How to use glmulti from python using rpy2? - r

Question

consider the following dataframe
import pickle
a='pickle.loads(b\'\\x80\\x03cpandas.core.frame\\nDataFrame\\nq\\x00)\\x81q\\x01}q\\x02(X\\x05\\x00\\x00\\x00_dataq\\x03cpandas.core.internals.managers\\nBlockManager\\nq\\x04)\\x81q\\x05(]q\\x06(cpandas.core.indexes.base\\n_new_Index\\nq\\x07cpandas.core.indexes.base\\nIndex\\nq\\x08}q\\t(X\\x04\\x00\\x00\\x00dataq\\ncnumpy.core.multiarray\\n_reconstruct\\nq\\x0bcnumpy\\nndarray\\nq\\x0cK\\x00\\x85q\\rC\\x01bq\\x0e\\x87q\\x0fRq\\x10(K\\x01K\\n\\x85q\\x11cnumpy\\ndtype\\nq\\x12X\\x02\\x00\\x00\\x00O8q\\x13K\\x00K\\x01\\x87q\\x14Rq\\x15(K\\x03X\\x01\\x00\\x00\\x00|q\\x16NNNJ\\xff\\xff\\xff\\xffJ\\xff\\xff\\xff\\xffK?tq\\x17b\\x89]q\\x18(X\\x0b\\x00\\x00\\x00priceToBookq\\x19X\\x04\\x00\\x00\\x00betaq\\x1aX\\x0e\\x00\\x00\\x00price to salesq\\x1bX\\x0c\\x00\\x00\\x00gross profitq\\x1cX\\x0c\\x00\\x00\\x0052WeekChangeq\\x1dX\\n\\x00\\x00\\x00market capq\\x1eX\\x04\\x00\\x00\\x00ebitq\\x1fX\\r\\x00\\x00\\x00total revenueq X\\x0c\\x00\\x00\\x00payout ratioq!X\\x08\\x00\\x00\\x00pe ratioq"etq#bX\\x04\\x00\\x00\\x00nameq$Nu\\x86q%Rq&h\\x07cpandas.core.indexes.range\\nRangeIndex\\nq\\\'}q((h$NX\\x05\\x00\\x00\\x00startq)K\\x00X\\x04\\x00\\x00\\x00stopq*K\\x07X\\x04\\x00\\x00\\x00stepq+K\\x01u\\x86q,Rq-e]q.h\\x0bh\\x0cK\\x00\\x85q/h\\x0e\\x87q0Rq1(K\\x01K\\nK\\x07\\x86q2h\\x12X\\x02\\x00\\x00\\x00f8q3K\\x00K\\x01\\x87q4Rq5(K\\x03X\\x01\\x00\\x00\\x00<q6NNNJ\\xff\\xff\\xff\\xffJ\\xff\\xff\\xff\\xffK\\x00tq7b\\x89B0\\x02\\x00\\x00\\xd1#,\\x9b9\\x8c)#Cz\\xe5\\xd5\\x94_\\xf5?\\x92(\\x0ffn9\\xf0?\\n+\\x15TT-\\x17# \\xd5\\xb0\\xdf\\x13\\x03%#u\\xdek\\xad\\xd4\\xb8\\xfb?\\x1c\\xee#\\xb7&\\xbd\\xf3?-\\x98\\xf8\\xa3\\xa8\\xf3\\xf3?H\\xfd\\xf5\\n\\x0b\\xae\\xf1?:;\\x19\\x1c%/\\xf1?\\x9f\\x93\\xde7\\xbe\\xf6\\xf0?\\xbb}V\\x99)\\xad\\xf3?\\xae\\xbby\\xaaC.\\xf3?\\xa5,C\\x1c\\xeb\\xe2\\xf9?d\\x94g^\\x0e\\x13\\x12#\\x9e\\xc7r\\\\\\xd7i\\x06#\\xe4\\xe0\\x0c\\xddp\\xc8\\xcc?%\\x95)\\xe6 \\x18 #\\xa1\\xf4\\x85\\x90\\xf3\\x1e!#y6P\\x85\\xe4\\x89\\x0e#.\\xd9\\xc2=\\xe0\\x1b\\x0c#\\x00\\x00\\x00\\xc6\\x9e\\xe86B\\x00\\x00\\x00fF\\xb83B\\x00\\x00\\x00.\\xdc\\xb6\\x0bB\\x00\\x00\\x80\\x954\\xa5%B\\x00\\x00#\\\'1O3B\\x00\\x00\\x00\\xec\\xed58B\\x00\\x00\\x80\\t\\x93\\xa64B\\xf1\\xda\\x84\\xff\\x9d\\x82\\xd5?f\\xb8>\\x028#\\xa0?\\xc8^\\xef\\xfex/\\xb0\\xbf\\xab\\xd5\\x91\\x02\\x8f\\x18\\xd6?\\xd7\\xc05\\xfb,d\\xd6?r\\x8e\\xb6\\x01\\n\\xbb\\xc8?\\xc0\\xd52\\x00\\xf1F\\xc9?\\x00\\x00\\x00 \\x8b\\x1bqB\\x00\\x00\\x00\\xa0\\x92HKB\\x00\\x00\\x00\\x80\\xcb\\x8a B\\x00\\x00\\x00\\x00\\x98)_B\\x00\\x00\\x00`\\xca+pB\\x00\\x00\\x00\\xa0N\\xe4WB\\x00\\x00\\x00\\x00\\xc0\\x9fQB\\x00\\x00\\x00\\xc5\\x0c\\xc5-B\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00lIv\\xf0A\\x00\\x00\\x00\\xd9\\xb83\\x17B\\x00\\x00\\x80\\xa3\\x1c\\x01$B\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\xc0\\x17\\xcaINB\\x00\\x00\\x00fF\\xb83B\\x00\\x00#\\xdcq\\xaaBB\\x00\\x00\\x00\\x87h\\x00*B\\x00\\x00\\xc0\\xca\\xd3L=B\\x00\\x00\\x00\\xec\\xed58B\\x00\\x00\\x80\\t\\x93\\xa64B\\xa1\\xf81\\xe6\\xae%\\xd0?\\x8b\\xfde\\xf7\\xe4a\\xd9?\\x00\\x00\\x00\\x00\\x00\\x00\\xf8?\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\xf1\\xf4JY\\x868\\xd6?>(\\xc5\\x1ap\\xce\\xd4?\\xc3\\xf5(\\\\\\x8f\\xc2\\xcd?\\xad\\xbf%\\x00\\xff\\xe05#\\xc8$#gaG\\\'#\\x9a\\x99\\x99\\x99\\x99\\x996#{Ic\\xb4\\x8e\\x82>#^+\\xa1\\xbb$\\x8a;#UL\\xa5\\x9fp\\xbe)#0G\\x8f\\xdf\\xdb\\x84(#q8tq9ba]q:h\\x07h\\x08}q;(h\\nh\\x0bh\\x0cK\\x00\\x85q<h\\x0e\\x87q=Rq>(K\\x01K\\n\\x85q?h\\x15\\x89]q#(h\\x19h\\x1ah\\x1bh\\x1ch\\x1dh\\x1eh\\x1fh h!h"etqAbh$Nu\\x86qBRqCa}qDX\\x06\\x00\\x00\\x000.14.1qE}qF(X\\x04\\x00\\x00\\x00axesqGh\\x06X\\x06\\x00\\x00\\x00blocksqH]qI}qJ(X\\x06\\x00\\x00\\x00valuesqKh1X\\x08\\x00\\x00\\x00mgr_locsqLcbuiltins\\nslice\\nqMK\\x00K\\nK\\x01\\x87qNRqOuaustqPbX\\x04\\x00\\x00\\x00_typqQX\\t\\x00\\x00\\x00dataframeqRX\\t\\x00\\x00\\x00_metadataqS]qTub.\')'
a=eval(a)
a
and I want to run the function known by glmulti in python. I tried lots of ways but I failed. I then did the hopeless act of going to r as follow
take the dataset to excel file as
a.to_excel('test1.xlsx')
Go to r studio
install.packages("glmulti", "rJava", "readxl")
library("glmulti", "rJava", "readxl")
getwd()
setwd(".Gp\\to\\the\\python directory where you are workingin")
my_data <- read_excel("test1.xlsx", sheet = 1)
Change the columns of the dataframe because it does not work with the main values of the data
j=1
for (i in paste0("x",1:length(my_data))){
names(my_data)[j]=i
j=j+1
}
Select my x variable and y variable
y=my_data[,6]
x=my_data[, names(my_data) != names(my_data)[6]]
finally, I run the function I want in r as
glmulti(names(y), names(x), data=my_data, method="h")
Is there an easier way to run it from python using rpy2? If so can you please advise on this?

Answer 1

Consider converting Pandas data frame into an R data frame with rpy2, and then call just as you do now the glmulti from imported package.
However, a few notes about R:
Every function or method derives from a package which is true of Python except standard library functions (e.g., list, sum, type). But in R, its standard library packages are loaded by default (e.g., utils, stats, base) for everyday methods (e.g., read.csv, head, summary).
Though you can qualify package names with each function call such as with base::names, it is not required as in Python but helpful in case of name collision with other packages.
You do not need a for loop to rename all columns but can vectorize with base::paste0 and assign using stats::setNames or base::colnames.
Python Processing
import pandas as pd
import pickle
df_py = eval('pickle.loads(...)')
# RE-ORDER COLUMNS BY MOVING SIXTH COLUMN TO FIRST POSITION
cols = df_py.columns.to_list()
new_order = [cols[5]] + cols[0:5] + cols[6:]
df_py = df_py.reindex(new_order, axis=1)
print(df_py.head(10))
R Processing
from rpy2.robjects import pandas2ri
from rpy2.robjects.packages import importr
utils = importr('utils')
base = importr('base')
stats = importr('stats')
glmulti = importr('glmulti') # DOES NOT REQUIRE rJava PACKAGE BUT DOES REQUIRE Java LANGUAGE
# CONVERT TO R DATAFRAME
pandas2ri.activate()
df_r = pandas2ri.py2ri(df_py) # USING ABOVE PANDAS DATA FRAME
# RENAME COLUMNS y, x1, x2, x3, ...
df_r = stats.setNames(df_r, base.c("y", base.paste0("x", base.seq(1,base.length(df_r)[0]-1))))
print(utils.head(df_r, 10))
# CALL glmulti()
glmulti.glmulti(y = base.names(df_r)[0],
xr = base.names(df_r)[1:],
data = df_r,
method = "h")