[R] step function stops with "subscript out of bounds"

[Prof Brian Ripley]

On 17/05/2012 09:25, David A Vavra wrote:
> I've been having a problem using the step function to evaluate models. I've
> simplified the code and get the same problem using the dataset Titanic. The
> relevant code and output is below. The problem disappears (i.e., 'step' runs
> correctly) if I rerun the code but change the 'loglm' call to explicitly
> reference Titanic instead of X (as in: loglm(as.formula(Y),data=Titanic)).
>
> What is causing this?

A lack of understanding of 'non-standard evaluation'.  X (or at least, 
the X you want) is not visible from the standard search path.

>
> TIA,
> DAV	
>
> ----------
>
>> catn<-function(...) cat(...,"\n")
>> local({  X<-Titanic; print(class(X));
>             Y<-paste('~',paste(names(dimnames(X)),collapse="*"));
>             print(Y);
>             sm<-loglm(as.formula(Y),data=X);
>             catn("SM"); print(sm); catn('running');
>             step(sm,direction='backward')  })

Which will tell you
Error in eval(expr, envir, enclos) : could not find function "loglm"

If you correct that and use a vanilla session you will get

Error in loglm(formula = ~Class + Sex + Age + Survived + Class:Sex + 
Class:Age +  :
   object 'X' not found

which is more informative.

So the solution is to

- use less easily masked names than 'X'.
- ensure the data object is visible on the search path.


> Output:
>
> [1] "table"
> [1] "~ Class*Sex*Age*Survived"
> SM
> Call:
> loglm(formula = as.formula(Y), data = X)
>
> Statistics:
>                   X^2 df P(>  X^2)
> Likelihood Ratio   0  0        1
> Pearson          NaN  0        1
> running
> Start:  AIC=64
> ~Class * Sex * Age * Survived
>
> Error in loglin(data, margins, start = start, fit = fitted, param = param,
> :
>    subscript out of bounds
>
> Enter a frame number, or 0 to exit
>
> 1: local({
>      X<- Titanic
>      print(class(X))
>      Y<- paste("~", paste(names(dimnames(X)), collapse = "*"))
>      print(Y)
>      sm<- loglm(as.formula(Y), data = X
>   2: eval.parent(substitute(eval(quote(expr), envir)))
>   3: eval(expr, p)
>   4: eval(expr, envir, enclos)
>   5: eval(quote({
>      X<- Titanic
>      print(class(X))
>      Y<- paste("~", paste(names(dimnames(X)), collapse = "*"))
>      print(Y)
>      sm<- loglm(as.formula(Y), dat
>   6: eval(expr, envir, enclos)
>   7: #1: step(sm, direction = "backward")
>   8: #1: drop1(fit, scope$drop, scale = scale, trace = trace, k = k, ...)
>   9: #1: drop1.default(fit, scope$drop, scale = scale, trace = trace, k = k,
> ...)
> 10: #1: update(object, as.formula(paste("~ . -", tt)), evaluate = FALSE)
> 11: #1: update.loglm(object, as.formula(paste("~ . -", tt)), evaluate =
> FALSE)
> 12: #1: eval.parent(call)
> 13: #1: eval(expr, p)
> 14: #1: eval(expr, envir, enclos)
> 15: #1: loglm(formula = ~Class + Sex + Age + Survived + Class:Sex +
> Class:Age + Sex:Age + Class:Survived + Sex:Survived + Age:Survived +
> Class:Sex:Age + Class:
> 16: #1: loglm1(formula, data, ..., .call = .call, .formula = .formula)
> 17: #1: loglm1.default(formula, data, ..., .call = .call, .formula =
> .formula)
> 18: #1: loglin(data, margins, start = start, fit = fitted, param = param,
> eps = eps, iter = iter, print = print)
>
> Selection: 0
>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595