Dear all, I have a question on how to set up the starting model in POLYCLASS and make sure the terms in the starting model retained in the final POLYCLASS model. In the function POLYMARS, this can be done using the STARTMODEL option. See below for example, I started with model y= b0 + b1*X1 + b2*X2 + b3*X4 + b4*X5 + b5*X2*X5 + e> m00 <- matrix(c(1, NA, 0, NA, 1, 2, NA, 0, NA, 1, 4, NA, 0, NA, 1, 5, NA, 0, NA, 1, 2, NA, 5, NA, 1),nrow = 5, ncol=5, byrow=TRUE);> m2 <- polymars(response=PID2$y, predictors=PID2[,1:7],startmodel=m00)> summary(m2)But I could not figure out how this works for POLYCLASS. There is an option FIT in POLYCLASS, which needs to be a POLYCLASS object though. Any suggestion or information is greatly appreciated. Sincerely, Xiaogang Su ===============================Xiaogang Su, Assistant Professor Department of Statistics and Actuarial Science University of Central Florida Orlando, FL 32816 (407) 823-2940 [O] xiaosu at mail.ucf.edu http://pegasus.cc.ucf.edu/~xsu/
I have not seen a reply, so I will offer a few suggestions, even
though I've never used the 'polspline' package. I scanned several
of
the help pages and looked in "~\library\polspline' where R is installed
on my hard drive and found no further documentation, and I found nothing
new from RSiteSearch("polyclass"). Googling for 'polyclass'
led me to
"http://bear.fhcrc.org/~clk/soft.html", the home page for Charles
Kooperberg, the author and maintainer. If it were my problem, I might
try writing him directly at the email address given in
help(package="polyclass"); I'm including him as a "cc"
on this reply.
I spent time looking at this, because 'polyclass', 'polymars'
and
'polspline' seem potentially related related to one of my secondary
interests. Unfortunately, I couldn't find sufficient documentation to
allow me to proceed with the time I felt I could afford to invest in
this right now.
If it were my problem, before I wrote another email about this, I'd
first list the function 'polyclass', make a local copy, then work
through an example line by line using 'debug(polyclass)'. This
'debug'
facility is remarkably powerful and easy to use. I've solved many
problems like this using 'debug' in this way.
If that failed to provide the necessary enlightenment, I'd submit
another post including a self-contained example based on a modification
of the 'iris' example featured in the 'polyclass' help page.
Your
example is NOT self contained, so I would NOT use that. Using the
'iris' example would make it much easier to explain clearly what you
want. It also makes it much easier for someone like me to experiment
with alternatives and describe what I did in terms of a tested example.
Hope this helps.
p.s. I suggest you also review the posting guide!
"www.R-project.org/posting-guide.html".
Xiaogang Su wrote:> Dear all,
>
> I have a question on how to set up the starting model in POLYCLASS and
> make sure the terms in the starting model retained in the final
> POLYCLASS model.
>
> In the function POLYMARS, this can be done using the STARTMODEL option.
> See below for example, I started with model
> y= b0 + b1*X1 + b2*X2 + b3*X4 + b4*X5 + b5*X2*X5 + e
>
>> m00 <- matrix(c(
> 1, NA, 0, NA, 1,
> 2, NA, 0, NA, 1,
> 4, NA, 0, NA, 1,
> 5, NA, 0, NA, 1,
> 2, NA, 5, NA, 1),nrow = 5, ncol=5, byrow=TRUE);
>
>> m2 <- polymars(response=PID2$y, predictors=PID2[,1:7],
> startmodel=m00)
>> summary(m2)
>
> But I could not figure out how this works for POLYCLASS. There is an
> option FIT in POLYCLASS, which needs to be a POLYCLASS object though.
>
> Any suggestion or information is greatly appreciated.
>
> Sincerely,
> Xiaogang Su
>
>
> ===============================> Xiaogang Su, Assistant Professor
> Department of Statistics and Actuarial Science
> University of Central Florida
> Orlando, FL 32816
> (407) 823-2940 [O]
> xiaosu at mail.ucf.edu
> http://pegasus.cc.ucf.edu/~xsu/
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
Dear Dr. Graves, Thanks for your information and kindness! I really appreciate it. According to my findings so far, POLYCLASS doesnot seem to allow for variables being forced into the model. Even the commercialized MARS doesnot have this function either. However, one ad hoc approach that they suggested is to fit linear (or logistic) model and form rediduals first and then run MARS with the residuals. Best regards, -XG Su ===============================Xiaogang Su, Assistant Professor Department of Statistics and Actuarial Science University of Central Florida Orlando, FL 32816 (407) 823-2940 [O] xiaosu at mail.ucf.edu http://pegasus.cc.ucf.edu/~xsu/>>> Spencer Graves <spencer.graves at pdf.com> 7/7/2006 5:49:05 AM >>>I have not seen a reply, so I will offer a few suggestions, even though I've never used the 'polspline' package. I scanned several of the help pages and looked in "~\library\polspline' where R is installed on my hard drive and found no further documentation, and I found nothing new from RSiteSearch("polyclass"). Googling for 'polyclass' led me to "http://bear.fhcrc.org/~clk/soft.html", the home page for Charles Kooperberg, the author and maintainer. If it were my problem, I might try writing him directly at the email address given in help(package="polyclass"); I'm including him as a "cc" on this reply. I spent time looking at this, because 'polyclass', 'polymars' and 'polspline' seem potentially related related to one of my secondary interests. Unfortunately, I couldn't find sufficient documentation to allow me to proceed with the time I felt I could afford to invest in this right now. If it were my problem, before I wrote another email about this, I'd first list the function 'polyclass', make a local copy, then work through an example line by line using 'debug(polyclass)'. This 'debug' facility is remarkably powerful and easy to use. I've solved many problems like this using 'debug' in this way. If that failed to provide the necessary enlightenment, I'd submit another post including a self-contained example based on a modification of the 'iris' example featured in the 'polyclass' help page. Your example is NOT self contained, so I would NOT use that. Using the 'iris' example would make it much easier to explain clearly what you want. It also makes it much easier for someone like me to experiment with alternatives and describe what I did in terms of a tested example. Hope this helps. p.s. I suggest you also review the posting guide! "www.R-project.org/posting-guide.html". Xiaogang Su wrote:> Dear all, > > I have a question on how to set up the starting model in POLYCLASSand> make sure the terms in the starting model retained in the final > POLYCLASS model. > > In the function POLYMARS, this can be done using the STARTMODELoption.> See below for example, I started with model > y= b0 + b1*X1 + b2*X2 + b3*X4 + b4*X5 + b5*X2*X5 + e > >> m00 <- matrix(c( > 1, NA, 0, NA, 1, > 2, NA, 0, NA, 1, > 4, NA, 0, NA, 1, > 5, NA, 0, NA, 1, > 2, NA, 5, NA, 1),nrow = 5, ncol=5, byrow=TRUE); > >> m2 <- polymars(response=PID2$y, predictors=PID2[,1:7], > startmodel=m00) >> summary(m2) > > But I could not figure out how this works for POLYCLASS. There is an > option FIT in POLYCLASS, which needs to be a POLYCLASS object though.> > Any suggestion or information is greatly appreciated. > > Sincerely, > Xiaogang Su > > > ===============================> Xiaogang Su, Assistant Professor > Department of Statistics and Actuarial Science > University of Central Florida > Orlando, FL 32816 > (407) 823-2940 [O] > xiaosu at mail.ucf.edu > http://pegasus.cc.ucf.edu/~xsu/ > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide!http://www.R-project.org/posting-guide.html
That's correct. The option is not there. You can force it in a starting model - but it can still be deleted, At some stage Insightful implemented a commercial set of polynomial spline functions in S-Plus that does have that option. They got it as far as a beta-library [quoting from my own homepage http://bear.fhcrc.org/~clk]: =========================== Doug Clarkson at Insightful Corp. has implemented commercial versions of hare, heft, logspline and a variety of related methods, with lots of additional features and options. See http://www.insightful.com/downloads/libraries/default.asp. Look for S+BEST. ===========================There are remaining bugs in this code.... Doug Clarkson is no longer at Insightful, and the code seems to be pretty much abbandoned. Charles Quoting Xiaogang Su <xiaosu at mail.ucf.edu>:> Dear Dr. Graves, > > Thanks for your information and kindness! I really appreciate it. > According to my findings so far, POLYCLASS doesnot seem to allow for > variables being forced into the model. Even the commercialized MARS > doesnot have this function either. However, one ad hoc approach that > they suggested is to fit linear (or logistic) model and form rediduals > first and then run MARS with the residuals. > > Best regards, > -XG Su > > > ===============================> Xiaogang Su, Assistant Professor > Department of Statistics and Actuarial Science > University of Central Florida > Orlando, FL 32816 > (407) 823-2940 [O] > xiaosu at mail.ucf.edu > http://pegasus.cc.ucf.edu/~xsu/ > > > >>> Spencer Graves <spencer.graves at pdf.com> 7/7/2006 5:49:05 AM >>> > I have not seen a reply, so I will offer a few suggestions, > even > though I've never used the 'polspline' package. I scanned several of > the help pages and looked in "~\library\polspline' where R is installed > > on my hard drive and found no further documentation, and I found > nothing > new from RSiteSearch("polyclass"). Googling for 'polyclass' led me to > > "http://bear.fhcrc.org/~clk/soft.html", the home page for Charles > Kooperberg, the author and maintainer. If it were my problem, I might > > try writing him directly at the email address given in > help(package="polyclass"); I'm including him as a "cc" on this reply. > > I spent time looking at this, because 'polyclass', 'polymars' > and > 'polspline' seem potentially related related to one of my secondary > interests. Unfortunately, I couldn't find sufficient documentation to > > allow me to proceed with the time I felt I could afford to invest in > this right now. > > If it were my problem, before I wrote another email about > this, I'd > first list the function 'polyclass', make a local copy, then work > through an example line by line using 'debug(polyclass)'. This 'debug' > > facility is remarkably powerful and easy to use. I've solved many > problems like this using 'debug' in this way. > > If that failed to provide the necessary enlightenment, I'd > submit > another post including a self-contained example based on a modification > > of the 'iris' example featured in the 'polyclass' help page. Your > example is NOT self contained, so I would NOT use that. Using the > 'iris' example would make it much easier to explain clearly what you > want. It also makes it much easier for someone like me to experiment > with alternatives and describe what I did in terms of a tested > example. > > Hope this helps. > p.s. I suggest you also review the posting guide! > "www.R-project.org/posting-guide.html". > > Xiaogang Su wrote: > > Dear all, > > > > I have a question on how to set up the starting model in POLYCLASS > and > > make sure the terms in the starting model retained in the final > > POLYCLASS model. > > > > In the function POLYMARS, this can be done using the STARTMODEL > option. > > See below for example, I started with model > > y= b0 + b1*X1 + b2*X2 + b3*X4 + b4*X5 + b5*X2*X5 + e > > > >> m00 <- matrix(c( > > 1, NA, 0, NA, 1, > > 2, NA, 0, NA, 1, > > 4, NA, 0, NA, 1, > > 5, NA, 0, NA, 1, > > 2, NA, 5, NA, 1),nrow = 5, ncol=5, byrow=TRUE); > > > >> m2 <- polymars(response=PID2$y, predictors=PID2[,1:7], > > startmodel=m00) > >> summary(m2) > > > > But I could not figure out how this works for POLYCLASS. There is an > > option FIT in POLYCLASS, which needs to be a POLYCLASS object though. > > > > > Any suggestion or information is greatly appreciated. > > > > Sincerely, > > Xiaogang Su > > > > > > ===============================> > Xiaogang Su, Assistant Professor > > Department of Statistics and Actuarial Science > > University of Central Florida > > Orlando, FL 32816 > > (407) 823-2940 [O] > > xiaosu at mail.ucf.edu > > http://pegasus.cc.ucf.edu/~xsu/ > > > > ______________________________________________ > > R-help at stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html >
Dear Prof. Kooperberg, Thanks a lot for your clarification! That is very helpful. I will check out the polynomial spline functions in S-Plus that you mentioned. Best regards, -XG Su ===============================Xiaogang Su, Assistant Professor Department of Statistics and Actuarial Science University of Central Florida Orlando, FL 32816 (407) 823-2940 [O] xiaosu at mail.ucf.edu http://pegasus.cc.ucf.edu/~xsu/>>> <clk at fhcrc.org> 07/10/06 4:01 PM >>>That's correct. The option is not there. You can force it in a starting model - but it can still be deleted, At some stage Insightful implemented a commercial set of polynomial spline functions in S-Plus that does have that option. They got it as far as a beta-library [quoting from my own homepage http://bear.fhcrc.org/~clk]: =========================== Doug Clarkson at Insightful Corp. has implemented commercial versions of hare, heft, logspline and a variety of related methods, with lots of additional features and options. See http://www.insightful.com/downloads/libraries/default.asp. Look for S+BEST. ===========================There are remaining bugs in this code.... Doug Clarkson is no longer at Insightful, and the code seems to be pretty much abbandoned. Charles Quoting Xiaogang Su <xiaosu at mail.ucf.edu>:> Dear Dr. Graves, > > Thanks for your information and kindness! I really appreciate it. > According to my findings so far, POLYCLASS doesnot seem to allow for > variables being forced into the model. Even the commercialized MARS > doesnot have this function either. However, one ad hoc approach that > they suggested is to fit linear (or logistic) model and form rediduals > first and then run MARS with the residuals. > > Best regards, > -XG Su > > > ===============================> Xiaogang Su, Assistant Professor > Department of Statistics and Actuarial Science > University of Central Florida > Orlando, FL 32816 > (407) 823-2940 [O] > xiaosu at mail.ucf.edu > http://pegasus.cc.ucf.edu/~xsu/ > > > >>> Spencer Graves <spencer.graves at pdf.com> 7/7/2006 5:49:05 AM >>> > I have not seen a reply, so I will offer a few suggestions, > even > though I've never used the 'polspline' package. I scanned several of > the help pages and looked in "~\library\polspline' where R isinstalled> > on my hard drive and found no further documentation, and I found > nothing > new from RSiteSearch("polyclass"). Googling for 'polyclass' led me to > > "http://bear.fhcrc.org/~clk/soft.html", the home page for Charles > Kooperberg, the author and maintainer. If it were my problem, I might > > try writing him directly at the email address given in > help(package="polyclass"); I'm including him as a "cc" on this reply. > > I spent time looking at this, because 'polyclass', 'polymars' > and > 'polspline' seem potentially related related to one of my secondary > interests. Unfortunately, I couldn't find sufficient documentation to > > allow me to proceed with the time I felt I could afford to invest in > this right now. > > If it were my problem, before I wrote another email about > this, I'd > first list the function 'polyclass', make a local copy, then work > through an example line by line using 'debug(polyclass)'. This'debug'> > facility is remarkably powerful and easy to use. I've solved many > problems like this using 'debug' in this way. > > If that failed to provide the necessary enlightenment, I'd > submit > another post including a self-contained example based on amodification> > of the 'iris' example featured in the 'polyclass' help page. Your > example is NOT self contained, so I would NOT use that. Using the > 'iris' example would make it much easier to explain clearly what you > want. It also makes it much easier for someone like me to experiment > with alternatives and describe what I did in terms of a tested > example. > > Hope this helps. > p.s. I suggest you also review the posting guide! > "www.R-project.org/posting-guide.html". > > Xiaogang Su wrote: > > Dear all, > > > > I have a question on how to set up the starting model in POLYCLASS > and > > make sure the terms in the starting model retained in the final > > POLYCLASS model. > > > > In the function POLYMARS, this can be done using the STARTMODEL > option. > > See below for example, I started with model > > y= b0 + b1*X1 + b2*X2 + b3*X4 + b4*X5 + b5*X2*X5 + e > > > >> m00 <- matrix(c( > > 1, NA, 0, NA, 1, > > 2, NA, 0, NA, 1, > > 4, NA, 0, NA, 1, > > 5, NA, 0, NA, 1, > > 2, NA, 5, NA, 1),nrow = 5, ncol=5, byrow=TRUE); > > > >> m2 <- polymars(response=PID2$y, predictors=PID2[,1:7], > > startmodel=m00) > >> summary(m2) > > > > But I could not figure out how this works for POLYCLASS. There is an > > option FIT in POLYCLASS, which needs to be a POLYCLASS objectthough.> > > > > Any suggestion or information is greatly appreciated. > > > > Sincerely, > > Xiaogang Su > > > > > > ===============================> > Xiaogang Su, Assistant Professor > > Department of Statistics and Actuarial Science > > University of Central Florida > > Orlando, FL 32816 > > (407) 823-2940 [O] > > xiaosu at mail.ucf.edu > > http://pegasus.cc.ucf.edu/~xsu/ > > > > ______________________________________________ > > R-help at stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html >