New subject: question on pscore matching using nnet or cart (fwd)

7 Mar 2005

Hi Soko,

We just fixed the nnet size default bug, so the next time that MatchIt
rebuilds, the size default will get pulled through to change the default.

The fact that extraneous arguments to nnet don't get a warning message is
due to the way nnet.formula internally handles (...) arguments.  For
example:

nnet.formula(treat~educ,data=lalonde,node=3,size=4,soko=4)

doesn't yield a warning.  This is something peculiar to the nnet package, so
just be careful in passing arguments when model="nnet."

Dan

----- Original Message ----- 
From: "Daniel E. Ho" &lt;daniel.ho(a)yale.edu&gt;
To: "S Setoguchi" &lt;soko(a)kuhp.kyoto-u.ac.jp&gt;
Cc: "Kosuke Imai" &lt;kimai(a)Princeton.Edu&gt;du>; "Elizabeth Stuart"
&lt;EStuart(a)Mathematica-Mpr.com&gt;
Sent: Monday, March 07, 2005 12:26 AM
Subject: Re: [matchit] question on pscore matching using nnet or cart (fwd)

...
  You're right.  This is a bug in distance, which
should be pulling through
 any (...) arguments to nnet but actually isn't.  The rpart implementation
 works this way:

ff<-matchit(treat~educ,data=lalonde,model="cart",cp=0.03)
 ff$assign$call  rpart(formula = treat ~ educ, data = lalonde, cp = 0.03)

 Sorry for the confusion, but we need to fix the nnet portion.

 Dan

 ----- Original Message ----- 
 From: "S Setoguchi" &lt;soko(a)kuhp.kyoto-u.ac.jp&gt;
 To: "'Daniel E. Ho'" &lt;daniel.ho(a)yale.edu&gt;
 Sent: Monday, March 07, 2005 12:09 AM
 Subject: RE: [matchit] question on pscore matching using nnet or cart (fwd)
...

 I see what was wrong.
 You used the term 'node' in your previous email

  > >
foo<-matchit(treat~educ,model="nnet",data=lalonde,node=4) 
 But now you are using 'size' in this reply.
 That was my question. I got confused with the term. I thought it was
'size'
...
  but you used 'node' once in your previous
email.
 I see you are using 'size' this time.

 Soko

 -----Original Message-----
 From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
 Sent: Monday, March 07, 2005 12:09 AM
 To: S Setoguchi; matchit(a)latte.harvard.edu
 Subject: Re: [matchit] question on pscore matching using nnet or cart (fwd)
...

 I'm not exactly sure what you are trying, but the problem might be with nnet
...
  itself.

 nnet uses some sort of random seed so you will get different answers with
 each neural net that you run.  For example:

  nnet(treat~educ,size=4,data=lalonde)  #
weights:  13
 initial  value 295.270340
 final  value 185.000000
 converged
 a 1-4-1 network with 13 weights
 inputs: educ
 output(s): treat
 options were -

  nnet(treat~educ,size=4,data=lalonde)  #
weights:  13
 initial  value 130.405931
 iter  10 value 128.240413
 iter  20 value 128.174714
 iter  30 value 127.232077
 iter  40 value 126.821942
 final  value 126.755841
 converged
 a 1-4-1 network with 13 weights
 inputs: educ
 output(s): treat
 options were -

 If you're running into a different problem, please feel free to send along a
...
  few lines to replicate the problem.

 Thanks,

 Dan

 ----- Original Message ----- 
 From: "S Setoguchi" &lt;soko(a)kuhp.kyoto-u.ac.jp&gt;
 To: "'Daniel E. Ho'" &lt;daniel.ho(a)yale.edu&gt;du>;
&lt;matchit(a)latte.harvard.edu&gt;
 Sent: Sunday, March 06, 2005 11:47 PM
 Subject: RE: [matchit] question on pscore matching using nnet or cart (fwd)
...

  Hi

 I was playing with psmatch for nnet.
 I realized that an argument to change size of nodes in the original
 nnet  is
  'size' but not 'node'.
 I tried both in matchit and both run but give me different results.
 Can you explain why this is??

 -----Original Message-----
 From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
 Sent: Sunday, March 06, 2005 10:48 PM
 To: S Setoguchi
 Subject: Re: [matchit] question on pscore matching using nnet or cart  (fwd)

 Great.  For some reason I wasn't getting the matchit@latte emails, so
 I'm just going to resend my answer to the listserv in case others
 might find  it
  helpful.

 Dan

 ----- Original Message -----
 From: "S Setoguchi" &lt;soko(a)kuhp.kyoto-u.ac.jp&gt;
 To: "'Daniel E. Ho'" &lt;daniel.ho(a)yale.edu&gt;du>;
"'Elizabeth Stuart'"
 &lt;stuart(a)stat.harvard.edu&gt;
 Cc: "'Kosuke Imai'" &lt;kimai(a)Princeton.Edu&gt;du>;
&lt;ssetoguc(a)hsph.harvard.edu&gt;
 Sent: Sunday, March 06, 2005 9:32 PM
 Subject: RE: [matchit] question on pscore matching using nnet or cart  (fwd)

  Thanks. It makes sense.
 Soko

 -----Original Message-----
 From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
 Sent: Sunday, March 06, 2005 8:46 PM
 To: Elizabeth Stuart
 Cc: Kosuke Imai; ssetoguc(a)hsph.harvard.edu
 Subject: Re: [matchit] question on pscore matching using nnet or
 cart  (fwd)

 Weird, for some reason I'm not getting any of these matchit
 messages.

 Yes, all of the usual tweaks can be used with nnet and cart.

 For example:

  data(lalonde)
 foo<-matchit(treat~educ,model="nnet",data=lalonde)
 foo<-matchit(treat~educ,model="nnet",data=lalonde,node=4)
 foo<-matchit(treat~educ,model="cart",data=lalonde)
 foo<-matchit(treat~educ,model="cart",data=lalonde,cp=0.02) 
 I hope that makes sense!

 Dan
 ----- Original Message -----
 From: "Elizabeth Stuart" &lt;stuart(a)stat.harvard.edu&gt;
 To: "Daniel E. Ho" &lt;daniel.ho(a)yale.edu&gt;
 Cc: "Kosuke Imai" &lt;kimai(a)Princeton.Edu&gt;
 Sent: Sunday, March 06, 2005 8:35 PM
 Subject: [matchit] question on pscore matching using nnet or cart
 (fwd)

  Hey Dan,
 I seem to remember that you played around with nnet and cart a
 little. My memory is that any of the nnet or cart options can be
 changed by just adding that to the options in the matchit command
 (that's what the "..." in the  matchit command is for).  Is that
 right?

 It was good talking to you tonight.  Good luck with your
 preparations!

 liz

 ---------- Forwarded message ----------
 Date: Sun, 6 Mar 2005 13:59:25 -0500
 From: Soko Setoguchi &lt;ssetoguc(a)hsph.harvard.edu&gt;
 To: matchit(a)latte.harvard.edu
 Subject: [matchit] question on pscore matching using nnet or cart

 Hi

 I have questions on propensity score matching using nnet or cart.
 For nnet, I know the default set by matchit is node=3 but how do
 you  change it
  to other values.
 Similarly for cart, I assume that matchit uses default setting of
 rpart.  How
  do you change the setting of rapart for example
cp, xval,
 minbucket etc...

 Thank you

 Soko

 Soko Setoguchi
 Harvard School of Public Health

 Soko Setoguchi MD MPH ScM
 Doctor of Public Health Candidate
 Department of Epidemiology
 Harvard School of Public Health

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