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Different result from nls in R-2.2.1 and R-2.3.1

2 messages · Frede Aakmann Tøgersen, Brian Ripley

Original
Frede Aakmann Tøgersen
# 
Short story: January 2006 I did some analysis in R-2.2.1 using nls. Repeating the exercise in R-2.3.1 yesterday produced somewhat different results. 

After some debugging I found that either nls is the problem or that mine understanding of environments or scoping rules is lacking something.

This is a short reproducing example.



x <- seq(0,5,len=20)

n <- 1
y <- 2*x^2 + n + rnorm(x)

xy <- data.frame(x=x,y=y)

myf <- function(x,a,b,n){
  res <- a*x^b + n
  ## a print for debugging purpose
  print(n)
  res
}

## This works as I expect it to do in R-2.2.1 but doesn't work in R-2.3.1. 
## n is somehow sat to nrow(xy) inside nls()
## Note that x and y is defined in the dataframe xy, whereas n is found in the global environment.
fit <- nls(y ~ myf(x,a,b,n), data=xy, start=c(a=1,b=1), trace=TRUE)

## this works in both versions
## x,y,n found in the .GlobalEnv
fit <- nls(y ~ myf(x,a,b,n), start=c(a=1,b=1), trace=TRUE)

## this works in both versions.
## x, y, n found in dataframe xyn
xyn <- data.frame(xy,n=n)
fit <- nls(y ~ myf(x,a,b,n), data=xyn, start=c(a=1,b=1), trace=TRUE)

## this works in both versions
## Now using the variable .n instead of n
## .n is found in .GlobaEnv
.n <- 1
fit <- nls(y ~ myf(x,a,b,.n), data=xy, start=c(a=1,b=1), trace=TRUE)


In my real case and the example above, I do have three or more parameters of which fitting is done only on few of theme. Is this a problem? Or should I ask, why is this a problem in R-2.3.1 but not in R-2.2.1?

Is my problem related to this difference between lines of code from nls:

R-2.2.1:     mf <- as.list(eval(mf, parent.frame()))

R-2.3.1:     mf <- eval.parent(mf)
             n <- nrow(mf)
             mf <- as.list(mf)

where n is being defined in the scope of nls in the latest version?

Best regards

Frede Aakmann T?gersen



Danish Institute of Agricultural Sciences
Research Centre Foulum
Dept. of Genetics and Biotechnology
Blichers All? 20, P.O. BOX 50
DK-8830 Tjele

Phone:   +45 8999 1900
Direct:  +45 8999 1878

E-mail:  FredeA.Togersen at agrsci.dk
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Brian Ripley
# 
The way nls looks for variables in its formula is very unusual.  For 
non-parameters it has

     for(var in varNames[!varIndex])
         mf[[var]] <- eval(as.name(var), data)

inside nls, and that means that the scoping rules are first 'data' then 
the body of nls().  That's surely not what one would expect here: 
fitting functions using model.frame look in 'data' and then the 
environment of the formula (if non-null) or the parent frame.

So to avoid surprises, put fixed values in 'data'.  (Your example did not 
work in 2.2.1 when run from a function.)

I'll try to find a bug fix for 2.4.0.
On Thu, 21 Sep 2006, Frede Aakmann T?gersen wrote: