,
>
>I am hoping someone can help me with the following multivariate issue:
>I have a model consisting of about 50 covariates.  I would like to 
>reduce this to about 5 covariate for the reduced model by combining 
>cofactors that are strongly correlated.  Is there a package or function

>that would help me with this in R?  I appreciate any suggestions.
>
>Thanks,
>Ian
>
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>
>
>  
>

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RE: [R] Sampling

2003-12-01 Thread Christian Mora
YourData[sample(209,106),]

Regards
Christian Mora


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Savano
Sent: Monday, December 01, 2003 9:38 AM
To: Lista R
Subject: [R] Sampling


UseRs,

I imported a table using "read.table". It has 209 observations, I want
to 
select a sample with 106 observations.  What function I use?

thanks.

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[R] Johnson's Sb distribution

2003-12-09 Thread Christian Mora
Hi all;

I'm working with the library SuppDists trying to fit a Johnson's Sb
distribution to a dataset. It works fine, but I need to set one of the
location parameters (epsilon) to zero. How can I do this using the
function JohnsonFit() or any other similar? ...and Is it possible to
define the type (SN,SL,SB,SU) or the library assumes the type
automatically depending on the data?

Thanks for any hint

Christian

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[R] mode

2003-12-11 Thread Christian Mora
How can I get the mode (most frequent value) from a dataset (continuos
variables)? I can obtain it when the data is discrete (by making a table
and looking at the higher frequency) but I don't know how obtain it
from, for example, a density plot of the data. Does anyone know how to
do it? Thanks
CM

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[R] 4-parameter logistic model

2003-02-21 Thread Christian Mora
Dear R users

I'm a new user of R and I have a basic question about the 4-parameter
logistic model. According to the information from Pinheiro & Bates the model
is:

y(x)=theta1+(theta2-theta1)/(1+exp((theta3-x)/theta4)) ==
y(x)=A+(B-A)/(1+exp((xmid-input)/scal))

from the graph in page 518 of the book of the same authors (mixed models in
S) theta 1 corresponds to the horizontal asymptote as x goes to infinity and
theta2 the horizontal asymptote as x goes to -infinity. When I use the
function SSfpl(input,A,B,xmid,scal), I'm not sure why the value of A is the
lower of the two asymptotes if according to the original function A should
be equal to theta1 (upper asymptote).. or maybe I'm wrong.

I'll appreciate any comment on this.

Best Regards

CM

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[R] Lattice graphs and legend

2003-08-09 Thread Christian Mora
Dear all,

I'm working with grouped data using the nlme package
in R. By using the function plot() I'm trying to
obtain a trellis-like graph but by default a legend is
placed on top of the plot. How can I remove this
legend?

Thanks for any hint

Christian Mora

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[R] Question about 'NA'

2003-08-09 Thread Christian Mora
Hi all,

Ive got a database with 10 columns (different
variables) for 100 subjects, each column with
different # of NA's. I'd like to know if it is
possible to use a function to exclude the NA's using
only a specific column, lets say:

Data2 <- omit.exclude(Data1$column1) ??, then
Data3 <- omit.exclude(Data1$column2) and so on 

I tried the code above but with no results

Thanks for any help

CM

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[R] gnls - Step halving....

2003-08-14 Thread Christian Mora
Hi all,

I'm working with a dataset from 10 treatments, each
treatment with 30 subjects, each subject measured 5
times. The plot of the dataset suggests that a
3-parameter logistic could be a reasonable function to
describe the data. When I try to fit the model using
gnls I got the message 'Step halving factor reduced
below minimum in NLS step'. I´m using as the initial
values of the parameters those obtained from the nls
fit. Is a problem of the initial estimates of the
parameters that I get the error or could be something
else?

The code for the nls fit was:

options(contrasts=c("contr.helmert","contr.poly")) 
VA1.lis<-nlsList(DRAM~SSlogis(MED,phi1,phi2,phi3)|TRAT,
data=VA1,na.action=na.omit)

The code for the gnls fit was (using a 'difference
parameterization' like SAS):

options(contrasts=c("contr.SAS","contr.poly")) 
VA1.gnls<-gnls(DRAM~SSlogis(MED,phi1,phi2,phi3),
data=VA1,params=list(phi1~TRAT,phi2~TRAT,phi3~TRAT), 
start=c(
23.36209,  avg of phi1 for the 10 trts *
-0.8549794,  * diff. between avg and nls
estimate of TRAT#2 **
.and so on

I´d appreciate any comment

Thanks
CM

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[R] gnls - Step halving....

2003-08-14 Thread Christian Mora
Hi all,

I'm working with a dataset from 10 treatments, each
treatment with 30 subjects, each subject measured 5
times. The plot of the dataset suggests that a
3-parameter logistic could be a reasonable function to
describe the data. When I try to fit the model using
gnls I got the message 'Step halving factor reduced
below minimum in NLS step'. I´m using as the initial
values of the parameters those obtained from the nls
fit. Is a problem of the initial estimates of the
parameters that I get the error or could be something
else?

The code for the nls fit was:

options(contrasts=c("contr.helmert","contr.poly")) 
VA1.lis<-nlsList(DRAM~SSlogis(MED,phi1,phi2,phi3)|TRAT,
data=VA1,na.action=na.omit)

The code for the gnls fit was (using a 'difference
parameterization' like SAS):

options(contrasts=c("contr.SAS","contr.poly")) 
VA1.gnls<-gnls(DRAM~SSlogis(MED,phi1,phi2,phi3),
data=VA1,params=list(phi1~TRAT,phi2~TRAT,phi3~TRAT), 
start=c(
23.36209,  avg of phi1 for the 10 trts *
-0.8549794,  * diff. between avg and nls
estimate of TRAT#2 **
.and so on

I´d appreciate any comment

Thanks
CM

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[R] custom loss function + nonlinear models

2005-04-04 Thread Christian Mora
Hi all;

I'm trying to fit a reparameterization of the
assymptotic regression model as that shown in
Ratkowsky (1990) page 96. 

Y~y1+(((y2-y1)*(1-((y2-y3)/(y3-y1))^(2*(X-x1)/(x2-x1/(1-((y2-y3)/(y3-y1))^2))

where y1,y2,y3 are expected-values for X=x1, X=x2, and
X=average(x1,x2), respectively.

I tried first with Statistica v7 by LS and
Gauss-Newton algorithm without success (no
convergence: predictors are redundant). Then I
tried with the option CUSTOM LOSS FUNCTION and several
algorithms like Quasi-Newton, Simplex, Hookes-Jeeves,
among others. In all these cases the model converged
to some values for the parameters in it.

My question is (after searching the help pages) : Is
there such a thing implemented in R or can it be
easily implemented? In other words, is it possible to
define which loss function to use and the algorithm to
find the parameters estimates? 

Thanks
Christian

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RE: [R] Non-Linear Regression Problem

2004-04-14 Thread Christian Mora
Working on the same idea, Ive generated a data grid with 4 vars, two of
them with its own sequence and two with fixed values. As Spencer pointed
out one option is to get the values from a simple loop. My question is:
How can jump from one set of starting values to the next (on the data
grid) in case they cause an invalid value in the model Im evaluating? In
my example, Ive 12 possible combinations of the 4 vars and in the 6th
combination I get an error and the loop is terminated so what Im looking
for is to skip this problem and continue from the 7th to 12th
combination of starting points

Ill appreciate any comment

Code:

data<-expand.grid(alpha=100,delta=4,beta=seq(1,2,by=0.5),gamma=seq(.1,.4
,by=.1))
for(i in 1:12){
fit<-nls(y~delta+(alpha-delta)/(1+exp(beta*log(rate/gamma))),data=base,s
tart=c(alpha=data$alpha[i],delta=data$delta[i],beta=data$beta[i],gamma=d
ata$gamma[i]),trace=T)
}

Thanks
CMora



-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Spencer Graves
Sent: Wednesday, April 14, 2004 12:27 PM
To: WilDscOp
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Non-Linear Regression Problem


1.  For the equation you mentioned, have you considered the following: 

DF <- data.frame(t.=c(1, 4, 16), Y=c(.8, .45, .04))
# I do NOT use "t" as a name, as it
# may conflict with the matrix transpose function.
fit0 <- lm(log(Y)~t.-1, DF)
fit0
Call:
lm(formula = log(Y) ~ t. - 1, data = DF)

Coefficients:
 t. 
-0.2012 


  If this is the problem you really wanted to solve AND you honestly

need NONLINEAR least squares, I would expect that (-0.2) should provide 
a reasonable starting value for nls: 

 > fit1 <- nls(Y~exp(-THETA*t.), data=DF, start=c(THETA=-0.2))
 > fit1
Nonlinear regression model
  model:  Y ~ exp(-THETA * t.)
   data:  DF
THETA
0.2034489
 residual sum-of-squares:  0.0003018337
 >

  2.  Alternatively, you could compute the sum of squares for all 
values of THETA = seq(0, .01, 100) in a loop, then find the minimum by 
eye. 

  3.  If this is just a toy example, and your real problem has 
several parameters, "expand.grid" will produce a grid, and you can 
compute the value of your function and the sum of squares of residuals 
at every point in the grid in a single loop, etc. 

  hope this helps.  spencer graves

WilDscOp wrote:

> Dear all,
>
> I was wondering if there is any way i could do a "Grid Search" on 
> a parameter space using R (as SAS 6.12 and higher can do it) to start 
> the Newton-Gauss Linearization least squares method when i have NO 
> prior information about the parameter.
> W. N. Venables and B. D. Ripley (2002) "Modern Applied Statistics with

> S", 4 th ed., page 216-7  has a topic "Self-starting non-linear 
> regressions" using negexp.SSival - but i can not solve my hypothetical

> problem using that - my problem is :
>
> Y = EXP(-(THETA * t)) with data below for estimating THETA:
>
> tY
> 10.80
> 4 0.45
> 16 0.04
>
> Whatever i could do, is in 
> http://www.angelfire.com/ab5/get5/nonlinear.PDF
>
> Any response / help / comment / suggestion / idea / web-link / replies

> will be greatly appreciated.
>
> Thanks in advance for your time.
>
> ___
>
> Mohammad Ehsanul Karim <[EMAIL PROTECTED]>
> Institute of Statistical Research and Training
> University of Dhaka, Dhaka- 1000, Bangladesh
>
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