There is a package in R that I need to use on my data. All my data preprocessing has already been done in python and all the modelling as well. The package in R is 'PMA'. I have used r2py before using Rs PLS package as follows
import numpy as np
from rpy2.robjects.numpy2ri import numpy2ri
import rpy2.robjects as ro
def Rpcr(X_train,Y_train,X_test):
ro.r('''source('R_pls.R')''')
r_pls=ro.globalenv['R_pls']
r_x_train=numpy2ri(X_train)
r_y_train=numpy2ri(Y_train)
r_x_test=numpy2ri(X_test)
p_res=r_pls(r_x_train,r_y_train,r_x_test)
yp_test=np.array(p_res[0])
yp_test=yp_test.reshape((yp_test.size,))
yp_train=np.array(p_res[1])
yp_train=yp_train.reshape((yp_train.size,))
ncomps=np.array(p_res[2])
ncomps=ncomps.reshape((ncomps.size,))
return yp_test,yp_train,ncomps
when I followed this format is gave an error that function numpy2ri does not exist.
So I have been working off of rpy2 manual and have tried a number of things with no success. The package I am working with in R is implemented like so:
library('PMA')
cspa=CCA(X,Z,typex="standard", typez="standard", K=1, penaltyx=0.25, penaltyz=0.25)
# X and Z are dataframes with dimension ppm and pXq
# cspa returns an R object which I need two attributes u and v
U<-cspa$u
V<-cspa$v
So trying to implement something like I was seeing on the rpy2 tried to load the module in python and use it in python like so
import rpy2.robjects as ro
from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage as STAP
from rpy2.robjects import numpy2ri
from rpy2.robjects.packages import importr
base=importr('base'
scca=importr('PMA')
numpy2ri.activate() # To turn NumPy arrays X1 and X2 to r objects
out=scca.CCA(X1,X2,typex="standard",typez="standard", K=1, penaltyz=0.25,penaltyz=0.25)
and got the following error
OMP: Error #15: Initializing libomp.dylib, but found libiomp5.dylib already initialized.
OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
Abort trap: 6
I also tried using R code directly using an example they had
string<-'''SCCA<-function(X,Z,K,alpha){
library("PMA")
scca<-CCA(X,Z,typex="standard",typez="standard",K=K penaltyx=alpha,penaltyz=alpha)
u<-scca$u
v<-scca$v
out<-list(U=u,V=v)
return(out)}'''
scca=STAP(string,"scca")
which as I understand can be used like an r function directly
numpy2ri.activate()
scca(X,Z,1,0.25)
this results in the same error as above.
So I do not know exactly how to fix it and have been unable to find anything similar.
