r tutorial - signal processing journal clubhehu/r_tutorial_spjc.pdf · what is r? why/why not r?...

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What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics with R Machine Learning & Statistical Learning with R Miscellaneous Stuff R TUTORIAL - Signal Processing Journal Club Oguzhan (Ouz) Gencoglu Department of Signal Processing Tampere University of Technology, Finland SPJC, November 2014 Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

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Page 1: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

R TUTORIAL - Signal Processing Journal Club

Oguzhan (Ouz) Gencoglu

Department of Signal ProcessingTampere University of Technology, Finland

SPJC, November 2014

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 2: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 3: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 4: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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.

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 5: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 6: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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 (Speech & Sandwich)

Most comprehensivestatistical analysisenvironment

Maintained by manystatisticians, scientists

Outstanding graphicalcapabilities

Almost 5000 packages

Cross-platform

Active user group

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 7: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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 (Speech & Sandwich)

Most comprehensivestatistical analysisenvironment

Maintained by manystatisticians, scientists

Outstanding graphicalcapabilities

Almost 5000 packages

Cross-platform

Active user group

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 8: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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 (Speech & Sandwich)

Most comprehensivestatistical analysisenvironment

Maintained by manystatisticians, scientists

Outstanding graphicalcapabilities

Almost 5000 packages

Cross-platform

Active user group

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 9: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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 (Speech & Sandwich)

Most comprehensivestatistical analysisenvironment

Maintained by manystatisticians, scientists

Outstanding graphicalcapabilities

Almost 5000 packages

Cross-platform

Active user group

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 10: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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 (Speech & Sandwich)

Most comprehensivestatistical analysisenvironment

Maintained by manystatisticians, scientists

Outstanding graphicalcapabilities

Almost 5000 packages

Cross-platform

Active user group

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 11: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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 (Speech & Sandwich)

Most comprehensivestatistical analysisenvironment

Maintained by manystatisticians, scientists

Outstanding graphicalcapabilities

Almost 5000 packages

Cross-platform

Active user group

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 12: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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 (Speech & Sandwich)

Most comprehensivestatistical analysisenvironment

Maintained by manystatisticians, scientists

Outstanding graphicalcapabilities

Almost 5000 packages

Cross-platform

Active user group

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 13: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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)

/ Learning Curve

/ Memory and Speed Issuesfor certain tasks

/ Ugly syntax (my opinion)- compare Python

/ Documentation style

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 14: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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)

/ Learning Curve

/ Memory and Speed Issuesfor certain tasks

/ Ugly syntax (my opinion)- compare Python

/ Documentation style

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 15: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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)

/ Learning Curve

/ Memory and Speed Issuesfor certain tasks

/ Ugly syntax (my opinion)- compare Python

/ Documentation style

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 16: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What exactly is this R thing?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)

/ Learning Curve

/ Memory and Speed Issuesfor certain tasks

/ Ugly syntax (my opinion)- compare Python

/ Documentation style

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 17: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 18: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 19: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 20: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 21: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 22: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 23: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 24: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 25: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

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)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 26: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Assignment, Lists, Arrays etc.

———————————————————————————–introduction.R, control structures.R———————————————————————————–

Assignment

Indexing

Arrays

List

Control structures

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 27: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Assignment, Lists, Arrays etc.

———————————————————————————–introduction.R, control structures.R———————————————————————————–

Assignment

Indexing

Arrays

List

Control structures

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 28: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Assignment, Lists, Arrays etc.

———————————————————————————–introduction.R, control structures.R———————————————————————————–

Assignment

Indexing

Arrays

List

Control structures

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 29: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Assignment, Lists, Arrays etc.

———————————————————————————–introduction.R, control structures.R———————————————————————————–

Assignment

Indexing

Arrays

List

Control structures

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 30: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Assignment, Lists, Arrays etc.

———————————————————————————–introduction.R, control structures.R———————————————————————————–

Assignment

Indexing

Arrays

List

Control structures

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 31: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Data Frames

———————————————————————————–data frames.R———————————————————————————–

Creating DFs

Using DFs

Aggregation

Reshaping

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 32: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Data Frames

———————————————————————————–data frames.R———————————————————————————–

Creating DFs

Using DFs

Aggregation

Reshaping

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 33: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Data Frames

———————————————————————————–data frames.R———————————————————————————–

Creating DFs

Using DFs

Aggregation

Reshaping

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 34: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Data Frames

———————————————————————————–data frames.R———————————————————————————–

Creating DFs

Using DFs

Aggregation

Reshaping

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 35: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

‘apply’ functions

———————————————————————————–apply functions.R———————————————————————————–

lapply

sapply

tapply

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 36: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

‘apply’ functions

———————————————————————————–apply functions.R———————————————————————————–

lapply

sapply

tapply

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 37: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

‘apply’ functions

———————————————————————————–apply functions.R———————————————————————————–

lapply

sapply

tapply

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 38: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 39: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 40: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 41: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

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

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 42: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What is a Markdown file?Markdown Example

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 43: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What is a Markdown file?Markdown Example

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.

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 44: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What is a Markdown file?Markdown Example

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.

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 45: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What is a Markdown file?Markdown Example

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.

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 46: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What is a Markdown file?Markdown Example

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.

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 47: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What is a Markdown file?Markdown Example

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.

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 48: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What is a Markdown file?Markdown Example

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 49: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

What is a Markdown file?Markdown Example

Markdown Example

0.0

0.1

0.2

0.3

−3 0 3values

dens

ity

type

1

2

3

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 50: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 51: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Base Plotting System

———————————————————————————–base introduction.R, base exploratory.R, maps example.R———————————————————————————–Idea: High-level graphing function followed by low-level modifyingfunctions + default parameters

Most common high-level ones: plot, hist, barplot, boxplot, curveMost common low-level ones: lines, text, axis, points, title, mtextGlobal graphics parameters: par()

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 52: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Base Plotting System

———————————————————————————–base introduction.R, base exploratory.R, maps example.R———————————————————————————–Idea: High-level graphing function followed by low-level modifyingfunctions + default parameters

Most common high-level ones: plot, hist, barplot, boxplot, curve

Most common low-level ones: lines, text, axis, points, title, mtextGlobal graphics parameters: par()

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 53: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Base Plotting System

———————————————————————————–base introduction.R, base exploratory.R, maps example.R———————————————————————————–Idea: High-level graphing function followed by low-level modifyingfunctions + default parameters

Most common high-level ones: plot, hist, barplot, boxplot, curveMost common low-level ones: lines, text, axis, points, title, mtext

Global graphics parameters: par()

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 54: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Base Plotting System

———————————————————————————–base introduction.R, base exploratory.R, maps example.R———————————————————————————–Idea: High-level graphing function followed by low-level modifyingfunctions + default parameters

Most common high-level ones: plot, hist, barplot, boxplot, curveMost common low-level ones: lines, text, axis, points, title, mtextGlobal graphics parameters: par()

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 55: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 56: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Lattice

Useful for trellis graphs, i.e., graphsthat display a variable or the relation-ship between variables, conditionedon one or more other variables.

formula argument: y ∼ x ∣ p * rwherey and x are primary variablesp and r are conditioning variables

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 57: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Lattice

Useful for trellis graphs, i.e., graphsthat display a variable or the relation-ship between variables, conditionedon one or more other variables.

formula argument: y ∼ x ∣ p * rwherey and x are primary variablesp and r are conditioning variables

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 58: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Lattice Introductory Example

———————————————————————————–lattice introduction.R———————————————————————————–

Plot Fiji earthquakes, i.e., plot lat-itude vs. longitude conditioned ondepth and magnitude.

Fiji Earthquakes

longitude

latit

ude

−35

−30

−25

−20

−15

−10

165 170 175 180 185

depthgroupmagnitude

165 170 175 180 185

depthgroupmagnitude

165 170 175 180 185

depthgroupmagnitude

depthgroupmagnitude

depthgroupmagnitude

−35

−30

−25

−20

−15

−10

depthgroupmagnitude

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 59: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 60: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Grammar of Graphics (ggplot2)

————————————————–ggplot2 introduction.R————————————————–

Plot galaxy clusters info with errorintervals.

1

0.01 0.10Radius (R500)

Sca

led

Tem

pera

ture

type

Cool core

Non−cool core

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 61: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Grammar of Graphics (ggplot2)

————————————————–ggplot2 example2.R————————————————–

Several simple plot examples onthe same dataset.

0

25

50

75

1997 1998 1999 2000 2001date

tem

p

factor(season)

autumn

spring

summer

winter

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 62: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 63: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

External Packages

Package: arcdiagram

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

star

death

attack

shield

luke

force

will

can

father

jedi

side

vader

emperor

became

luke

going

back

get

just

one

pull

right

side

jedi

mine

come

eat

will

will

now

young

friends

skywalker

side

can

good

dark

fleet

leader

gold

get

chewie

going

got

come

well

right

like

kid

hey

will

han

right

get

vader

han

fighters

chewie

leia

lord

shield

star

luke

get

know

come

kenobi

going

help

hope

chewie

obiwan

know

going

right

come

back

can

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

can

obiwan

admiral

skywalker

master

emperor

force

leader

red

two

will

force

yes

must

dark

jedi

mind

now

Star Wars: Character DialoguesArc−diagram

Episodes

IVVVI

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 64: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

External Packages

Packages: maptools, geosphere

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 65: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Base Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

Graphing Roadmap

Task Graphing Tool

Exploratory Analysis base

Simple 2D Plots base

Quick Plotting base

Trellis Graphs lattice

Formal Plotting ggplot2

Beautiful (?) Plots ggplot2

Unconventional Plots external packages

Graphing Roadmap

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 66: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Useful Packages and Examples

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 67: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Useful Packages and Examples

Some useful packages:

caret : General machine learning

nnet : Neural networks

randomForest : Decision trees/random forests

bigrf : Random forests for large datasets

gbm : Gradient boosting

lars, lasso2, glmnet : Regularized methods

e1071, kernlab : SVMs and kernel methods

rgp, rgenoud : Genetic algorithms

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 68: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Useful Packages and Examples

Logistic Regression Example

———————————————————————————–logistic regression.R———————————————————————————–

Predict graduate school admissionprobabilities using logistic regres-sion.

0.0

0.2

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0.6

0.8

200 400 600 800gre

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Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 69: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Useful Packages and Examples

Neural Network Example

———————————————————————————–neural net.R———————————————————————————–

Binary classification using a verysimple neural network classifier. −2 0 1 2 3

−2

01

23

x[,1]

x[,2

]

nnet with 1 hidden units

−2 0 1 2 3

−2

01

23

x[,1]

x[,2

]

nnet with 2 hidden units

−2 0 1 2 3

−2

01

23

x[,1]

x[,2

]

nnet with 3 hidden units

−2 0 1 2 3

−2

01

23

x[,1]

x[,2

]

nnet with 4 hidden units

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 70: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Useful Packages and Examples

Random Forest Example

———————————————————————————–random forest.R———————————————————————————–Binary classification using a very simple random forest classifier.

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 71: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 72: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Miscellaneous StuffInteractive Plotting and Documentation

———————————————————————————–shakespeare.R———————————————————————————–Conduct document analysis on Shakespeare’s plays in aninteractive way using the shiny package.

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 73: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 74: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Miscellaneous StuffAPI Interaction

Data mining on Twitter using twitteR package.

datagoogle

pandamining

machinelearning

trendsguys

book

googles

algorithm

awar

dbirddodo

machine learning

series

softwarewingflapping

action

playing

reviewartificial intelligence

data mining

guess

languagengram

view

er

named

prokoppmanning

popu

lar

programmers bookwatchiprog

via

amp

clas

s

computation

hard

cove

r

pattern

recognition

conference

developer

using

brief

adaptive airborne

job

advanced

arxi

v breuderink

classifier technology and the illusionof progress

connection

euro

pean

httptcowse

shortteaching

tools

elton

coursera

editionintroduction

produced

scala

statistics

techniques created

declining

informationkaufmann

morgan

onlin

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practical

readingre

sear

ch

time

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attainable

engineer

free

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taking

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approach

bioinformatics

computer

java

join

looking

module

neural

nlp

programming

science

sign

summer

apacheapplications

curalate

discovery

eltons

international

knowledge

mahout

math

name

practice

python

twitter

artificial

business

chapman

course

ecml

hallcrc

jobs

lectures

level logi

c

machineguided

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ity

set

statistical

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algorithmic

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example

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if young graduates want to build a future in the big data era i have one word for you ok two machine learning

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musical

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scho

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scientific

search

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computational databases

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Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 75: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Outline1 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 Introductory Examples & the R Paradigm

3 MarkdownWhat is a Markdown file?Markdown Example

4 Plotting and Graphics with RBase Plotting SystemLattice Plotting SystemGrammar of Graphics (ggplot2) Plotting SystemExternal Packages

5 Machine Learning & Statistical Learning with RUseful Packages and Examples

6 Miscellaneous StuffInteractive ApplicationsAPI InteractionAnd more...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 76: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Miscellaneous StuffAnd more...

One can

get data out of a database : RMySQL, RMongoDB, rhdf5,ROracle

teach in R : swirl

interact with C or Python : Rcpp, rPython

embed R code into LATEX : sweave

and more ...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 77: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Miscellaneous StuffAnd more...

One can

get data out of a database : RMySQL, RMongoDB, rhdf5,ROracle

teach in R : swirl

interact with C or Python : Rcpp, rPython

embed R code into LATEX : sweave

and more ...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 78: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Miscellaneous StuffAnd more...

One can

get data out of a database : RMySQL, RMongoDB, rhdf5,ROracle

teach in R : swirl

interact with C or Python : Rcpp, rPython

embed R code into LATEX : sweave

and more ...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 79: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Miscellaneous StuffAnd more...

One can

get data out of a database : RMySQL, RMongoDB, rhdf5,ROracle

teach in R : swirl

interact with C or Python : Rcpp, rPython

embed R code into LATEX : sweave

and more ...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 80: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Miscellaneous StuffAnd more...

One can

get data out of a database : RMySQL, RMongoDB, rhdf5,ROracle

teach in R : swirl

interact with C or Python : Rcpp, rPython

embed R code into LATEX : sweave

and more ...

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club

Page 81: R TUTORIAL - Signal Processing Journal Clubhehu/R_tutorial_spjc.pdf · What is R? Why/Why not R? Practical Issues. Introductory Examples & the R Paradigm Markdown Plotting and Graphics

What is R? Why/Why not R? Practical Issues.Introductory Examples & the R Paradigm

MarkdownPlotting and Graphics with R

Machine Learning & Statistical Learning with RMiscellaneous Stuff

Interactive ApplicationsAPI InteractionAnd more...

Questions / Comments / Suggestions

The Zen of Python

Beautiful is better than ugly.Explicit is better than implicit.Simple is better than complex.Complex is better than complicated.Flat is better than nested.Sparse is better than dense.Readability counts.(...)

Oguzhan (Ouz) Gencoglu R TUTORIAL - Signal Processing Journal Club