Python for ecologists

Key Points

Programming in Python (Introduction)
Data Analysis in Python
Indexing, Slicing and Subsetting DataFrames in Python
Data Types and Formats
Combining DataFrames with Pandas
Repeating Actions with Loops	Use for variable in sequence to process the elements of a sequence one at a time. The body of a for loop must be indented. Use len(thing) to determine the length of something that contains other values.
Making Plots With ggplot	plotnine is python implementation of The Gramma of Graphics ggplot is a set of gramma rules to make publication quality plots ggplot has idea of layer, building a plot is just adding different layers together
Data Ingest and Visualization - Matplotlib and Pandas
Accessing SQLite Databases Using Python and Pandas

Glossary

0-based indexing

is a way of assigning indices to elements in a sequential, ordered data structure starting from 0, i.e. where the first element of the sequence has index 0.

CSV (file)

is an acronym which stands for Comma-Separated Values file. CSV files store tabular data, either numbers, strings, or a combination of the two, in plain text with columns separated by a comma and rows by the carriage return character.

database

is an organized collection of data.

dataframe

is a two-dimensional labeled data structure with columns of (potentially) different type.

data structure

is a particular way of organizing data in memory.

data type

is a particular kind of item that can be assigned to a variable, defined by by the values it can take, the programming language in use and the operations that can be performed on it.

dictionary

is an unordered Python data structure designed to contain key-value pairs, where both the key and the value can be integers, floats or strings. Elements of a dictionary can be accessed by their key and can be modified.

docstring

is an optional documentation string to describe what a Python function does.

faceting

is the act of plotting relationships between set variables in multiple subsets of the data with the results appearing as different panels in the same figure.

float

is a Python data type designed to store positive and negative decimal numbers by means of a floating point representation.

function

is a group of related statements that perform a specific task.

integer

is a Python data type designed to store positive and negative integer numbers.

interactive mode

is an online mode of operation in which the user writes the commands directly on the command line one-by-one and execute them immediately by pressing a button on the keyword, usually Enter.

join key

is a variable or an array representing the column names over which pandas.DataFrame.join() merge together columns of different data sets.

library

is a set of functions and methods grouped together to perform some specific sort of tasks.

list

is a Python data structure designed to contain sequences of integers, floats, strings and any combination of the previous. The sequence is ordered and indexed by integers, starting from 0. Elements of a list can be accessed by their index and can be modified.

loop

is a sequence of instructions that is continually repeated until a condition is satisfied.

NaN

is an acronym for Not-a-Number and represents that either a value is missing or the calculation cannot output any meaningful result.

None

is an object that represents no value.

scripting mode

is an offline mode of operation in which the user writes the commands to be executed in a text file (with .py extension for Python) which is then compiled or interpreted to run the program. Notes that Python interprets script on run-time and compiles a binary version of the program to speed up the execution time.

Sequential (data structure)

is an ordered group of objects stored in memory which can be accessed specifying their index, i.e. their position, in the structure.

SQL

or Structured Query Language, is a domain-specific language for managing data stored in a relational database management system (RDBMS).

SQLite

is a self-contained, public domain SQL database engine.

string

is a Python data type designed to store sequences of characters.

tuple

is a Python data structure designed to contain sequences of integers, floats, strings and any combination of the previous. The sequence is ordered and indexed by integers, starting from 0. Elements of a tuple can be accessed by their index but cannot be modified.