R from Python – an rpy2 tutorial

rpy2 tutorial

Recently I found the Python module rpy2. This module offers a Python interface to R. Obviously; rpy2 requires that you have both R (version 3.2+) and Python (versions 2.7 and 3.3) installed.¬† There are pre-compiled binaries available for Linux and Windows (unsupported and unofficial, however). In this short tutorial, I will show you how to do carry out a repeated measures ANOVA (rmANOVA) using the r-packages ‘afex‘ and ‘lsmeans‘, Python, and rpy2.https://open.spotify.com/album/6XJujBkWZYlhTtxYRcDHr3


First, we start the tutorial with installing rpy2. I installed rpy2 on Ubuntu 14.04 using pip:


sudo pip install rpy2

When we have a working installation, we continue the tutorial with importing¬† the methods that we are going to use. In this rpy2 example we are going to use ‘afex’ to do the within-subject ANOVA and ‘lsmeans’ to do the follow-up analysis.


import rpy2.robjects as robjects
import rpy2.robjects.packages as rpackages
from rpy2.robjects.vectors import StrVector

We also need to check whether the needed packages are installed. Note that the following script will install the r-package if needed. However, it might be good to know how to carry out a repeated measrues ANOVA using the function ez_aov.


packageNames = ('afex', 'lsmeans')

if all(rpackages.isinstalled(x) for x in packageNames):

    have_packages = True

else:

   have_packages = False

if not have_packages:

    utils = rpackages.importr('utils')
    utils.chooseCRANmirror(ind=1)

    packnames_to_install = [x for x in packageNames if not rpackages.isinstalled(x)]

    if len(packnames_to_install) > 0:

        utils.install_packages(StrVector(packnames_to_install))

For this tutorial we borrow a data set from the package Psych. In this case, we use the r-function read.table to get the data.


data = robjects.r('read.table(file = "http://personality-project.org/r/datasets/R.appendix3.data", header = T)')

 

repeated measures ANOVA

In this part of the rpy2 tutorial we will carry out the actual analysis. However, before conducting our ANOVA for within-subjects design, we need to import the r-package (i.e., afex). When this is done, we will use the function aov_ez to conduct the analysis.


afex = importr('afex') 
model = afex.aov_ez('Subject', 'Recall', data, within='Valence')
print model

The last line above prints the results. A main effect of Valence was found.


   Effect         df  MSE          F ges p.value
1 Valence 1.15, 4.60 9.34 189.11 *** .93  < .0001

Follow-up analysis

Typically we are interested in following up the main effect, and with rpy2, we can do that using the r-package ‘lsmeans’. First, we need to import the package and then we do a pairwise contrast and adjust for familywise error using Holm-Bonferroni correction.


lsm  = importr('lsmeans')
pairwise = lsm.lsmeans(model, "Valence", contr="pairwise", adjust="holm")

That was easy, right. Particularly, if you are used to doing analysis in R. Although, rpy2 is relatively easy to use I don’t think it will replace learning R. That is, you will have to know some R to make use of it. However, if you are a Python programmer and want to use available R-scripts, it might be useful and hopefully this rpy2 tutorial have made it somewhat easier for you. Noteworthy, I am not aware of any Python implementations of rmANOVA (except for the linear-mixed effects approach maybe). In fact, that is why I learned how to use rpy2 in the first place; to use Python, and R, to conduct the analysis.

Update: In this rpy2 tutorial you learned how to do a repeated measures ANOVA with Python and R. I have now found a Python package that allows Python ANOVA for within-subjects design (i.e., Python native); see my tutorial Repeated Measures ANOVA using Python.

 

 

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