> Introduction to Nelson Rios, Tulane University Biodiversity Informatics Training Workshop Boulder, CO

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

Getting R www.r-project.org Available for Windows, Macintosh, Linux & as Source Code Current release (30 Mar 2012): R 2.15.0

RGui

Working directory Default location used to save and retrieve files. Use getwd() to determine current working directory Use setwd(new_path) to change current working directory

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.

Logical Operators == Equal to > Greater than < Less than <= Less than or equal to >= Greater than or equal to <> or != Not equal to

Example Code

Getting Help ?fxn or help(fxn) > ?round

Arrays

Matrices > (m*n)[2,4] > (m*n)[8] or

Conditional Execution: if Statements Syntax: if (expr1) expr2 else expr3 Use logical operators in if statements: ==, >, <, <=, >=, <>

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

Expression is repeated until break is called repeat Loops Syntax: repeat expr Expression is repeated until break is called

Getting Data from a File

Selecting Columns

Data source can also be on web

Extending R Via user-created packages available from repositories CRAN (Comprehensive R Archive Network) Bioconductor

Installing and using Packages Use GUI to select mirror, select package and install package 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 After installing use library() or GUI to load packages prior to use. Use search() to view active packages.

Using Packages Rectangular projection Bonne equal-area projection

U.S. Census State Boundaries Results from Georeferencing

Filtering Data Use logical operators in filter expression: ==, >, <, <=, >=, <> StateProvince==“Missouri”

Editing records in your data frame

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