From: "Bonate, Peter"  
Subject: [NMusers] SAS vs S-Plus
Date: Wed, December 8, 2004 2:35 pm

I guess it's time to stir up the pot a bit.  While I agree with
Mike Fossler that every modeler should learn a higher-order programming
language (and there are many: S-Plus, IML in SAS, Matlab, Gauss, O-matrix),
I disagree that S-plus should be the language of choice.  Matlab, Gauss, and
O-matrix are useful but they all suffer in that statistical analyses are
not easily implemented.  In the case of Matlab and O-matrix additional
modules must be purchased to do any kind of statistical analysis so
they aren't really useful for what we do.  Also, they don't do mixed
effects modeling.  So really it comes down to SAS and S-plus.  S-plus
early on became the program of choice because it had better graphics,
it still does over SAS, and has some procedures like GAM that SAS did
not.  However, the analysis gap has closed - both offer nonlinear mixed
effects models, GAM analysis, etc.  They are virtually the same.  S-plus
still has the edge graphics wise. 

However, of all the programming languages I have studied, S-plus is one
of the craziest and not the most easy to learn.  SAS is far easier to
learn and has the advantage in the all statistical analyses in support
of an NDA will be done within SAS.  Most companies have a site license
for SAS and so using it will not cost a department much, if anything. 
S-plus is a couple of thousand dollars.  I also have to say that SAS
has the regulatory edge in terms of acceptance over S-plus.



Peter L. Bonate, PhD, FCP 
Director, Pharmacokinetics 
ILEX Oncology 
4545 Horizon Hill Blvd 
San Antonio, TX  78229 
phone: 210-949-8662 
fax: 210-949-8219 

From:  "Bachman, William (MYD)"
Subject: RE: [NMusers] $A$ vs S-Plus 
Date: Wed, December 8, 2004 3:05 pm

You forgot the biggest one - cost.  Only major pharma can afford to implement
it across the board.  S-Plus is affordable, R is free.
William J. Bachman, Ph.D. 
Manager, Pharmacometrics Research and Development 
The Strategic Pharmaceutical Development Division of ICON plc 
7250 Parkway Drive, Suite 430 
Hanover, MD 21076 

From: "Sam Liao"
Subject: RE: [NMusers] $A$ vs S-Plus 
Date: Wed, December 8, 2004 3:50 pm

Hi Bill and nmv users:

I would like to ask if any S-Plus or R users in this group
know of any function to use in solving differential equations in PKPD models.

I prefer to use S-Plus in Monte Carlo simulation of PKPD models. 
But, so far only limited to models with explicit functions.


PharMax Research   

From: "Pravin Jadhav"
Subject: Re: [NMusers] $A$ vs S-Plus
Date: Wed, December 8, 2004 4:55 pm 

Sam and others,

R has nlmeODE package developed by Christoffer Tornoe that allows one
to write differential equations and tie-up with NLME. However, as I
understand NLME in R has not been updated for long time compared to
NLME in S-Plus (supported by Insightful).

Joga and his group is developing a website that will have various
kinds of NONMEM codes as well as R codes(to the extent possible) used
in PK -PD modeling.

About the other discussion, choice of softwares will differ between
users. I agree that S-Plus is limited by the memory requirement but I
hardly had a problem. There are ways to make codes more efficient.
Also, I find S-Plus very flexible for running simple models because
all the traditional diagnostic plots and random effects versus
covariates plots etc. can be created by ONE line code.

my 2cents.