[R] nls() and loop

[Jeff Newmiller]

?tryCatch
-- 
Sent from my phone. Please excuse my brevity.

On October 20, 2017 7:37:12 AM PDT, Evangelina Viotto <evangelinaviotto at gmail.com> wrote:
>Hello I´m need fitt growth curve with data length-age. I want to
>evaluate
>which is the function that best predicts my data, to do so I compare
>the
>Akaikes of different models. I'm now need to evaluate if changing the
>initial values changes the parameters and which do not allow to
>estimate
>the model.
>To do this I use the function nls(); and I randomize the initial values
>(real positive number).  To that I put it inside a function that every
>time
>q is executed it changes the initial parameters and affter and then do
>a
>loop  y and  save a list of the results that interest me in the
>function.
>this problem is does not converge by the initial values, the loop stops
>and
>throws error.
>I need to continue and  save initial values with the error that
>generates
>those values
>
>
>Cheers
>
>Vangi
>
>
>
>ANO<- c( 1.65, 1.69, 1.72, 1.72, 1.72, 1.72, 1.73, 2.66 ,2.66, 2.66,
>2.66,
>2.76, 2.76, 2.76 ,2.76, 2.78, 2.8, 3.65, 3.65 ,3.65, 3.78, 3.78, 5.07,
>7.02,
>7.1, 7.81, 8.72, 8.74, 8.78, 8.8, 8.8, 8.83, 8.98, 9.1, 9.11, 9.75,
>9.82,
>9.84, 9.87, 9.87, 10.99, 11.67, 11.8, 11.81, 13.93, 14.83, 15.82,
>15.99,
>16.87, 16.88, 16.9, 17.68, 17.79, 17.8, 17.8)
>
>
>SVL<-c(26.11,29.02,41.13,30.96,37.74,29.02,33.38,24.18,34.35,35.8,29.99,42.59,27.57,47.43,46.95,30.47,29.75,35.8,40.65,36.29,34.83,29.02,43.5,75,68,70,67.5,80,77.5,68,68,73.84,72.14,68,64.5,58.5,72.63,78.44,71.17,70.69,77,79,78,68.5,69.72,71.66,77,77,79,76.5,78.5,79,73,80,69.72)
>
>data<-data.frame (SVL, ANO)# creo data frame
>data
>> Logiscorri<-function(){
>+   a<-runif(1, min=0, max=150)#devuelve 1 al azar dentro de un max y
>un
>min
>+   b<-runif(1, min=0, max=100)
>+   g<-runif (1, min=0, max=1)
>+   d<-runif (1,min=0, max=100)
>+
>+   ## estimo la curva de distribucion de mis datos
>+   caiman<-nls(SVL~DE+(alfa/(1+exp(-gamma*ANO))),
>+               data=data,
>+               start=list(alfa= a  ,gamma= g, DE= d),
>+               control=nls.control(maxiter = 100, warnOnly=TRUE),
>+               trace=FALSE)
>+   caimansum<-summary(caiman)#ME DA LOS PARAMETROS ESTIMADO, EL NUM DE
>ITERACIONES
>+   ## analizamos akaike
>+   akaike<-AIC(caiman)
>+   Bayesiano<-BIC(caiman)
>+   alfa<-coef(caiman)[1]
>+   beta<-coef(caiman)[2]
>+   gamma<- coef(caiman)[3]
>+   DE<- coef(caiman)[4]
>+   formu<-formula(caiman)
>+
>+   ValoresIniciales<-c(a, g, d)
>+   resultados<-list(formu, caimansum, ValoresIniciales, akaike,
>Bayesiano)
>+   return(resultados)
>+ }
>> Logiscorri()
>[[1]]
>SVL ~ DE + (alfa/(1 + exp(-gamma * ANO)))
><environment: 0x16a6b89c>
>
>[[2]]
>
>Formula: SVL ~ DE + (alfa/(1 + exp(-gamma * ANO)))
>
>Parameters:
>      Estimate Std. Error t value Pr(>|t|)
>alfa  133.0765     6.9537  19.138  < 2e-16 ***
>gamma   0.2746     0.0371   7.401 1.13e-09 ***
>DE    -54.0467     7.1047  -7.607 5.34e-10 ***
>---
>Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>Residual standard error: 6.821 on 52 degrees of freedom
>
>Number of iterations to convergence: 30
>Achieved convergence tolerance: 4.995e-06
>
>
>[[3]]
>[1] 112.2528283   0.4831461  38.5151401
>
>[[4]]
>[1] 372.2001
>
>[[5]]
>[1] 380.2294
>
>> resultados<-list()
>> resultados
>list()
>> for(i in 1:10){
>+   resultados[i]<- list(Logiscorri())
>+ }
>Error in chol2inv(object$m$Rmat()) :
>  element (2, 2) is zero, so the inverse cannot be computed
>In addition: Warning message:
>In nls(SVL ~ DE + (alfa/(1 + exp(-gamma * ANO))), data = data, start =
>list(alfa = a,  :
>  singular gradient
>> names(resultados)<- 1:10
>Error in names(resultados) <- 1:10 :
>  'names' attribute [10] must be the same length as the vector [4]
>> parametros<- t(sapply(LogisticoConCorri, "[[", "parámetros")) #estp
>lo
>que hace es ir item por item de la lista y sacar los parámetros
>Error in FUN(X[[i]], ...) : subscript out of bounds
>> colnames(parametros)<- c("alfa", "beta", "gamma", "DE")
>Error in dimnames(x) <- dn :
>  length of 'dimnames' [2] not equal to array extent
>> akaikefinal<- sapply(LogisticoConCorri, "[[", "akaike")#esto va item
>por
>item de la lista y saca el akaike
>Error in FUN(X[[i]], ...) : subscript out of bounds
>> bayesfinal<- sapply(LogisticoConCorri, "[[", "Bayesiano")
>Error in FUN(X[[i]], ...) : subscript out of bounds
>>
>> --
>Biól. Evangelina V. Viotto
>Laboratorio Ecología Animal
>Centro de investigaciones Científicas y de Transferencias de
>Tecnología Aplicada a la Producción
>(CICyTTP-CONICET-UADER)
>Diamante, Entre Ríos
>Argentina
>
>	[[alternative HTML version deleted]]
>
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