Category: Programming

Programming related posts

In this category you will find posts that are related to programming and should be interesting for psychologists, cognitive scientists, and neuroscientists. Well, almost every researcher would probably find some of the information useful at some time!

Every research psychologist, cognitive scientist, and neuroscientist, should know how to program.. Knowing how to program and write scripts will make many of a researchers everyday tasks much easier. For instance, instead of going through line after line of raw data you can write a Python script that runs through each cell in each column. Furthermore, you get the possibility to use more advanced, and cutting edge, statistical techniques by using R statistical programming environment.

Another example might be to create experiments using PsychoPy (either by coding using Python or using the drag-and-drop interface) and the cheap and open-source Arduino microcontroller. Also, coding is fun and relaxing!

How to Use Binder and R for Reproducible Research

Erik Marsja

September 15, 2019

Leave a Comment

How to Use Binder and R for Reproducible Research

In a previous post, we learned how to use Binder and Python for reproducible research. Now we are going to learn how to create a Binder for our data analysis in R, so it can be fully reproduced by other researchers. More specifically, in this post we will learn how to use Binder for reproducible research.

Many researchers upload their code for data analysis and visualization using git (e.g., to GitHub, Gitlab).

No doubt, uploading your R scripts is great. However, we also need to make sure that we share the complete computational environment so that our code can be re-run and so that others can reproduce the results. That is, to have a fully reproducible example, we need a way to capture the different versions of the R packages we were using, at that particular time.

How to Read & Write SPSS Files in Python using Pandas

Erik Marsja

September 8, 2019

2 Comments

How to Read & Write SPSS Files in Python using Pandas

In this post we are going to learn 1) how to read SPSS (.sav) files in Python, and 2) how to write to SPSS (.sav) files using Python.

Python is a great general-purpose language as well as for carrying out statistical analysis and data visualization. However, Python is not really user-friendly for data storage. Thus, often our data will be archived using Excel, SPSS or similar software.

Python MANOVA Made Easy using Statsmodels

Erik Marsja

August 26, 2019

Leave a Comment

Python MANOVA Made Easy using Statsmodels

In previous posts, we learned how to use Python to detect group differences on a single dependent variable. However, there may be situations in which we are interested in several dependent variables. In these situations, the simple ANOVA model is inadequate.

One way to examine multiple dependent variables using Python would, of course, be to carry out multiple ANOVA. That is, one ANOVA for each of these dependent variables. However, the more tests we conduct on the same data, the more we inflate the family-wise error rate (the greater chance of making a Type I error).

This is where MANOVA comes in handy. MANOVA, or Multivariate Analysis of Variance, is an extension of Analysis of Variance (ANOVA). However, when using MANOVA we have two, or more, dependent variables.

MANOVA and ANOVA is similar when it comes to some of the assumptions. That is, the data have to be:

normally distributed dependent variables
equal covariance matrices)

In this post will learn how carry out MANOVA using Python (i.e., we will use Pandas and Statsmodels). Here, we are going to use the Iris dataset which can be downloaded here.

The Easiest Data Cleaning Method using Python & Pandas

Erik Marsja

August 19, 2019

Leave a Comment

The Easiest Data Cleaning Method using Python & Pandas

In this post we are going to learn how to do simplify our data preprocessing work using the Python package Pyjanitor. More specifically, we are going to learn how to:

Add a column to a Pandas dataframe
Remove missing values
Remove an empty column
Cleaning up column names

That is, we are going to learn how clean Pandas dataframes using Pyjanitor. In all Python data manipulation examples, here we are also going to see how to carry out them using only Pandas functionality.

Repeated Measures ANOVA in R and Python using afex & pingouin

Erik Marsja

August 12, 2019

2 Comments

Repeated Measures ANOVA in R and Python using afex & pingouin

In this post we will learn how to carry out repeated measures Analysis of Variance (ANOVA) in R and Python. To be specific, we will use the R package afex and the Python package pingouin to carry out one-way and two-way ANOVA f or within subject’s design. The structure of the following data analysis tutorial is as follows; a brief introduction to (repeated measures) ANOVA, carrying out within-subjects ANOVA in R using afex and in Python using pingouin. In the end, there will be a comparison of the results and the pros and cons using R or Python for data analysis (i.e., ANOVA).

How to Make a Scatter Plot in Python using Seaborn

Erik Marsja

August 5, 2019

Leave a Comment

How to Make a Scatter Plot in Python using Seaborn

Data visualization is a big part of the process of data analysis. In this post, we will learn how make a scatter plot using Python and the package Seaborn. In detail, we will learn how to use the Seaborn methods scatterplot, regplot, lmplot, and pairplot to create scatter plots in Python.

If you are interested in learning about more Python data visualization methods see the post “9 Data Visualization Techniques You Should Learn in Python“.

More specifically, we will learn how to make scatter plots, change the size of the dots, change the markers, the colors, and change the number of ticks. Furthermore, we will learn how to plot a regression line, add text, plot a distribution on a scatter plot, among other things. Finally, we will also learn how to save Seaborn plots in high resolution. That is, we learn how to make print-ready plots.

How to Read and Write JSON Files using Python and Pandas

Erik Marsja

July 31, 2019

3 Comments

How to Read and Write JSON Files using Python and Pandas

In this post, we will learn how to read and write JSON files using Python. In the first part, we are going to use the Python package json to create a JSON file and write a JSON file. After that, we are going to use Pandas json method to load JSON files into Pandas dataframe. Here, we will learn how to read from a JSON file locally and from an URL as well as how to read a nested JSON file using Pandas.

Finally, as a bonus, we will also learn how to manipulate data in Pandas dataframes, rename columns, and plot the data using Seaborn.

How to Use Binder and Python for Reproducible Research

Erik Marsja

July 22, 2019

Leave a Comment

How to Use Binder and Python for Reproducible Research

In this post we will learn how to create a binder so that our data analysis, for instance, can be fully reproduced by other researchers. That is, in this post we will learn how to use binder for reproducible research.

In previous posts, we have learned how to carry out data analysis (e.g., ANOVA) and visualization (e.g., Raincloud plots) using Python. The code we have used have been uploaded in the forms of Jupyter Notebooks.

For users of R Statistical Environment;

How to Use Binder and R for Reproducible Research

Although this is great, we also need to make sure that we share our computational environment so our code can be re-run and produce the same output. That is, to have a fully reproducible example, we need a way to capture the different versions of the Python packages we’re using.

9 Data Visualization Techniques You Should Learn in Python

Erik Marsja

July 15, 2019

6 Comments

9 Data Visualization Techniques You Should Learn in Python

With ever increasing volume of data, it is impossible to tell stories without visualizations. Data visualization is an art of how to turn numbers into useful knowledge. Using Python we can learn how to create data visualizations and present data in Python using the Seaborn package.

In this post we are going to learn how to use the following 9 plots:

Scatter Plot
Histogram
Bar Plot
Time Series Plot
Box Plot
Heat Map
Correlogram
Violin Plot
Raincloud Plot

Python Data Visualization Tutorial: Seaborn

As previously mentioned in this Python Data Visualization tutorial we are mainly going to use Seaborn but also Pandas, and Numpy. However, to create the Raincloud Plot we are going to have to use the Python package ptitprince.

Python Raincloud Plot using the ptitprince package

Probabilistic Programming in Python

Erik Marsja

January 14, 2019

2 Comments

Learn about probabilistic programming in this guest post by Osvaldo Martin, a researcher at The National Scientific and Technical Research Council of Argentina (CONICET) and author of Bayesian Analysis with Python: Introduction to statistical modeling and probabilistic programming using PyMC3 and ArviZ, 2nd Edition.

This post is based on an excerpt from the second chapter of the book that I have slightly adapted so it’s easier to read without having read the first chapter.