Matchit March 2005

matchit@lists.gking.harvard.edu

3 participants
4 discussions

Re: [matchit] question on pscore matching using nnet or cart (fwd)

by Daniel E. Ho

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/

19 years, 1 month

Re: [matchit] question on pscore matching using nnet or cart (fwd)

by Daniel E. Ho

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/

19 years, 1 month

Re: [matchit] question on pscore matching using nnet or cart (fwd)

by Daniel E. Ho

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) Dan > ---------- 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/

19 years, 1 month

question on pscore matching using nnet or cart

by Soko Setoguchi

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/

19 years, 1 month

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