Introduction to

Introduction toBiodiversity Informatics Training Workshop

Boulder, CO

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What is R

• Open source interpreted programming language and development environment

• Initially release in 1993• Influenced by the S programming language• Focus on statistics, data analysis & graphics• Extensible via user contributed packages

Why R?

• Reproducible, RepeatableTherefore a perfect tool for science

• Method to track data and analytic flowTherefore a perfect tool for scientists

Why Open?

Rasters: GeoTiff, .ASC, .BIL,

Vectors: Shapefiles

{dismo}, {rgdal}, {rVertnet}

• GetData• Prepare• Filter• Subset• Analyse• Model

• Map Data

• Derive surfaces

• Subset• Create

visuals

R & QGIS Integration

Getting

• www.r-project.org• Available for Windows, Macintosh, Linux & as

Source Code• Current release (14 June 2013): R 3.0.1

RGui

Object-based functional language

• What that means to users:Commands have three parts: arguments, body and its environment. A function is invoked by its name, followed by arguments, which can be named, positional or have defaults if omitted

myvariable <- read.table(x, file = ”data.csv”, sep = ”,”)

Objects

• Used to store values• Case sensitive• Named with alphanumeric characters• Cannot start with a number• Persistent until reassigned or removed from

objects list. User rm(obj_name) to remove.• Values can be assigned to variables via <- or = • Use objects() or ls() to view list of objects in the

current environment.

Getting Help

• ?fxn or help(fxn)

> ?round

Extending R• Via user-created packages available from

repositories– CRAN (Comprehensive R Archive Network)– Bioconductor

Installing and using Packages• Over 4,600 packages available. • Package: maps

– Draw lines and polygons as specified by a map database.• Package: mapproj

– Converts latitude and longitude into projected coordinates. Required by maps package, if we want to use projections other than default (rectangular).

• Package: maptools– Set of tools for manipulating and reading geographic data, in particular

ESRI shapefiles. Also installs package sp.• Package: sp

– A package providing classes and methods for spatial data: points, lines, polygons and grids

Bonne equal-area projection

Rectangular projection

Using Packages

U.S. Census State Boundaries

Results fromGeoreferencing

Filtering Data

StateProvince==“Missouri”

Use logical operators in filter expression: ==, >, <, <=, >=, <>

Editing records in your data frame

or

FishNet 2 Collaborative Georeferencing Project

• http://geolocate.fishnet2.net/workflow.html

More Information

http://cran.r-project.org/doc/manuals/R-intro.pdf

for Loops

Syntax: for (name in expr1) expr2

Breaking out of Loops

next can be used to discontinue the rest of a particular cycle and skip to the next iteration in the loop

while Loops

Syntax: while (condition) expr

repeat Loops

Syntax: repeat expr

Expression is repeated until break is called