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How to do one-way ANOVA for repeated measures In Python

How to carry out one-way ANOVA with Python. First, brief theory on ANOVA and then a practical example on how to do Python Anova.

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How to do one-way ANOVA for repeated measures In Python

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  1. How to do one-way ANOVA using Python Originally posted by Python Psychologist

  2. 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 substracted out of the error term. ● ○

  3. 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.

  4. 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:

  5. 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

  6. Doing one-way ANOVA in Python import pandas as pd In the code to the left we import the needed python librares. import numpy as np from scipy import stats I also created a function to calculate the grand mean. 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

  7. Doing one-way ANOVA in Python ##For createing example data I then create some data using 3 lists and Pandas DataFrame. X1 = [6,4,5,1,0,2] X2 = [8,5,5,2,1,3] After data creation we calculate the grand mean, subject mean, and column means. X3 = [10,6,5,3,2,4] df = pd.DataFrame({‘Subid’:xrange(1, len(X1)+1), “X1”:X1, “X2”:X2, “X3”:X3}) All means are, later, going to be used in the ANOVA calculation. #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)

  8. Doing one-way ANOVA in Python n = len(df['Subid’]) We now go on to get the sample size and the number of levels of the within-subject factor. k = len(['X1’, 'X2’, 'X3’]) #Degree of Freedom After this is done we need to calculate the degree of freedoms. ncells = df[['X1’,'X2’,'X3’]].size dftotal = ncells - 1 dfbw = 3 - 1 All of these are going to be used in the calculation of sum of squares and means square, and finally the F-ratio. dfsbj = len(df['Subid’]) - 1 dfw = dftotal - dfbw dferror = dfw - dfsbj

  9. 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]) ●

  10. 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’]])])) ●

  11. 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’]]) ●

  12. Doing one-way ANOVA in Python Sum of Squares Error is calculated using this formula: ● Python code: SSerror = SSwithin - SSsubject ●

  13. 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... ● ●

  14. 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

  15. 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. ● I blog images related to data, Python, statistics, and psychology related stuff on my tumblr: ● http://pythonpsychologist.tumblr.com/

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