Data Analysis and Visualization in Python for Ecologists: Key Points

Before we start

Python is an open source and platform independent programming language.
Jupyter Notebook and the Spyder IDE are great tools to code in and interact with Python. With the large Python community it is easy to find help on the internet.

Python is an interpreted language which can be used interactively (executing one command at a time) or in scripting mode (executing a series of commands saved in file).
One can assign a value to a variable in Python. Those variables can be of several types, such as string, integer, floating point and complex numbers.
Lists and tuples are similar in that they are ordered lists of elements; they differ in that a tuple is immutable (cannot be changed).
Dictionaries are data structures that provide mappings between keys and values.

Libraries enable us to extend the functionality of Python.
Pandas is a popular library for working with data.
A Dataframe is a Pandas data structure that allows one to access data by column (name or index) or row.
Aggregating data using the groupby() function enables you to generate useful summaries of data quickly.
Plots can be created from DataFrames or subsets of data that have been generated with groupby().

In Python, portions of data can be accessed using indices, slices, column headings, and condition-based subsetting.
Python uses 0-based indexing, in which the first element in a list, tuple or any other data structure has an index of 0.
Pandas enables common data exploration steps such as data indexing, slicing and conditional subsetting.

pandas uses other names for data types than Python, for example: object for textual data.
A column in a DataFrame can only have one data type.
The data type in a DataFrame’s single column can be checked using dtype.
Make conscious decisions about how to manage missing data.
A DataFrame can be saved to a CSV file using the to_csv function.

Pandas’ merge and concat can be used to combine subsets of a DataFrame, or even data from different files.
join function combines DataFrames based on index or column.
Joining two DataFrames can be done in multiple ways (left, right, and inner) depending on what data must be in the final DataFrame.
to_csv can be used to write out DataFrames in CSV format.

Loops help automate repetitive tasks over sets of items.
Loops combined with functions provide a way to process data more efficiently than we could by hand.
Conditional statements enable execution of different operations on different data.
Functions enable code reuse.

The data, aes variables and a geometry are the main elements of a plotnine graph
With the + operator, additional scale_*, theme_*, xlab/ylab and facet_* elements are added

Matplotlib is the engine behind plotnine and Pandas plots.
The object-based nature of matplotlib plots enables their detailed customization after they have been created.
Export plots to a file using the savefig method.

sqlite3 provides a SQL-like interface to read, query, and write SQL databases from Python.
sqlite3 can be used with Pandas to read SQL data to the familiar Pandas DataFrame.
Pandas and sqlite3 can also be used to transfer between the CSV and SQL formats.