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 Pe?aloza
Biolog?a y Manejo de Recursos Acu?ticos
Centro Nacional Patag?nico(CENPAT).
CONICET
Bvd. Brown s/n?.
(U9120ACV)Pto. Madryn
Chubut
Argentina
Tel: 54-2965/451301/451024/451375/45401 (Int:277)
Fax: 54-29657451543
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