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How to do one-way ANOVA

using Python
Originally posted by Python Psychologist

What is repeated measures ANOVA?

A repeated-measures ANOVA (rmANOVA) is extending the analysis of variance tosituations


using repeated-measures research designs. (e.g., in which all subjects have been through each
condition)

Logic of rmANOVA and independent measures ANOVA is similar;


many formulas are, basically the same,

Second stage of analysis in rmANOVA to get the individual differences subst


the error term.

What is repeated measures ANOVA?

A repeated-measures design eliminates individual differences from the between-treatments


variability because the same subjects go through each treatment condition.

The F-ratio needs to be balanced with the calculation such that the individual differences are
eliminated from the F-ratio.

In the end we get a similar test statistic as in an ordinary ANOVA but all individual differences
are removed. Thus, there are no individual differences between treatments.

What is repeated measures ANOVA?

The variability due to individual differences is not a component of the numerator of the F-ratio.

Individual differences must also be removed from the denominator of the F ratio to maintain a balanced ratio with an
expected value of 1.00 when there is no treatment effect:

What is repeated measures ANOVA?


This can be accomplished by two stages. Note, SS stands for Sum of Squares.
1.

First, the total variability (SS total) is partitioned into variability between-treatments (SS between)
and within-treatments (SS within). Individual differences do not appear in SS between due to that
the same sample of subjects were measured in every treatment. Individual differences do play a
role in SS total because the sample contains different subjects.

2.

Second, we measure the individual differences by calculating the variability between subjects, or
SS subjects. SS value is subtracted from SS within and we obtain variability due to sampling
error, SS erro

Doing one-way ANOVA in Python

import pandas as pd
import numpy as np

In the code to the left we import the needed


python librares.

from scipy import stats


def calc_grandmean(data, columns):
"
Takes a pandas dataframe and calculates the grand mean
data = dataframe
columns = list of column names with the response variables
"
gm = np.mean(data[columns].mean())
return gm

I also created a function to calculate the grand


mean.

Doing one-way ANOVA in Python


##For createing example data
X1 = [6,4,5,1,0,2]

I then create some data using 3 lists and


Pandas DataFrame.

X2 = [8,5,5,2,1,3]
X3 = [10,6,5,3,2,4]
df = pd.DataFrame({Subid:xrange(1, len(X1)+1), X1:X1, X2:X2,

After data creation we calculate the grand mean,


subject mean, and column means.

X3:X3})
#Grand mean
grand_mean = calc_grandmean(df, ['X1, 'X2, 'X3])
df['Submean] = df[['X1, 'X2, 'X3]].mean(axis=1)
column_means = df[['X1, 'X2, 'X3]].mean(axis=0)

All means are, later, going to be used in the


ANOVA calculation.

Doing one-way ANOVA in Python


n = len(df['Subid])
k = len(['X1, 'X2, 'X3])

We now go on to get the sample size and the


number of levels of the within-subject factor.

#Degree of Freedom
ncells = df[['X1,'X2,'X3]].size
dftotal = ncells - 1

After this is done we need to calculate the


degree of freedoms.

dfbw = 3 - 1
dfsbj = len(df['Subid]) - 1
dfw = dftotal - dfbw
dferror = dfw - dfsbj

All of these are going to be used in the


calculation of sum of squares and means
square, and finally the F-ratio.

Doing one-way ANOVA in Python

Sum of Squares Between is calculated using this formula:

Python code: SSbetween = sum(n*[(m - grand_mean)**2 for m in column_means])

Doing one-way ANOVA in Python

Sum of Squares Within is calculated using this formula:

Python code: SSwithin = sum(sum([(df[col] - column_means[i])**2 for i, col in enumerate(df[['X1, 'X2, 'X3]])]))

Doing one-way ANOVA in Python

Sum of Squares Subjects is calculated using this formula:

Python code: SSsubject = sum(k*[(m -grand_mean)**2 for m in df['Submean]])

Doing one-way ANOVA in Python

Sum of Squares Error is calculated using this formula:

Python code: SSerror = SSwithin - SSsubject

Doing one-way ANOVA in Python

We can also calculate the SS total (i.e., The sum of squared deviations of all observations from the grand mean):

Python code: SStotal = SSbetween + SSwithin


Although it is not entirely necessary...

Doing one-way ANOVA in Python

After we have calculated the Mean square error and Mean square between we can obtain the F-statitistica:

msbetween = SSbetween/dfbetween
mserror = SSerror/dferror
F = msbetween/mserror

Doing one-way ANOVA in Python

By using SciPy we can obtain a p-value. We start by setting our alpha to .05 and then we get our p-value.
alpha = 0.05
p_value = stats.f.sf(F, 2, dferror)

That was it! If you have any question please let me know.

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