[R] Lexical scoping for step and add1 functions

[Jeff Newmiller]

In a nutshell, formulas carry the environment in which they are 
defined along with the variable names, and your dfr was defined in the 
test.FN environment, but the formulas were defined in the global 
environment. I got this to work by defining the formula character strings 
in the global environment, and then converting those strings to formulas 
in the function. I don't think you can trick lm into referring to the 
global environment from within test.FN so that summaries refer to the 
X.des data frame instead of dfr (but someone could prove me wrong).

################################

test.FN <- function( dfr, scope, k = 2 ) {
   scp <- list( lower = as.formula( scope$lower )
 	     , upper = as.formula( scope$upper )
 	     )
   temp.lm <- lm( scp$lower
                , data = dfr
                )
   step( temp.lm
       , scope = scp
       , k=k
       )
}

# Begin by setting the rng seed.
set.seed( 523 )

# Generate a design matrix and response.
X.des <- matrix( abs( rnorm( 50 * 20, sd = 4 ) ), nrow = 50 )
Y <- 20 + X.des[, 1:3 ] %*% matrix( c( 3, -4, 2 ), nrow = 3 ) + rnorm( 50 )
X.des <- cbind( as.data.frame( X.des ), Y )

# Create the lower and upper formula components of a list.
test.scope <- list( lower = "Y ~ 1"
 		  , upper = paste( "Y ~"
 				 , paste( names( X.des )[ 1:20 ]
 					, collapse = " + "
 					)
 				 , sep=""
 				 )
 		  )
# Run 'test.FN'.
test.FN( dfr = X.des
        , scope = test.scope
        )


On Mon, 7 Mar 2016, Louisell, Paul T PW wrote:

> Hi,
>
> I've run into a problem calling the step function from within a function; I sent this to the R development list first, but the moderator said it was better suited to R help. My OS is Windows 7 and I'm using R version 3.2.3.
>
> Here's a simple function to help reproduce the error:
>      > test.FN
>      function(dfr, scope, k=2){
>      temp.lm=lm(scope$lower, data=dfr)
>      step(temp.lm, scope=scope$upper, k=k)
>      }
>
> And here's the code that gives the error when calling the function above:
>      # Begin by setting the rng seed.
>      > set.seed(523)
>
>      # Generate a design matrix and response.
>      > X.des=matrix(abs(rnorm(50*20, sd=4)), nrow=50)
>      > Y=20 + X.des[, 1:3] %*% matrix(c(3, -4, 2), nrow=3) + rnorm(50)
>      > X.des=cbind(as.data.frame(X.des), Y)
>
>      # Create the lower and upper formula components of a list.
>      > test.scope=list(lower=as.formula(Y ~ 1), upper=as.formula(paste("Y ~ ", paste(names(X.des)[1:20], collapse=" + "), sep="")))
>
>      # Run 'test.FN'.
>      > test.FN(dfr=X.des, scope=test.scope)
>      Start:  AIC=257.58
>      Y ~ 1
>
>      Error in is.data.frame(data) : object 'dfr' not found
>      > traceback()
>      11: is.data.frame(data)
>      10: model.frame.default(formula = Y ~ V1 + V2 + V3 + V4 + V5 + V6 +
>              V7 + V8 + V9 + V10 + V11 + V12 + V13 + V14 + V15 + V16 +
>              V17 + V18 + V19 + V20, data = dfr, drop.unused.levels = TRUE)
>      9: stats::model.frame(formula = Y ~ V1 + V2 + V3 + V4 + V5 + V6 +
>             V7 + V8 + V9 + V10 + V11 + V12 + V13 + V14 + V15 + V16 +
>             V17 + V18 + V19 + V20, data = dfr, drop.unused.levels = TRUE)
>      8: eval(expr, envir, enclos)
>      7: eval(fcall, env)
>      6: model.frame.lm(fob, xlev = object$xlevels)
>      5: model.frame(fob, xlev = object$xlevels)
>      4: add1.lm(fit, scope$add, scale = scale, trace = trace, k = k,
>             ...)
>      3: add1(fit, scope$add, scale = scale, trace = trace, k = k, ...)
>      2: step(temp.lm, scope = scope$upper, k = k) at #3
>      1: test.FN(dfr = X.des, scope = test.scope)
>
> The call to the traceback function indicates add1 doesn't see the dataframe dfr  passed to test.FN. The step function runs fine when I do everything in the global environment without using test.FN. I know the lexical scoping rules are different for objects involving model formulae, but despite a fair amount of experimentation, I haven't found any way to make the step / add1 functions see the dataframe that's passed to test.FN. Any help would be greatly appreciated.
>
> Thanks,
>
> Paul Louisell
> Statistical Specialist
> Paul.Louisell at pw.utc.com<mailto:Paul.Louisell at pw.utc.com>
> 860-565-8104
>
> Still, tomorrow's going to be another working day, and I'm trying to get some rest.
> That's all, I'm trying to get some rest.
> Paul Simon, "American Tune"
>
>
>
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>
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