R help - Aug 2008 - Simple programming problem with 'with' or 'data ='

Hello

I wrote a simple program to modify a boxplot:

<<<

gdsbox <- function(indvar){
boxplot(indvar~gds3lev, 
   main = paste('Boxplot of', substitute(indvar), "for GDS
groups"),
   names = c('1', '3', '4, 5, 6'))
}
>>>
If I attach the dataframe gdsgraph, this works fine. However, I've been
warned against attach.  When I tried to run this program using 'with',
it did not work.

e.g. 

           with(gdsgraph, gdsbox(BReT3T5T))

produced an error that gds3level was not found

but if I try

          with(gdsgraph, boxplot(BReT3T5T~gds3lev))

it works fine.

Similar problems occurred when I tried to use data 
What am I missing?

Thanks

Peter




Peter L. Flom, PhD
Brainscope, Inc.
212 263 7863 (MTW)
917 488 7176 (ThF)



	[[alternative HTML version deleted]]

On 8/27/2008 1:15 PM, Peter Flom wrote:
> Hello
> 
> I wrote a simple program to modify a boxplot:
> 
> <<<
> 
> gdsbox <- function(indvar){
> boxplot(indvar~gds3lev, 
>    main = paste('Boxplot of', substitute(indvar), "for GDS
groups"),
>    names = c('1', '3', '4, 5, 6'))
> }
> 
>>>>
> 
> If I attach the dataframe gdsgraph, this works fine. However, I've been
warned against attach.  When I tried to run this program using 'with',
it did not work.
> 
> e.g. 
> 
>            with(gdsgraph, gdsbox(BReT3T5T))
> 
> produced an error that gds3level was not found
> 
> but if I try
> 
>           with(gdsgraph, boxplot(BReT3T5T~gds3lev))
> 
> it works fine.
> 
> Similar problems occurred when I tried to use data > 
> What am I missing?
You defined your gdsbox function in the global environment, which means 
it will go looking for non-local variables there.  It doesn't matter 
where you call it from, R uses lexical scoping.

To get what you want, you could define your function within the with, i.e.

with(gdsgraph, {

  gdsbox <- function(indvar){
  boxplot(indvar~gds3lev,
     main = paste('Boxplot of', substitute(indvar), "for GDS
groups"),
     names = c('1', '3', '4, 5, 6'))
  }

  gdsbox(BReT3T5T)
})

but this misses the point of defining gdsbox once, and using it in many 
places.  So I'd say the best thing to do is to change the definition of 
it to use the data argument, i.e.

gdsbox <- function(indvar, data) {
     boxplot(indvar~gds3lev,
     main = paste('Boxplot of', substitute(indvar), "for GDS
groups"),
     names = c('1', '3', '4, 5, 6'), data=data)
  }

and call it as

gdsbox(BReT3T5T, gdsgraph)

There are ways to make your function act as though it doesn't use 
lexical scoping (parent.env, etc.), but they are ugly, and I don't think 
they're necessary here.

Duncan Murdoch

with(gdsgraph, boxplot(BReT3T5T ~ gds3lev)) is equivalent to 
boxplot(gdsgraph$BReT3T5T ~ gdsgraph$gds3lev), so all the terms are found.

gds1lev is not found within the scope of the function gdsbox(). This 
function has too many hard codings to be of much use generically.

Consider rewriting it as (untested function)

gdsbox <- function(y, x, data, main.title=NULL, ...){

   if(is.null(main.title)){
     main.title <- paste('Boxplot of', substitute(y), "for GDS
groups") }

   boxplot( data$y ~ data$x, main=main.title, ... )
}

but why bother when you call the more robust, well tested and well 
documented boxplot() ?

If you still want help, can you give a simple reproducible example?

Regards, Adai



Peter Flom wrote:
> Hello
> 
> I wrote a simple program to modify a boxplot:
> 
> <<<
> 
> gdsbox <- function(indvar){
> boxplot(indvar~gds3lev, 
>    main = paste('Boxplot of', substitute(indvar), "for GDS
groups"),
>    names = c('1', '3', '4, 5, 6'))
> }
> 
> 
> If I attach the dataframe gdsgraph, this works fine. However, I've been
warned against attach.  When I tried to run this program using 'with',
it did not work.
> 
> e.g. 
> 
>            with(gdsgraph, gdsbox(BReT3T5T))
> 
> produced an error that gds3level was not found
> 
> but if I try
> 
>           with(gdsgraph, boxplot(BReT3T5T~gds3lev))
> 
> it works fine.
> 
> Similar problems occurred when I tried to use data > 
> What am I missing?
> 
> Thanks
> 
> Peter
> 
> 
> 
> 
> Peter L. Flom, PhD
> Brainscope, Inc.
> 212 263 7863 (MTW)
> 917 488 7176 (ThF)
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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