[R] nls does not accept start values

[Uwe Ligges]

Petr PIKAL wrote:
> Thank you
> 
> It was simplified version of my problem. I want to elaborate a function 
> which can take predefined list of formulas, some data and evaluate which 
> formulas can fit the data. I was inspired by some article in Chemical 
> engineering in which some guy used excel solver for such task. I was 
> curious if I can do it in R too. I am not sure if nls is appropriate tool 
> for such task but I had to start somewhere.
> 
> Here is a function which takes list of formulas and data and gives a 
> result for each formula.
> 
> modely <- function(formula, data, ...){
> ll <- length(formula)   #no of items in formula list
> result2 <- vector("list", ll) #prepare results
> result1 <- rep(NA, ll)
> for(i in 1:ll) {
> fit<-try(nls(formula[[i]], data))
> if( class(fit)=="try-error") result1[i] <- NA  else result1[i] <- 
> sum(resid(fit)^2)
> if( class(fit)=="try-error") result2[[i]] <- NA  else result2[[i]] <- 
> coef(fit)
> }
> 
> ooo<-order(result1) #order results according to residual sum
> 
> #combine results into one list together with functions used
> 
> result <- mapply(c, "sq.resid" = result1, result2) 
> names(result) <- as.character(formula)
> # output
> result[ooo]
> }
> 
> # data
> x <-1:10
> y <-1/(.5-x)+rnorm(10)/100
> 
> # list of formulas
> fol <- structure(list(a = y ~ 1/(a - x), b = y ~ a * x^2 + b * log(x), 
>     c = y ~ x^a), .Names = c("a", "b", "c"))
> 
> modely(fol, data.frame(x=x, y=y)
> 
> does not use "correct" model because when using default start values it 
> results in
> 
>> nls(fol[[1]], data.frame(x=x, y=y))
> Error in numericDeriv(form[[3]], names(ind), env) : 
>   Missing value or an infinity produced when evaluating the model
> 
> however
> 
>  nls(fol[[1]], data.frame(x=x, y=y), start=list(a=mean(y)))
> 
> gives correct result. Therefore I started think about how to add a 
> "better" starting value for some fits as a second part of my formula list 
> to define structure like>
> 
> list(a= formula1, start.formula1, b=formula2, start.formula2, ....)
> 
> I wonder If you can push me to better direction.


You can make up a list of lists (each containing one formula and its 
starting values) or specify formulas in one list and starting values in 
a corresponding second list.
You need just the corresponding subsetting in your call to nls such as 
in the simple case I suggested already.

Best,
Uwe



> Thanks again
> Best regards
> Petr
> 
> 
> 
> 
> Uwe Ligges <ligges at statistik.tu-dortmund.de> napsal dne 02.03.2009 
> 09:41:45:
> 
>> Petr PIKAL wrote:
>>> Hi to all
>>>
>>> OK as I did not get any response and I really need some insight I try 
>>> again with different subject line
>>>
>>> I have troubles with correct evaluating/structure of nls input
>>>
>>> Here is an example
>>>
>>> # data
>>> x <-1:10
>>> y <-1/(.5-x)+rnorm(10)/100
>>>
>>> # formula list
>>> form <- structure(list(a = list(quote(y ~ 1/(a - x)), 
> "list(a=mean(y))")), 
>>>  .Names = "a")
>>>
>>> # This gives me an error due to not suitable default starting value
>>>
>>> fit <- nls(form [[1]] [[1]], data.frame(x=x, y=y))
>>>
>>> # This works and gives me a result
>>>
>>> fit <- nls(form [[1]] [[1]], data.frame(x=x, y=y), 
> start=list(a=mean(y)))
>>> *** How to organise list "form" and call to nls to enable to use other 
> 
>>> then default starting values***.
>>>
>>> I thought about something like
>>>
>>> fit <- nls(form [[1]] [[1]], data.frame(x=x, y=y), start=get(form 
> [[1]] 
>>> [[2]]))
>>>             ^^^^^^^^^^^^^^^^^^^ 
>>> but this gives me an error so it is not correct syntax. (BTW I tried 
> eval, 
>>> assign, sustitute, evalq and maybe some other options but did not get 
> it 
>>> right.
>>>
>>> I know I can put starting values interactively but what if I want them 
> 
>>> computed by some easy way which is specified by second part of a list, 
> 
>>> like in above example.
>> If you really want to orgnize it that way, why not simpler as in:
>>
>> form <- list(y ~ 1/(a - x), a = mean(y))
>> fit <- nls(form[[1]], data.frame(x=x, y=y), start = form[2])
>>
>>
>> Uwe Ligges
>>
>>
>>> If it matters
>>> WXP,  R2.9.0 devel.
>>>
>>> Regards
>>> Petr
>>>
>>> petr.pikal at precheza.cz
>>>
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>