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

2. 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

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

4. RGui

5. 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

6. 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.

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

8. Example Code

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

10. Arrays

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

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

13. for Loops
Syntax: for (name in expr1) expr2

14. 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

15. while Loops
Syntax: while (condition) expr

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

17. Getting Data from a File

20. Selecting Columns

22. Data source can also be on web

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

24. 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.

25. Using Packages
Rectangular projection
Bonne equal-area projection

26. U.S. Census State Boundaries
Results from Georeferencing

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

28. Editing records in your data frame

29. More Information