?????Hi Soko,
Could you provide a replicable example of this, say with the lalonde data? It's hard to guess at what might be going on without some dataset.
Dan
----- Original Message -----
From: S Setoguchi
To: 'Daniel E. Ho'
Sent: Wednesday, May 18, 2005 12:23 AM
Subject: Proepensity score matching using nnet
Hi Dan
Would like your help for one more thing.
I cannot figure out what is going on my program and you might have an insight.
I created the dataset called W and doing propensity score matching using nnet.W is the data with 12 varibales named w1 through w10, a, and y.
I get the following error message. Do you have any idea what is going on?
Soko
> is.data.frame(W)
[1] TRUE
> psmatch<- matchit(a~w1+w2+w3+w4+w5+w6+w7+w8+w9+w10,model="nnet",data=W,size=5)
Calculating propensity score...# weights: 37
initial value 502.266699
iter 10 value 393.923293
iter 20 value 390.399478
iter 30 value 387.433295
iter 40 value 384.763135
iter 50 value 383.245161
iter 60 value 382.258124
iter 70 value 381.175506
iter 80 value 380.259462
iter 90 value 379.869123
iter 100 value 378.775436
final value 378.775436
stopped after 100 iterations
Error: Data W must be a dataframe
> traceback()
8: stop("Data ", cl$data, " must be a dataframe", call. = FALSE)
7: matchit(a ~ w1 + w2 + w3 + w4 + w5 + w6 + w7 + w8 + w9 + w10,
model = "nnet", data = W, size = 10, caliper = 0.1)
6: summary.nnet(res)
5: summary(res)
4: distance(formula = a ~ w1 + w2 + w3 + w4 + w5 + w6 + w7 + w8 +
w9 + w10, model = "nnet", data = W, size = 5)
3: eval(expr, envir, enclos)
2: eval(as.call(mf), sys.frame(sys.parent()))
1: matchit(a ~ w1 + w2 + w3 + w4 + w5 + w6 + w7 + w8 + w9 + w10,
model = "nnet", data = W, size = 5)
Great, glad it worked. You're right -- updating doesn't seem to work as
described.
Thanks,
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Tuesday, May 17, 2005 11:47 PM
Subject: RE: Updating matchit
It did.
I followed the instruction from your website.
http://gking.harvard.edu/matchit/docs/Loading_M_SMALL_ATCH_S.html, where it
had "I" in lowercases.
You might want to change it.
What do you think about the error message on 'udate.packages("MatchI")'? Are
we getting the error message because there is nothing to update?
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Tuesday, May 17, 2005 11:45 PM
To: S Setoguchi
Cc: matchit(a)latte.harvard.edu
Subject: Re: Updating matchit
Does it work if you capitalize the "I" in MatchIt?
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Tuesday, May 17, 2005 11:38 PM
Subject: RE: Updating matchit
Dan
This is what I tried.
> install.packages("MatchIt")
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 27996 bytes opened URL
downloaded 27Kb
trying URL
`http://cran.r-project.org/bin/windows/contrib/2.0/MatchIt_1.0-1.zip'
Content type `application/zip' length 154470 bytes
opened URL
downloaded 150Kb
package 'MatchIt' successfully unpacked and MD5 sums checked
Delete downloaded files (y/N)? y
updating HTML package descriptions
> library(Matchit)
Error in library(Matchit) : There is no package called 'Matchit'
#If I used the pull-down menu to load the package, it works...
> update.packages("Matchit")
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 27996 bytes opened URL
downloaded 27Kb
Error in old.packages(lib.loc = lib.loc, contriburl = contriburl, method =
method, :
no installed.packages for (invalid?) lib.loc=Matchit
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Tuesday, May 17, 2005 11:06 PM
To: S Setoguchi
Cc: matchit(a)latte.harvard.edu
Subject: Re: Updating matchit
Hi Soko,
I'd just try a full reinstall...
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Tuesday, May 17, 2005 10:35 PM
Subject: Updating matchit
Hi Dan
I tried to update matchit and it gives me the following message.
> update.packages("Matchit")
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 27996 bytes opened URL
downloaded 27Kb
Error in old.packages(lib.loc = lib.loc, contriburl = contriburl, method =
method, :
no installed.packages for (invalid?) lib.loc=Matchit
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Monday, March 07, 2005 12:46 AM
To: S Setoguchi
Subject: Re: [matchit] question on pscore matching using nnet or cart (fwd)
No problem. Thanks for pointing out the bug,
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Monday, March 07, 2005 12:41 AM
Subject: RE: [matchit] question on pscore matching using nnet or cart (fwd)
Hi
I did not know that nnet does not give a warning message for etraneous
arguments...I will be careful.
Thanks for your quick response and the fix.
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Monday, March 07, 2005 12:40 AM
To: S Setoguchi
Cc: matchit(a)latte.harvard.edu
Subject: Re: [matchit] question on pscore matching using nnet or cart (fwd)
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" <daniel.ho(a)yale.edu>
To: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
Cc: "Kosuke Imai" <kimai(a)Princeton.Edu>; "Elizabeth Stuart"
<EStuart(a)Mathematica-Mpr.com>
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" <soko(a)kuhp.kyoto-u.ac.jp>
> To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
> 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" <soko(a)kuhp.kyoto-u.ac.jp>
> To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>; <matchit(a)latte.harvard.edu>
> 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" <soko(a)kuhp.kyoto-u.ac.jp>
> > To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>; "'Elizabeth Stuart'"
> > <stuart(a)stat.harvard.edu>
> > Cc: "'Kosuke Imai'" <kimai(a)Princeton.Edu>;
> > <ssetoguc(a)hsph.harvard.edu>
> > 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" <stuart(a)stat.harvard.edu>
> > > To: "Daniel E. Ho" <daniel.ho(a)yale.edu>
> > > Cc: "Kosuke Imai" <kimai(a)Princeton.Edu>
> > > 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 <ssetoguc(a)hsph.harvard.edu>
> > > > 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
> > > >
> > > >
> > > > -
> > > > MatchIt mailing list served by Harvard-MIT Data Center List
> > > > Address: matchit(a)latte.harvard.edu
> > > > Subscribe/Unsubscribe:
> > > > http://lists.hmdc.harvard.edu/?info=matchit
> > > > MatchIt Software and Documentation:
> > > > http://gking.harvard.edu/matchit/
> > >
> > >
> > >
> >
> >
> >
>
>
>
-
MatchIt mailing list served by Harvard-MIT Data Center
List Address: matchit(a)latte.harvard.edu
Subscribe/Unsubscribe: http://lists.hmdc.harvard.edu/?info=matchit
MatchIt Software and Documentation: http://gking.harvard.edu/matchit/
Does it work if you capitalize the "I" in MatchIt?
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Tuesday, May 17, 2005 11:38 PM
Subject: RE: Updating matchit
Dan
This is what I tried.
> install.packages("MatchIt")
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 27996 bytes
opened URL
downloaded 27Kb
trying URL
`http://cran.r-project.org/bin/windows/contrib/2.0/MatchIt_1.0-1.zip'
Content type `application/zip' length 154470 bytes
opened URL
downloaded 150Kb
package 'MatchIt' successfully unpacked and MD5 sums checked
Delete downloaded files (y/N)? y
updating HTML package descriptions
> library(Matchit)
Error in library(Matchit) : There is no package called 'Matchit'
#If I used the pull-down menu to load the package, it works...
> update.packages("Matchit")
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 27996 bytes
opened URL
downloaded 27Kb
Error in old.packages(lib.loc = lib.loc, contriburl = contriburl, method =
method, :
no installed.packages for (invalid?) lib.loc=Matchit
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Tuesday, May 17, 2005 11:06 PM
To: S Setoguchi
Cc: matchit(a)latte.harvard.edu
Subject: Re: Updating matchit
Hi Soko,
I'd just try a full reinstall...
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Tuesday, May 17, 2005 10:35 PM
Subject: Updating matchit
Hi Dan
I tried to update matchit and it gives me the following message.
> update.packages("Matchit")
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 27996 bytes opened URL
downloaded 27Kb
Error in old.packages(lib.loc = lib.loc, contriburl = contriburl, method =
method, :
no installed.packages for (invalid?) lib.loc=Matchit
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Monday, March 07, 2005 12:46 AM
To: S Setoguchi
Subject: Re: [matchit] question on pscore matching using nnet or cart (fwd)
No problem. Thanks for pointing out the bug,
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Monday, March 07, 2005 12:41 AM
Subject: RE: [matchit] question on pscore matching using nnet or cart (fwd)
Hi
I did not know that nnet does not give a warning message for etraneous
arguments...I will be careful.
Thanks for your quick response and the fix.
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Monday, March 07, 2005 12:40 AM
To: S Setoguchi
Cc: matchit(a)latte.harvard.edu
Subject: Re: [matchit] question on pscore matching using nnet or cart (fwd)
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" <daniel.ho(a)yale.edu>
To: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
Cc: "Kosuke Imai" <kimai(a)Princeton.Edu>; "Elizabeth Stuart"
<EStuart(a)Mathematica-Mpr.com>
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" <soko(a)kuhp.kyoto-u.ac.jp>
> To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
> 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" <soko(a)kuhp.kyoto-u.ac.jp>
> To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>; <matchit(a)latte.harvard.edu>
> 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" <soko(a)kuhp.kyoto-u.ac.jp>
> > To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>; "'Elizabeth Stuart'"
> > <stuart(a)stat.harvard.edu>
> > Cc: "'Kosuke Imai'" <kimai(a)Princeton.Edu>;
> > <ssetoguc(a)hsph.harvard.edu>
> > 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" <stuart(a)stat.harvard.edu>
> > > To: "Daniel E. Ho" <daniel.ho(a)yale.edu>
> > > Cc: "Kosuke Imai" <kimai(a)Princeton.Edu>
> > > 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 <ssetoguc(a)hsph.harvard.edu>
> > > > 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
> > > >
> > > >
> > > > -
> > > > MatchIt mailing list served by Harvard-MIT Data Center List
> > > > Address: matchit(a)latte.harvard.edu
> > > > Subscribe/Unsubscribe:
> > > > http://lists.hmdc.harvard.edu/?info=matchit
> > > > MatchIt Software and Documentation:
> > > > http://gking.harvard.edu/matchit/
> > >
> > >
> > >
> >
> >
> >
>
>
>
-
MatchIt mailing list served by Harvard-MIT Data Center
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MatchIt Software and Documentation: http://gking.harvard.edu/matchit/
Hi Soko,
I'd just try a full reinstall...
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Tuesday, May 17, 2005 10:35 PM
Subject: Updating matchit
Hi Dan
I tried to update matchit and it gives me the following message.
> update.packages("Matchit")
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 27996 bytes
opened URL
downloaded 27Kb
Error in old.packages(lib.loc = lib.loc, contriburl = contriburl, method =
method, :
no installed.packages for (invalid?) lib.loc=Matchit
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Monday, March 07, 2005 12:46 AM
To: S Setoguchi
Subject: Re: [matchit] question on pscore matching using nnet or cart (fwd)
No problem. Thanks for pointing out the bug,
Dan
----- Original Message -----
From: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
Sent: Monday, March 07, 2005 12:41 AM
Subject: RE: [matchit] question on pscore matching using nnet or cart (fwd)
Hi
I did not know that nnet does not give a warning message for etraneous
arguments...I will be careful.
Thanks for your quick response and the fix.
Soko
-----Original Message-----
From: Daniel E. Ho [mailto:daniel.ho@yale.edu]
Sent: Monday, March 07, 2005 12:40 AM
To: S Setoguchi
Cc: matchit(a)latte.harvard.edu
Subject: Re: [matchit] question on pscore matching using nnet or cart (fwd)
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" <daniel.ho(a)yale.edu>
To: "S Setoguchi" <soko(a)kuhp.kyoto-u.ac.jp>
Cc: "Kosuke Imai" <kimai(a)Princeton.Edu>; "Elizabeth Stuart"
<EStuart(a)Mathematica-Mpr.com>
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" <soko(a)kuhp.kyoto-u.ac.jp>
> To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>
> 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" <soko(a)kuhp.kyoto-u.ac.jp>
> To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>; <matchit(a)latte.harvard.edu>
> 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" <soko(a)kuhp.kyoto-u.ac.jp>
> > To: "'Daniel E. Ho'" <daniel.ho(a)yale.edu>; "'Elizabeth Stuart'"
> > <stuart(a)stat.harvard.edu>
> > Cc: "'Kosuke Imai'" <kimai(a)Princeton.Edu>;
> > <ssetoguc(a)hsph.harvard.edu>
> > 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" <stuart(a)stat.harvard.edu>
> > > To: "Daniel E. Ho" <daniel.ho(a)yale.edu>
> > > Cc: "Kosuke Imai" <kimai(a)Princeton.Edu>
> > > 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 <ssetoguc(a)hsph.harvard.edu>
> > > > 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
> > > >
> > > >
> > > > -
> > > > MatchIt mailing list served by Harvard-MIT Data Center List
> > > > Address: matchit(a)latte.harvard.edu
> > > > Subscribe/Unsubscribe:
> > > > http://lists.hmdc.harvard.edu/?info=matchit
> > > > MatchIt Software and Documentation:
> > > > http://gking.harvard.edu/matchit/
> > >
> > >
> > >
> >
> >
> >
>
>
>
-
MatchIt mailing list served by Harvard-MIT Data Center
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Subscribe/Unsubscribe: http://lists.hmdc.harvard.edu/?info=matchit
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