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Introduction to. >. 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 - PowerPoint PPT Presentation
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Introduction toBiodiversity 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
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