R TUTORIAL - PHI (Session 1) · The Good, The Bad & the Ugly (Sides of R) Practical Issues What is R? Why/Why not R? Practical Issues. The Good, The Bad & the Ugly (Sides of R) Free

What is R? Why/Why not R? Practical Issues.Basic Examples

MarkdownDecisions, Roadmap & Comparisons

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R TUTORIAL - PHI (Session 1)

Oguzhan (Ouz) Gencoglu

Department of Signal ProcessingTampere University of Technology, Finland

Personal Health Informatics Team, October 2014

Oguzhan (Ouz) Gencoglu R TUTORIAL - PHI (Session 1)



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Outline

1 What is R? Why/Why not R? Practical Issues.What exactly is this R thing?The Good, The Bad & the Ugly (Sides of R)Practical Issues

2 Basic ExamplesAssignment, Lists, Arrays etc.Data Frames‘apply’ functionsStatistical Tools

3 MarkdownWhat is a Markdown file?Markdown Example

4 Decisions, Roadmap & Comparisons




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What exactly is this R thing?The Good, The Bad & the Ugly (Sides of R)Practical Issues

Outline








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What is R? Why/Why not R? Practical Issues.What exactly is this R thing?

R is a language and environment for statistical computing andgraphics. It provides a wide variety of statistical (linear andnonlinear modeling, classical statistical tests, time-series analysis,classification, clustering, ...) and graphical techniques, and ishighly extensible.




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What is R? Why/Why not R? Practical Issues.The Good, The Bad & the Ugly (Sides of R)

Free (Speech & Sandwich)

Most comprehensivestatistical analysisenvironment

Maintained by manystatisticians, scientists

Outstanding graphicalcapabilities

Almost 5000 packages

Cross-platform

Active user group




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Cross-platform

Active user group




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Cross-platform

Active user group




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Cross-platform

Active user group




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Cross-platform

Active user group




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Cross-platform

Active user group




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Cross-platform

Active user group




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/ Learning Curve

/ Memory and Speed Issuesfor certain tasks

/ Ugly syntax (my opinion)- compare Python

/ Documentation style




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/ Learning Curve







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/ Learning Curve







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/ Learning Curve







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What is R? Why/Why not R? Practical Issues.Starting the Journey

R - http://ftp.sunet.se/pub/lang/CRAN/

RStudio IDE - http://www.rstudio.com/

Case sensitive

Expressions are printed, assignments not

Assigning with <- (or ->)

Commenting with #

Indexing starts from 1

NaN (not a number), NA (not available)


http://ftp.sunet.se/pub/lang/CRAN/

http://www.rstudio.com/



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Case sensitive



Commenting with #








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Case sensitive



Commenting with #








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Case sensitive



Commenting with #








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Case sensitive



Commenting with #








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Case sensitive



Commenting with #








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Case sensitive



Commenting with #








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Case sensitive



Commenting with #








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Assignment, Lists, Arrays etc.Data Frames‘apply’ functionsStatistical Tools

Outline








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Assignment, Lists, Arrays etc.

introduction.Rcontrol structures.R

Assignment

Indexing

Arrays

List

Control structures




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Assignment

Indexing

Arrays

List

Control structures




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Assignment

Indexing

Arrays

List

Control structures




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Assignment

Indexing

Arrays

List

Control structures




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Assignment

Indexing

Arrays

List

Control structures




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Data Frames

data frames.R

Creating DFs

Using DFs

Aggregation

Reshaping




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Data Frames

data frames.R

Creating DFs

Using DFs

Aggregation

Reshaping




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Data Frames

data frames.R

Creating DFs

Using DFs

Aggregation

Reshaping




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Data Frames

data frames.R

Creating DFs

Using DFs

Aggregation

Reshaping




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‘apply’ functions

apply functions.R

lapply

sapply

tapply




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apply functions.R

lapply

sapply

tapply




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apply functions.R

lapply

sapply

tapply




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Statistical Tools

Prefix d for density value (pdf)

Prefix p for cumulative probability (cdf)

Prefix q for quantile values

Prefix r for random values from the distribution




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Statistical Tools








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Statistical Tools








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Statistical Tools








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What is a Markdown file?Markdown Example

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What is a Markdown file?

R Markdown enables easy authoring of reproducible web reportsfrom R. It offers:

Easy creation of web reports from R that can be automaticallyregenerated whenever underlying code or data changes.

A highly accessible syntax (markdown) which lower thebarriers to entry for reproducible research.

Output of a standalone HTML file (with images embeddeddirectly in the file) that is easy to share using email, Dropbox,or by deploying to a web server.

Support for publishing dynamic and interactive web content.




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Markdown Example

0.0

0.1

0.2

0.3

−3 0 3values

dens

ity

type

1

2

3




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Decisions, Roadmap & Comparisons

Task Language (software)

Exploratory Analysis R

Casual Publishing R

Filter Design MATLAB

Casual Plotting MATLAB/Python/R

Simple Numeric Matrix MATLAB/Python/R

Many Plots Python

Error Handling Python

Formal Plotting R

Machine Learning Python/(R)

Roadmap




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Image Processing MATLAB

Memory Python

Pure Speed C++

Object Oriented Programming C++/Python

Garbage Collection Python

String Processing Python/Perl

GPU Python

Parallel Processing Python

Roadmap




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Biomedical Signal Processing MATLAB/Python/R

Dynamic Plotting Python

Neat Coding Python

Own License and Library Python/R

Contribution Externally Python

Simple GUI MATLAB

Having Fun Whatever floats your boat

Roadmap




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ACKBAR BEN BIGGS CREATURE EMPEROR GOLD LEADER HAN JABBA LANDO LEIA LUKE OWEN PIETT RED LEADER TARKIN THREEPIO TROOPER VADER WEDGE YODA

star

death

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emperor

became

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skywalker

side

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fighters

chewie

leia

lord

shield

star

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come

kenobi

going

help

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chewie

obiwan

know

going

right

come

back

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just

well

got

father

luke

one

take

need

lord

yes

vader

red

copy

just

will

rebel

station

vader

yes

sir

artoo

master

going

luke

think

wait

jabba

help

sure

right

blast

will

ship

now

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obiwan

admiral

skywalker

master

emperor

force

leader

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two

will

force

yes

must

dark

jedi

mind

now

Star Wars: Character DialoguesArc−diagram

●

●

●

Episodes

IVVVI




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Questions / Comments ?


R TUTORIAL - PHI (Session 1) · The Good, The Bad & the Ugly (Sides of R) Practical Issues What is R? Why/Why not R? Practical Issues. The Good, The Bad & the Ugly (Sides of R) Free

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