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From: Skipper Seabold <jsseabold@gm...>  20090623 21:26:05

Hello all, I am relatively new to R and Rpy and have a question about obtaining the covariance matrix after doing a glm estimation so that I can get the standard errors. I'm sure I'm missing something simple, but I haven't been able to find a solution searching the web or the ML archives. I have y and x which are two numpy arrays. y is a binary response variable and x contains my regressors plus a prepended column of ones. I estimate the model as follows which goes fine. from rpy import r des_cols = ['x.%d' % (i+1) for i in range(x.shape[1])] formula = r('y~%s1' % '+'.join(des_cols)) frame = r.data_frame(y=y, x=x) results = r.glm(formula, data=frame, family='binomial') results['coefficients'] is as expected judging from other software, so I assume this was all done correctly. I searched and found out that I should be able to obtain the covariance matrix with r.vcov[results] But when I try this command I receive the following error RPy_RException: Error in UseMethod("vcov") : no applicable method for "vcov" Any ideas? Cheers, Skipper 
From: Laurent Gautier <lgautier@gm...>  20090623 19:01:50

Sebastian Żurek wrote: > BEGIN PGP SIGNED MESSAGE > Hash: SHA1 > > Thanks for the fast answer, Laurent! > The anonymous function solution is OK, when one needs to work > occasionally with some piece of code. Unfortunately  my problem is a > little bit different: > > I will be given a whole library of custom R functions, I need to access > them with Python, provide some arguments and gather some results. All R > code is maintained by my colleague who is R master and there's no option > he will code R in Python, it's my task to provide RtoPython > interface, which is a part of a bigger system, which written purely in > Python. That's a typical usecase for rpy/rpy2, I think. I hope to find the time to write more about that in the near future (and I have to admit that I do not see where the problem is). > Any other suggestion are greatly welcome! > > I'm a R newbie (it's my first hours with this language, though), I guess > one can provide a package (library) of functions and register them in R > namespace  the question is: if I provide such a mechanism with rpy2 > (using the R "library" function) will all the functions became visible > for rpy2? Apparently so. By default R is loading a number of packages (libraries) when you just start it. The documentation has a toy example showing how to check where a symbol is coming from: http://rpy.sourceforge.net/rpy2/doc/html/rinterface.html#rpackagesasenvironments Otherwise, the upcoming 2.1 version will be proposing a place where R packages can be given tailored python representations (that's still quite rough, but the earlier people try to break it the better). L. > I'm going to check this in a minute... > > Laurent Gautier pisze: >> Sebastian Żurek wrote: >>> Hi! >>> >>> I want to use rpy2 in my Python software to make a use of some custom >>> Rscripts/functions. >>> >>> Is it possible, to call a custom R function with rpy2? >>> For example, having the custom (taken from R tutorial) definition: >>> >>> twosam < function(y1, y2) { >>> n1 < length(y1); n2 < length(y2) >>> yb1 < mean(y1); yb2 < mean(y2) >>> s1 < var(y1); s2 < var(y2) >>> s < ((n11)*s1 + (n21)*s2)/(n1+n22) >>> tst < (yb1  yb2)/sqrt(s*(1/n1 + 1/n2)) >>> tst >>> } >>> >>> how to call it with rpy2? I guess, there should be a Rpackaged that >>> contains it implemented and loaded? >>> >>> In python code, I want to use something like: >>> >>> twosam = robjects.r['twosam'] >> If you only want to access your function from Python, having making it >> an anonymous R function might one way to go. >> >> twosam = robjects.r(''' >> function(y1, y2) { >> n1 < length(y1); n2 < length(y2) >> yb1 < mean(y1); yb2 < mean(y2) >> s1 < var(y1); s2 < var(y2) >> s < ((n11)*s1 + (n21)*s2)/(n1+n22) >> tst < (yb1  yb2)/sqrt(s*(1/n1 + 1/n2)) >> tst >> } >> ''') >> >> >> >> twosam(robjects.IntVector(range(10)), >> robjects.IntVector(range(10))) >> >> >> >> L. >> >> >>> Thanks for *any* clues! >>> Sebastian >>> >>>  >>> Are you an open source citizen? Join us for the Open Source Bridge conference! >>> Portland, OR, June 1719. Two days of sessions, one day of unconference: $250. >>> Need another reason to go? 24hour hacker lounge. Register today! >>> http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org >>> _______________________________________________ >>> rpylist mailing list >>> rpylist@... >>> https://lists.sourceforge.net/lists/listinfo/rpylist >> >>  >> Are you an open source citizen? Join us for the Open Source Bridge conference! >> Portland, OR, June 1719. Two days of sessions, one day of unconference: $250. >> Need another reason to go? 24hour hacker lounge. Register today! >> http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org >> _______________________________________________ >> rpylist mailing list >> rpylist@... >> https://lists.sourceforge.net/lists/listinfo/rpylist > > BEGIN PGP SIGNATURE > Version: GnuPG v2.0.11 (GNU/Linux) > Comment: Using GnuPG with Mozilla  http://enigmail.mozdev.org > > iEYEARECAAYFAkpBHXEACgkQGAS1N8/5iJ54YQCfTdmCeOtaLdyM81YN3I5r+qrB > XzwAn1TTB7vVOymt2imTbq0bY9APsTEa > =Mrnm > END PGP SIGNATURE > > >  > _______________________________________________ > rpylist mailing list > rpylist@... > https://lists.sourceforge.net/lists/listinfo/rpylist 
From: Sebastian Żurek <sebzur@se...>  20090623 18:25:09

BEGIN PGP SIGNED MESSAGE Hash: SHA1 Thanks for the fast answer, Laurent! The anonymous function solution is OK, when one needs to work occasionally with some piece of code. Unfortunately  my problem is a little bit different: I will be given a whole library of custom R functions, I need to access them with Python, provide some arguments and gather some results. All R code is maintained by my colleague who is R master and there's no option he will code R in Python, it's my task to provide RtoPython interface, which is a part of a bigger system, which written purely in Python. Any other suggestion are greatly welcome! I'm a R newbie (it's my first hours with this language, though), I guess one can provide a package (library) of functions and register them in R namespace  the question is: if I provide such a mechanism with rpy2 (using the R "library" function) will all the functions became visible for rpy2? I'm going to check this in a minute... Laurent Gautier pisze: > Sebastian Żurek wrote: >> Hi! >> >> I want to use rpy2 in my Python software to make a use of some custom >> Rscripts/functions. >> >> Is it possible, to call a custom R function with rpy2? >> For example, having the custom (taken from R tutorial) definition: >> >> twosam < function(y1, y2) { >> n1 < length(y1); n2 < length(y2) >> yb1 < mean(y1); yb2 < mean(y2) >> s1 < var(y1); s2 < var(y2) >> s < ((n11)*s1 + (n21)*s2)/(n1+n22) >> tst < (yb1  yb2)/sqrt(s*(1/n1 + 1/n2)) >> tst >> } >> >> how to call it with rpy2? I guess, there should be a Rpackaged that >> contains it implemented and loaded? >> >> In python code, I want to use something like: >> >> twosam = robjects.r['twosam'] > > If you only want to access your function from Python, having making it > an anonymous R function might one way to go. > > twosam = robjects.r(''' > function(y1, y2) { > n1 < length(y1); n2 < length(y2) > yb1 < mean(y1); yb2 < mean(y2) > s1 < var(y1); s2 < var(y2) > s < ((n11)*s1 + (n21)*s2)/(n1+n22) > tst < (yb1  yb2)/sqrt(s*(1/n1 + 1/n2)) > tst > } > ''') > > > > twosam(robjects.IntVector(range(10)), > robjects.IntVector(range(10))) > > > > L. > > >> Thanks for *any* clues! >> Sebastian >> >>  >> Are you an open source citizen? Join us for the Open Source Bridge conference! >> Portland, OR, June 1719. Two days of sessions, one day of unconference: $250. >> Need another reason to go? 24hour hacker lounge. Register today! >> http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org >> _______________________________________________ >> rpylist mailing list >> rpylist@... >> https://lists.sourceforge.net/lists/listinfo/rpylist > > >  > Are you an open source citizen? Join us for the Open Source Bridge conference! > Portland, OR, June 1719. Two days of sessions, one day of unconference: $250. > Need another reason to go? 24hour hacker lounge. Register today! > http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org > _______________________________________________ > rpylist mailing list > rpylist@... > https://lists.sourceforge.net/lists/listinfo/rpylist BEGIN PGP SIGNATURE Version: GnuPG v2.0.11 (GNU/Linux) Comment: Using GnuPG with Mozilla  http://enigmail.mozdev.org iEYEARECAAYFAkpBHXEACgkQGAS1N8/5iJ54YQCfTdmCeOtaLdyM81YN3I5r+qrB XzwAn1TTB7vVOymt2imTbq0bY9APsTEa =Mrnm END PGP SIGNATURE 
From: Laurent Gautier <lgautier@gm...>  20090623 15:16:33

Sebastian Żurek wrote: > Hi! > > I want to use rpy2 in my Python software to make a use of some custom > Rscripts/functions. > > Is it possible, to call a custom R function with rpy2? > For example, having the custom (taken from R tutorial) definition: > > twosam < function(y1, y2) { > n1 < length(y1); n2 < length(y2) > yb1 < mean(y1); yb2 < mean(y2) > s1 < var(y1); s2 < var(y2) > s < ((n11)*s1 + (n21)*s2)/(n1+n22) > tst < (yb1  yb2)/sqrt(s*(1/n1 + 1/n2)) > tst > } > > how to call it with rpy2? I guess, there should be a Rpackaged that > contains it implemented and loaded? > > In python code, I want to use something like: > > twosam = robjects.r['twosam'] If you only want to access your function from Python, having making it an anonymous R function might one way to go. twosam = robjects.r(''' function(y1, y2) { n1 < length(y1); n2 < length(y2) yb1 < mean(y1); yb2 < mean(y2) s1 < var(y1); s2 < var(y2) s < ((n11)*s1 + (n21)*s2)/(n1+n22) tst < (yb1  yb2)/sqrt(s*(1/n1 + 1/n2)) tst } ''') twosam(robjects.IntVector(range(10)), robjects.IntVector(range(10))) L. > > Thanks for *any* clues! > Sebastian > >  > Are you an open source citizen? Join us for the Open Source Bridge conference! > Portland, OR, June 1719. Two days of sessions, one day of unconference: $250. > Need another reason to go? 24hour hacker lounge. Register today! > http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org > _______________________________________________ > rpylist mailing list > rpylist@... > https://lists.sourceforge.net/lists/listinfo/rpylist 
From: Sebastian Żurek <sebzur@se...>  20090623 14:46:08

Hi! I want to use rpy2 in my Python software to make a use of some custom Rscripts/functions. Is it possible, to call a custom R function with rpy2? For example, having the custom (taken from R tutorial) definition: twosam < function(y1, y2) { n1 < length(y1); n2 < length(y2) yb1 < mean(y1); yb2 < mean(y2) s1 < var(y1); s2 < var(y2) s < ((n11)*s1 + (n21)*s2)/(n1+n22) tst < (yb1  yb2)/sqrt(s*(1/n1 + 1/n2)) tst } how to call it with rpy2? I guess, there should be a Rpackaged that contains it implemented and loaded? In python code, I want to use something like: twosam = robjects.r['twosam'] Thanks for *any* clues! Sebastian 