R-Python-MATLAB 7/19/2023

Collaborative Online Training Program on

“Prospects and Applications of Artificial Intelligence in Livestock Sector”

INTRODUCTION TO PYTHON, R AND

MATLAB

CS Mukhopadhyay, PhD
Senior Scientist
College of Animal Biotechnology,
Guru Angad Dev Veterinary and Animal Sciences University 1
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INTRODUCTION
 Programming language: A set of computer understandable
instructions (in form of syntactical notations) to execute some
task by the computer system
 Two components of PL:
 Semantics: meaning assigned to a code by strings and syntax

 Syntax: writing rules, including use of symbols, indentations, etc

 Low vs. High-level languages:

 Low-level PL: computer understandable binary language

 High level PL: human understandable English code, to be

assembled/translated to binary

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GENERATIONS OF PROG. LANGUAGES

 First Generation PL: the machine level languages, now not
used
 Entered through the front panel system of the computer
system
 Second Generation PL: These are assembly languages
 Codes are read & written by programmer

 2nd GLs: used in kernels & device drivers, need

extremely intensive processing (viz. games, graphics etc)
 3 GL: these are programmer friendly & more refined version
of the 2GLs.
 It is also called the High Level Language
 Example: ALGOL, COBOL, FORTRAN, later, C, C++, C#,
Java etc.
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GENERATIONS OF PROG. LANGUAGES

 4GL: Its improved version of the 3GLs that attempt to get
closer to human language, form of thinking &
conceptualization
 4GLs: high-level specification programming language or
environment
 Example: SQL, R, SPSS, SAS etc.

 5 GL: a programming language based on solving problems,

using constraints given to the program, rather than using
an algorithm written by a programmer
 AI is the main concern in developing the 5GLs

 Example: Prolog, OPS5, & Mercury

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R PROGRAMMING ENVIRONMENT
 R has been used primarily in academics & research

 Mainly used for statistical analysis and exploratory data analysis.

 R is a widely used tool for making beautiful graphs & visualizations.

 R packages are available at:

 Comprehensive R Archive Network (CRAN)

 Bioconductor: An open source repository for packages on bioinformatics.

 GitHub: Web-based Git repository hosting service.

 Most of the R libraries have dependencies

 Less popular than Python for deep learning & NLP

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R PROGRAMMING ENVIRONMENT
 Integrated development environment (IDE): either through command line or
RStudio (an integrated environment comprising of a data editor, debugging
support, & a graphics-window).
 Anaconda IDE is also used but less popular than using Anaconda for Python
(jupyter notebook and Spyder / Scientific PYthon Development EnviRonment
for Python)
 Jupyter Notebook: an application, used for creating and editing scripts to
display the input and output of a Python or R language script. The notebook
files
 R is preferred for standalone computing or related analysis
 To initiate R in jupyter: open Anaconda prompt 3 and install R using the
following code: “C:\Users\csmbi>conda install -c r r-irkernel”
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R PROGRAMMING ENVIRONMENT

R Studio

R Console

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PYTHON LANGUAGE

 1991: Python was released as a general-purpose, interpreted

high-level programming language whose design philosophy
emphasizes code readability.

 It was developed by Guido van Rossum

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PYTHON LANGUAGE
 Python is preferred by programmers, data analysts, data scientists
and by developers.

 Coding & debugging is easy because of the simple syntax.

 The indentation of code is critical as any change could alter its

meaning

 Python is preferred when Web-integration of data analysis tasks by

web apps

 Python is used more because of its superior code readability,

speed, & many functionalities, syntactically clear & elegant, easily
interpretable, & easy to type
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PYTHON LANGUAGE
 Python: suitable for most of mathematical computation & learning how
algorithms work

 The Python Package Index (PyPi) & Anaconda are repositories of Python
software with all libraries

 BioPython is for bioinformatics analysis.

 Data Visualizations are more convoluted in Python than in R, & results are
less eye-pleasing or informative

 Jupyter Notebooks & Spyder are popular, & mostly preferred IDEs in Python

 Python package rpy2 which is 'an interface to R running embedded in a

Python process' or it allows you to call R from Python
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MATLAB

 1984: MATLAB was developed by MathWorks,

 MATLAB allows matrix manipulations, plotting of functions &
data, implementation of algorithms,
 It is used for creation of user interfaces, & interfacing with
programs written in other languages, including C, C++, Java,
& Fortran
 It is a commercial software

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ANACONDA NAVIGATOR

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JUPYTER NOTEBOOK

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CONFUSION MATRIX GENERATED (BY PYTHON)

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POPULAR LIBRARIES AND PACKAGES: R

 dplyr, tidyr and data.table to easily manipulate data

 stringr to manipulate strings

 zoo to work with regular and irregular time series

 ggplot2 to visualize

 datacaret for machine learning.. And many

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POPULAR LIBRARIES AND PACKAGES: R

 pandas to easily manipulate

 statsmodels to explore data, estimate statistical models, and

perform statistical tests and unit tests

 scipy and numpy for scientific computing

 scikit-learn for machine learning

 matplotlib and seaborn to make graphics

 biopython for sequence analysis

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MATLAB TOOLBOXES: AI-ML-DL

 Bioinformatics Toolbox

 Database Toolbox

 Deep Learning Toolbox

 Medical Imaging Toolbox

 Signal Processing Toolbox

 Statistics and Machine Learning Toolbox

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COMPARATIVE BETWEEN R & PYTHON CODING

R-Coding Python

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LET US DO SOME PRACTICAL HANDS ON

 1. Installation of R and Anaconda

 2. Create one dataframe in R and Python

 3. Import *.csv file using R and Python

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1. INSTALLATION OF R AND ANACONDA

 R Download & Installation (Windows OS):

https://cran.r-project.org/bin/windows/base/
 Install R (Linux OS):
sudo apt update
sudo apt install r-base r-base-dev –y
 Download and Install Anaconda (Windows OS):
https://www.anaconda.com/
 Install Anaconda (Linux OS):
Multiple steps for various kinds of Linux at:
https://docs.anaconda.com/free/anaconda/install/linux/
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2. CREATE ONE DATAFRAME IN R AND PYTHON

 R:
DF_Name =
data.frame(
Name=c("AA", "BB", "CC", 'DD', 'EE', 'FF'),
Age= c(20, 25, 30, 20, 20, 30),
Ph.D.= c(TRUE, FALSE, T, T, TRUE, F))

 Python:
import pandas as pd

DF_Name_0 =
pd.DataFrame({
"Name" : ["AA", "BB", "CC", "DD", "EE", "FF"],
"Age" : [20, 25, 30, 20, 20, 30],
"Ph.D.": [True, False, True, "TRUE", "T", "FALSE"]})

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DF_Name = data.frame(Name=c("AA", "BB", "CC",

'DD', 'EE', 'FF'), Age= c(20, 25, 30, 20, 20, 30),
Ph.D.= c(TRUE, FALSE, T, T, TRUE, F))

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3. IMPORT *.CSV FILE USING R AND PYTHON

 R:
DF_Name<- read.csv(“path/file_name.csv",
header = FALSE, sep = "\t")

 Python:

import pandas
DF_Name = pandas.read_csv(“path/1_Age_Wt_Ht.csv")
DF_Name

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 IASRI Talk: GWAS Hands On 22/02/2016

ACKNOWLEDGMENTS: PROF JAMES REECY, DR. JAMES KOLTES , DR. J. R. TAIT & ERIC
FRITZ ALONG WITH TWO OTHER TRAINEES FROM PAKISTAN (DR SAIF-UR RAHMAN) AND
CHINA (XEURONG YANG)

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 22/02/2016

Thanks for your patient hearing

IASRI Talk: GWAS Hands On

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