Accessing A R User Defined Function In Python
So I need to do Principle Component Regression with cross validation and I could not find a package in Python that would do so. I wrote my own PCR class but when tested against R's
Solution 1:
Consider importing the abitrary R user-defined function as a package with rpy2's SignatureTranslatedAnonymousPackage (STAP):
from rpy2.robjects.numpy2ri import numpy2ri, pandas2ri
from rpy2.robjects.packages import STAP
# for rpy2 < 2.6.1# from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage as STAP
r_fct_string = """
R_pls <- function(X_train, y_train, X_test){
library(pls)
X <- as.matrix(X_train)
y <- as.matrix(y_train)
xt <- as.matrix(X_test)
tdata <- data.frame(y,X=I(X))
REGmodel <- pls::pcr(y~X,scale=FALSE,data=tdata,validation="CV")
B <- RMSEP(REGmodel)
C <- B[[1]]
q <- length(C)
degs <- c(1:q)
allvals <- C[degs%%2==0]
allvals <- allvals[-1]
comps <- which.min(allvals)
ndata <- data.frame(X=I(xt))
ypred_test <- as.data.frame(predict(REGmodel,ncomp=comps,newdata=ndata,se.fit=TRUE))
ntdata <- data.frame(X=I(X))
ypred_train <- as.data.frame(predict(REGmodel,ncomp=comps,newdata=ntdata,se.fit=TRUE))
data_out <- list(ypred_test=ypred_test, ypred_train=ypred_train)
return(data_out)
}
"""
r_pkg = STAP(r_fct_string, "r_pkg")
# CONVERT PYTHON NUMPY MATRICES TO R OBJECTS
r_X_train, r_y_train, r_X_test = map(numpy2ri, py_X_train, py_y_train, py_X_test)
# PASS R OBJECTS INTO FUNCTION (WILL NEED TO EXTRACT DFs FROM RESULT)
p_res = r_pkg.R_pls(r_X_train, r_y_train, r_X_test)
Alternatively, you can source the function as @agstudy shows here if function is saved in a separate .R script then call it like any Python function.
import rpy2.robjects as ro
robjects.r('''source('my_R_pls_func.r')''')
r_pls = ro.globalenv['R_pls']
# CONVERT PYTHON NUMPY MATRICES TO R OBJECTS
r_X_train, r_y_train, r_X_test = map(numpy2ri, py_X_train, py_y_train, py_X_test)
# PASS R OBJECTS INTO FUNCTION (WILL NEED TO EXTRACT DFs FROM RESULT)
p_res = r_pls(r_X_train, r_y_train, r_X_test)
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