April Lindeman <[email protected]> wrote on 09/04/2012 01:43:06 PM:
>
> I am trying to compare Vbert growth curves from several years of
> fish data. I am following the code provided by: http://
> www.ncfaculty.net/dogle/fishR/gnrlex/VonBertalanffy/VonBertalanffy.pdf
> . Specifically the section on VBGM Comparisons between groups.
>
> This code is pretty cut and dry. I am able to run it perfectly with
> the "fake" data that is provided. But when I run it with my own data
> I get stuck with this line:
> fitGen <- nls(vbGen,data=LMB,start=svGen)
>
> I get this error code: Error in numericDeriv(form[[3L]], names(ind),
> env) : Missing value or an infinity produced when evaluating the model.
>
>
> Does anyone know how to fix it? I have no missing values and do not
> know how to fix the infinity produced.
>
> Here is my data set: structure(list(Age = c(1L, 2L, 3L, 5L, 1L, 2L,
> 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L,
> 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L), MM = c(155.
> 79, 296.37, 325.77, 374.65, 181.46, 258.31, 321.88, 355.6, 139.75,
> 230.72, 319.61, 344.84, 130.92, 236.34, 290.53, 360.33, 400.61, 155.
> 33, 240.87, 315.46, 345.05, 378.2, 134.71, 256.66, 333.71, 362.99,
> 381.46, 153.91, 217.21, 287.8, 357.28, 385.62, 222.25, 288.93, 294.
> 05, 332.79, 367.39), Year = c(2005L, 2005L, 2005L, 2005L, 2006L,
> 2006L, 2006L, 2006L, 2007L, 2007L, 2007L, 2007L, 2008L, 2008L,
> 2008L, 2008L, 2008L, 2009L, 2009L, 2009L, 2009L, 2009L, 2010L,
> 2010L, 2010L, 2010L, 2010L, 2011L, 2011L, 2011L, 2011L, 2011L,
> 2012L, 2012L, 2012L, 2012L, 2012L)), .Names = c("Age", "MM",
> "Year"), class = "data.frame", row.names = c(NA, -37L))
As another person commented, you skipped the step where you attached the
data
attach(LMB)
> In case it's helpful here is all my code before this point:
> str(LMB)
Why are you carrying out these as.integer() conversions? It's not clear
to me that they are necessary.
> MMi=as.integer(MM)
> Yearf=as.factor(Year)
> Agei=as.integer(Age)
As another person commented, you skipped the step where you attached the
needed packages. I found I had to install and attach 7 packages to get
your code to run! But this could have been avoided by simply supplying us
with the starting values:
svCom <- list(Linf=430, K=0.5, t0=0)
> ( svCom <- vbStarts(MMi~Agei,data=LMB))
You copied this code from the example in the pdf, but in that example they
had only 2 groups. You have 8 years. So, this should be:
svGen <- lapply(svCom, rep, length(unique(Year)))
> ( svGen <- lapply(svCom,rep,2) )
Wow. I didn't know you use the extraction function, [], in a formula.
This is very good to know! Thanks for educating me!!
> vbGen <- MMi~Linf[Yearf]*(1-exp(-K[Yearf]*(Age-t0[Yearf]))+error)
> fitGen <- nls(vbGen,data=LMB,start=svGen)
>
>
> Thank you, April
Here's the whole reproducible snippet of code ...
# the data
LMB <- structure(list(Age = c(1L, 2L, 3L, 5L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L,
3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L), MM = c(155.79, 296.37, 325.77, 374.65,
181.46, 258.31, 321.88, 355.6, 139.75, 230.72, 319.61, 344.84, 130.92,
236.34, 290.53, 360.33, 400.61, 155.33, 240.87, 315.46, 345.05, 378.2,
134.71, 256.66, 333.71, 362.99, 381.46, 153.91, 217.21, 287.8, 357.28,
385.62, 222.25, 288.93, 294.05, 332.79, 367.39), Year = c(2005L, 2005L,
2005L, 2005L, 2006L, 2006L, 2006L, 2006L, 2007L, 2007L, 2007L, 2007L,
2008L, 2008L, 2008L, 2008L, 2008L, 2009L, 2009L, 2009L, 2009L, 2009L,
2010L, 2010L, 2010L, 2010L, 2010L, 2011L, 2011L, 2011L, 2011L, 2011L,
2012L, 2012L, 2012L, 2012L, 2012L)), .Names = c("Age", "MM", "Year"),
class = "data.frame", row.names = c(NA, -37L))
# attach the data
attach(LMB)
# provide starting values
svCom <- list(Linf=430, K=0.5, t0=0)
# repeat the starting values for each year
svGen <- lapply(svCom, rep, length(unique(Year)))
# define a new variable, uniquely numbered for each year
Yearf <- as.factor(Year)
# fit a single model with different parameter estimates for each year
fitGen <- nls(MM ~ Linf[Yearf]*(1-exp(-K[Yearf]*(Age-t0[Yearf]))),
data=LMB, start=svGen)
fitGen
Jean
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