[R] data transformation

From: gabriela escati peñaloza <gescati_at_yahoo.com.ar>
Date: Wed 24 May 2006 - 23:19:12 EST


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 am going to display the growth functions so as they were entered and a "nlme" call example:

# differents growth function

#vonBertlalanffy

vonBert<- function(x, Linf, K, t0)
Linf*(1-exp(-K*(x-t0)))

size ~ vonBert(age, Linf, K,t0)

vonBert <-deriv(~ Linf*(1-exp(-K*(x-t0))),

      c("Linf","K","t0"),function(x,Linf,K,t0){})

vonBertInit <- function(mCall, LHS, data)   {
xy <- sortedXyData(mCall[["x"]], LHS, data)

    Linf <- 900
    if (Linf != max(xy[,"y"])) Linf <- -Linf     K <- 0.3
    t0<-0
    value <- c(Linf, K, t0)
    names(value) <- mCall[c("Linf", "K","t0")]     value
 }

vonBert <- selfStart(vonBert, initial = vonBertInit)

class(vonBert)

#Richards

Rich <- function(x, Linf, K, t0, m)
Linf*(1-exp(-K*(x-t0)))^(1/(1-m))

size ~ Rich(age, Linf, K, t0, m)  

Rich <-deriv(~ Linf*(1-exp(-K*(x-t0)))^(1/(1-m)),      

c("Linf","K","t0","m"),function(x,Linf,K,t0,m){})

RichInit <- function(mCall, LHS, data)
  {
xy <- sortedXyData(mCall[["x"]], LHS, data)

    Linf <- 900
    if (Linf != max(xy[,"y"])) Linf <- -Linf

    K <- 0.3
    t0<-0
    m <- 0.3

    value <- c(Linf, K, t0, m)
    names(value) <- mCall[c("Linf", "K","t0","m")]     value
 }

Rich <- selfStart(Rich, initial = RichInit)

class(Rich)

#call

Rich.nlme <- nlme(size ~ Rich(age, Linf, K, t0, m),

	data = L.gd,
	fixed = Linf + K +t0 +m~ 1,
      start = list(fixed = c(900, 0.3,-3,0.9)))

#error message

Error: Singularity in backsolve at level 0, block 1 In addition: Warning message:
NaNs produced in: log(x)

What is the problem? I do not understand that it is what is bad: the data, the entered growth functions, some specification...
I will thank for any contribution of information.

Lic. Gabriela Escati Peñaloza
Biología y Manejo de Recursos Acuáticos
Centro Nacional Patagónico(CENPAT).
CONICET
Bvd. Brown s/nº.
(U9120ACV)Pto. Madryn
Chubut
Argentina

Tel: 54-2965/451301/451024/451375/45401 (Int:277) Fax: 54-29657451543                 



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