Myles English wrote: > Hello, > > rpy 1.25 > ubuntu 6.10 > python 2.4 > > The code below can be copied and pasted in the R interpreter or an empty > file, as appropriate, to be run easily. The python code imports > dataframe.py that is included as an example in the rpy distribution. > > My question is: > > Running the R code in the interpreter prints the list of hubertgamma > values as: > 0.6982304 0.6501113 0.5739095 0.5301628 0.4861548 0.4826513 > 0.4579655 0.4465557 0.4329692 0.4092727 > > Running the RPy code in a shell prints the list of hubertgamma values > as: > [0.052761567599982385, -0.0045159859941235163, -0.047153537691912426, > -0.018242422413064344, -0.022733831895949543, -0.0033926040834361161, > -0.020580660750514498, -0.018014109040888696, -0.012575979384130119] > > Why aren't these two lists the same? I think I am missing something in > the conversion.
It doesn't look like you are setting the seed to the R random number generator to 1 in the Python code - are you? If not, you will be using two different sets of input values -> two different sets of answers. Tim C > # R code > #================================================================ > # from http://addictedtor.free.fr/packages > require(fpc) > require(A2R) > d.usa <- dist(USArrests, "euc") > h.usa <- hclust(d.usa, method="ward") > set.seed(1) > some.factor <- letters[1:4][rbinom(50, prob=0.5, size=3)+1] > hubertgamma <- rep(0,10) > for(i in 1:10){ > hubertgamma[i] <- cluster.stats(d.usa, > cutree(h.usa, k=i+1), > G2 = FALSE, > G3 = FALSE, > silhouette = FALSE)$hubertgamma > } > A2Rplot(h.usa, > k=3, > fact.sup=some.factor, > criteria=hubertgamma, > boxes = FALSE, > col.up = "gray", > col.down = c("orange","royalblue","green3")) > hubertgamma > #prints 0.6982304 0.6501113 0.5739095 0.5301628 > # 0.4861548 0.4826513 0.4579655 > # 0.4465557 0.4329692 0.4092727 > > # python code using RPy to put in a module > #========================================= > from rpy import * > from dataframe import * # dataframe.py comes with the rpy > distribution > class_table['data.frame'] = DataFrame > > class A(object): > def build(self): > set_default_mode(NO_CONVERSION) # so that, hclust finds more > than one item in rdist > d = r('USArrests') > self.rdist = r.dist(d, method = "euclidean") > self.dend = r.hclust(self.rdist, method="ward") > r.require('fpc') > r.require('A2R') > hubertgamma = [] > set_default_mode(CLASS_CONVERSION) > f=['a','b','c','d'] > self.somefactor = [f[int(i)] for i in r.rbinom(50, prob=0.5, > size=3)] > self.hubertgamma = [] > for i in range(1,10): # not zero-based, could cause a problem > self.hubertgamma.append(r.cluster_stats(self.rdist, > r.cutree(self.dend, k=i+1), > G2 = False, > G3 = False, > silhouette = False)['hubertgamma']) > r.x11() > r.A2Rplot(self.dend, > k = 3, > fact_sup=self.somefactor, > criteria=self.hubertgamma, > boxes = True, > col_up = "gray", > col_down = ["orange","royalblue", "green3"]) > #r.dev_off() > return self.hubertgamma > > if __name__ == '__main__': > obj = A() > print obj.build() > #prints [0.052761567599982385, -0.0045159859941235163, > # -0.047153537691912426, -0.018242422413064344, > # -0.022733831895949543, -0.0033926040834361161, > # -0.020580660750514498, -0.018014109040888696, > # -0.012575979384130119] > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > rpy-list mailing list > rpy-list@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rpy-list > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
