 Dear Robert,
 
The differences have to do with diffent scaling defaults.
 
lrm by default standardizes the covariates to unit sd before applying
penalization. penalized by default does not do any standardization, but
if asked standardizes on unit second central moment. In your example:
 
x = c(-2, -2, -2, -2, -1, -1, -1, 2, 2, 2, 3, 3, 3, 3)
z = c(0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1)
 
You got:
 
> g = lrm(z ~ x, penalty = 1)
> g$coefficients
 Intercept          x 
-0.1620727  0.3241454 
 
Now:
 
> coef(penalized(z ~ x, lambda2 = 1,standardize=T))
 
(Intercept)           x 
 -0.1651565   0.3303130 
 
is already more similar. To counter the difference between dividing by n
(penalized) or n-1 (lrm), do
 
> coef(penalized(z ~ x, lambda2 = 14/13,standardize=T))
 
(Intercept)           x 
 -0.1620727   0.3241454 
 
The glmnet case should be similar, but I don't know the details here. It
seems glmnet uses its own peculiar way of defining the penalty, but some
choice of scaling should be able to bring glmnet in line as well.
 
Kind regards,
 
Jelle
 
 



________________________________

	From: Robert V (Bob) Sasseen [mailto:sasseen@ai.sri.com] 
	Sent: 29 October 2009 19:32
	To: Goeman, J.J. (MSTAT)
	Subject: different L2 regularization behavior between lrm,
glmnet, and penalized? (original question)
	
	
	Jelle,
	
	Below is the original question. The formatting apparently got a
bit messed up when it was parsed by the list server. This may be easier
to read.
	
	Bob
	
	
------------------------------------------------------------------------
---------
	
	The following R code using different packages gives the same
results for a simple logistic regression without regularization, but
different results with regularization. This may just be a matter of
different scaling of the regularization parameters, but if anyone
familiar with these packages has insight into why the results differ,
I'd appreciate hearing about it. I'm new to R. Thanks. (Version info
below. Same results on Windows and Solaris 8, except that I haven't
gotten glmnet to compile on the latter.)
	
	Robert V (Bob) Sasseen
	sasseen@ai.sri.com
	
	
	> # Some x values (predictive var).
	> x = c(-2, -2, -2, -2, -1, -1, -1, 2, 2, 2, 3, 3, 3, 3)
	
	> # Some z values--the observed outcome.
	> # Effect is that for 
	> # x = -2, p = 1/4; 
	> # x = -1, p = 1/3; 
	> # x =  2, p = 2/3; 
	> # x =  3, p = 3/4.
	> z = c(0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1)
	
	
	> library(Design)
	> g = lrm(z ~ x)
	> g$coefficients
	 Intercept          x 
	-0.2224842  0.4449685 
	
	> g = lrm(z ~ x, penalty = 1)
	> g$coefficients
	 Intercept          x 
	-0.1620727  0.3241454 
	
	
	> library(glmnet)
	> g = glmnet(cbind(x), cbind(1-z, z), family = "binomial",
lambda = 0, standardize = FALSE)
	> coef(g)
	           1
	  -0.2224843
	x  0.4449687
	
	> g = glmnet(cbind(x), cbind(1-z, z), family = "binomial",
lambda = 1, alpha = 0, standardize = FALSE)
	> coef(g)
	           1
	  -0.1098361
	x  0.2196721
	
	
	> library(penalized)
	> fit = penalized(z ~ x)
	> coefficients(fit, "all")
	(Intercept)           x 
	 -0.2224843   0.4449687 
	
	> fit = penalized(z ~ x, lambda2 = 1)
	> coefficients(fit, "all")
	(Intercept)           x 
	 -0.2060658   0.4121315 
	
	
	> sessionInfo()
	R version 2.9.2 (2009-08-24) 
	i386-pc-mingw32 
	
	locale:
	LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
	
	attached base packages:
	[1] splines   stats     graphics  grDevices utils     datasets
methods  
	[8] base     
	
	other attached packages:
	[1] penalized_0.9-26   glmnet_1.1-3       Matrix_0.999375-30
lattice_0.17-25   
	[5] Design_2.3-0       Hmisc_3.7-0        survival_2.35-4   
	
	loaded via a namespace (and not attached):
	[1] cluster_1.12.0 grid_2.9.2    
	
	
	-- 
	
Robert V (Bob) Sasseen 
Senior Software Engineer 
Advanced Analytics 
Artificial Intelligence Center 
SRI International 


      


3661 Valley Centre Drive, Suite 150 
San Diego, CA 92130 
robert.sasseen@sri.com 
(858) 350-2035 

	


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