From therneau at mayo.edu  Tue Jan 13 00:12:31 2009
From: therneau at mayo.edu (Terry Therneau)
Date: Mon, 12 Jan 2009 17:12:31 -0600 (CST)
Subject: [Rd] irrelevant warning message
Message-ID: <200901122312.n0CNCVg10854@hsrnfs-101.mayo.edu>

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
  - 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.



[Rd] irrelevant warning message
Terry Therneau