Using R in Kepler Dan Higgins – NCEAS Prepared for: Ecoinformatics Training for Ecologists LTER...

Using R in Kepler

Dan Higgins – NCEAS

Prepared for:

Ecoinformatics Training for Ecologists

LTER (Albuquerque)

January 8-12, 2007

http://www.kepler-project.org

What is R?

• R is a language and environment for data manipulation, statistical computing, and graphics.

• R is open-source and thus can be freely downloaded and used at no cost

• The R Project for Statistical Computing– http://www.r-project.org/

• NCEAS R Programming Language Resource Center– http://www.nceas.ucsb.edu/scicomp/RProgTutorialsLatest.html– http://www.nceas.ucsb.edu/scicomp/RShortCourse.html

RGui

RGui (Windows)

R Example

With only 3 lines, one can read a data table,plot all combinations of column data, andsummarize the data

Kepler and R

• R language has many similarities to the Kepler expression language

• R language emphasizes operations on vectors, matrices, and tables (‘data frames’) rather than scalars. (This eliminates many explicit looping statements)

• Many detailed statistical operations and data manipulation routines already exist in R

• R has ability to create sophisticated graphic displays

• Being able to call R routines from Kepler greatly simplifies many workflows

Simple R Workflow

Just drag an RExpression actor to the work area, add a director, and connect the outputs to a display and imageJ actors

Display is the same as one sees running the R script from the command line

RExpression Actor Parameters

Arrays and Graphical Output

R Script:ccc <- aaa + bbbcccplot(aaa,bbb)

Adding ports automatically creates R objects withthe port name [e.g. aaa <- c(1,2,3,4)]

Graphics automatically saved as images and sent to‘graphicsFileName’ output port (as file name)

R text output automatically sent to ‘output’ port

Adding ports creates R objectsfrom Kepler tokens

R script is a parameter of theRExpression actor whichuses port names

RExpression – Ports & Parameters

Tables are represented as ‘Data Frame’ objects in ‘R’

A Ptolemy ‘Record of Arrays’ can also represent a table

R Script: summary(df)

where ‘df’ is the Rdataframe createdautomatically whena record of arrays ispassed to an input port

AAA BBB

one 1

two 2

three 3

four 4

Array Records and Data Frames

R Dataframes

AAA BBB

one 1

two 2

three 3

four 4

In R, a ‘dataframe’ represents a table

A dataframe is a list of column vectors

Each column has the same kind of data(e.g. a number or a string)

Each column can have a name (e.g.‘AAA’ or ‘BBB’ )

AAA <- c(“one”,”two”,”three”,”four”)BBB <- c(1,2,3,4)df <- data.frame(aaa,bbb)Creating a dataframe df

1st Column: df[1,], df[‘AAA’,]

2nd Row: df[,2], df[AAA==‘two’,]

Selecting Parts of a dataframe

Using Multiple R Actors

Using Multiple R Actors - Result

R Summarize Table By Species

R Pairs Plot

Configuring an EML Datasourcefor Use in RExpression

Use “As Column Vector” topass the entire column atone time (i.e. an R vector)

Custom RExpression Actors

RExpression actors withpre-built R scripts canbe added to the Kepleractor list. Examples ofcurrent customs actorsare shown here.

This provides tools forusers that are unfamiliarwith R scripts

Acknowledgements•This material is based upon work supported by:

•The National Science Foundation under Grant Numbers 9980154, 9904777, 0131178, 9905838, 0129792, and 0225676.

•Collaborators: NCEAS (UC Santa Barbara), University of New Mexico (Long Term Ecological Research Network Office), San Diego Supercomputer Center, University of Kansas (Center for Biodiversity Research), University of Vermont, University of North Carolina, Napier University, Arizona State University, UC Davis

•The National Center for Ecological Analysis and Synthesis, a Center funded by NSF (Grant Number 0072909), the University of California, and the UC Santa Barbara campus.

•The Andrew W. Mellon Foundation.

•Kepler contributors: SEEK, Ptolemy II, SDM/SciDAC, GEON