From murdoch at stats.uwo.ca  Tue Jan 13 01:33:10 2009
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Mon, 12 Jan 2009 19:33:10 -0500
Subject: [Rd] irrelevant warning message
In-Reply-To: <200901122312.n0CNCVg10854@hsrnfs-101.mayo.edu>
References: <200901122312.n0CNCVg10854@hsrnfs-101.mayo.edu>
Message-ID: <496BE146.3030201@stats.uwo.ca>

On 12/01/2009 6:12 PM, Terry Therneau wrote:
> Context: 
>   R version 2.7.1 (2008-06-23)
>   I don't know when this was upgraded in the department, I just ran into the 
> aberrent behavior today.
>   
> Problem:
>   
>   Our group BY CHOICE does not change character variables into factors by 
> default.  I can get into a long arguement as to why later, and will give one 
> example of why below.
>   
>   The default behavior of S, Splus and R has been to create dummy variables for 
> factor, character, and logical variables.  This is good.  
>   
>   Why has R suddenly gotton a compulsion to put out a warning message for any 
> model where we do this?  I contend that it is

I think you need to be more specific.  I just tried

x <- sample(letters[1:4], 100, rep=T)
y <- rnorm(x)
lm(y ~ x)

and got a warning in all R versions I tried back to 2.4.1.  In 2.3.1 
this was an error.

So I suspect the change you saw was to some other modelling function 
besides lm(), and I would guess that it came from making it consistent 
with lm().

But it would help if you told use which function, and which version 
you're comparing 2.7.1 with.

Now, it probably does make sense to suppress that warning.  I guess it 
was probably introduced because we used to give an error, and someone 
was being conservative and didn't think error-ful behaviour should go to 
accepted behaviour in one step.  But maybe it's time for the second step.

Duncan Murdoch

>   - confusing
>   - unnecessary
>   - and wrong.
>   
>   It is certainly confusing, as it implies a behavior change when there has been 
> no change.  
>   The fact that the "factor" command was used behind the scenes is irrelevant to 
> anyone - who cares that HOW the rules are implemented.  Is there going to soon 
> be a message of WARNING: logical variable turned into numeric?  It is the 
> sensible next step.
>   Wrong because the data element in question is not converted - not at the user 
> level at least.  It would be much more proper to say "was treated as a factor by 
> model.matrix"; but that is a semantic issue.
>   
>   
>   In any case- to the real question.
>   
>   1.What is the easiest way to eliminate this?  I would prefer not to have to 
> change the source code and recompile the local versions.  Because of namespaces 
> it is not as easy as adding a repaired copy to our local library and loading it 
> first.  I remember some discussion about forcing a change into another name 
> space but I've lost the link to it. 
>   I'll do this if we must, but it is such a hassle to keep updating the change 
> with new releases of the package.  It might still be less than dealing with the 
> training/answer questions burden for our group, which is quite large.
>   
>   2. Is there any hope of undoing this?   Its only real impact is to annoy, and 
> I've always disliked systems that preach at me.  (Detested is more like it, I 
> still remember how hard it was to delete certain files in Digital's TOPS os, 
> which was sure you ``didn't actually want to do that''.)  Allowing some global 
> "stop preaching" option would be a fix, or in the same vein to have it look at 
> the existing stringsAsFactors option for a "this person knows so don't bother 
> him hint".
>     If this addition followed on some discussion, please point me to it.
> 
>   The reaction of other experienced users in our group has been the same, when I 
> pointed this out.  So I am not alone in the "why?"
>   
>   	Terry Therneau
>   	
> 
> PS. Here are two interrelated reasons we don't autoconvert:
> 
>   1. Subject id.  Factors give no advantage for a unique id, and some clear 
> problems.  In particular when one creates as subset - everyone over 60 say - 
> there is no good reason to remember all the ids you didn't select.
>   2. Subject id.  I work on a lot of studies of fractures and fracture risk.  A 
> time-trend model might be
>   	gam(fracture ~ subject + x1 + x2 + ..., subset=(sex='F'))
>   
>   Fracture risk for males and females is so different that separate models are 
> the sensible thing.  If subject is a factor before the call, then my model has a 
> zillion unneeded levels.  There are other ways out of this issue, but avoiding 
> factors is the easiest.
> 
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[Rd] irrelevant warning message
Duncan Murdoch