NCEAS R Programming Language Special Topics
This page presents in-depth discussions of specific R Language analysis and programming topics, as well as documentation to optional (Add-On) R packages of interest to ecologists. This information is intended for the experienced R user.
PDF files require Adobe Acrobat Reader. Click here to get Acrobat
Graphics and Plotting techniques
Preface to Murrell text on Graphics and Plotting in R (150 kb)
Describes the contents and approach taken by Paul Murrell's R Graphics and Plotting textbook.
Chap 1 of Murrell text on Graphics and Plotting in R (850 kb PDF)
The first chapter of Paul Murrell's book summarizes the R Language graphics subsystem.
In-Depth Analysis and Programming techniques
Wickham: Reshaping Data in R (260 kb)
This paper discusses a conceptual framework for data reshaping, and describes an implementation of these principles in the reshape R package
Anselin: An Introduction to Spatial Regression (100 kb)
This research note contains introduction and tutorial (with worked-out example) for the R spdep package for spatial regression.
Anselin: Review of Cluster Analysis Software (700 kb PDF)
A review of R and three other open-source software packages for performing spatial analysis of cancer clusters.
Anselin: Spatial Regression Analysis in R: A Workbook (450 kb PDF)
A set of laboratory exercises developed for graduate Spatial Econometrics course at U of Illinois Urbana-Champaign.
Baddeley and Turner: spatstat: An R Package for Analyzing Spatial Point Patterns (1000 kb)
Article describes in detail and demonstrates model fitting and simulation using the spstat package for spatial point pattern analysis.
This presentation discusses the current status of R spatial data analysis and prospects for future development, including GIS integration.
Paper describing the integration of PostgreSQL, GRASS GIS and R software packages to solve disease risk-classification problem.
Peng: Multidimensional Point Process Models in R (190 kb)
This paper describes the R add-on ptproc package for performing multidimensional point process analysis. Examples: Earthquake / wildfire occurrence data.
Demonstration and discussion of the major features of the R language geoR geostatistical data analysis package.
R News Summaries: R Spatial Statistics and geoR Packages (3000 kb)
Two brief newsletter articles that summarize many of the R spatial analysis add-on packages. A good place to start learning about them.
R Spatial Data Processing and Analysis Packages: A Summary
The Spatial Data in R website: discusses the SP data package and other packages.
R Data Import and Export Utilities: A Summary
A description of utilities for importing and exporting standard scientific data formats into the R environment.
Documentation for R 'add-on' Geospatial Analysis packages
Technical Reference Manuals for a sampling of the most popular spatially-aware R package downloads
clim.pact package manual (420 kb)
clim.pact: retrieves and downscales monthly climate data for global-scale analyses
maps: contains map datasets and routines to plot them.
maptools package manual (90 kb)
maptools: A useful package for reading and writing spatial data files in ESRI Shape File format.
PBSmapping:Pacific Biological Station-developed package with GIS-like mapping and plotting methods
RArcInfo package manual (90 kb)
RArcInfo: Functions to import data from ESRI Arc Map GIS Version 7.x binary coverages.
hdf5: Package for reading and writing Hierarchical Data Format (hdf) files.
NetCDF Data package manual (140 kb)
RNetCDF:implementation of Unidata's NetCDF (Network Common Data Form) file access tools.
RColorBrewer package manual (420 kb)
RColorBrewer: Contains color palettes for drawing high-quality thematic maps.
Rgdal Data Abstraction Library (70 kb)
rgdal: R language bindings to Geospatial Data Abstraction Library (GDAL) and Proj4 map projection library..
shapefiles package manual (420 kb)
shapefiles: core classes for spatial (point/line/polygon) data file processing.
spgrass6 map projection package (40 kb)sp: core classes for spatial (point/line/polygon) data file processing.
spgrass6:The interface between R and the GRASS 6.0 Geographic Information System.
splancs package manual (420 kb)
splancs: Spatial and Space-Time Point Pattern Analysis methods.
spdep: collection of functions to create spatial weights matrix object from polygon continuities.
spatstat package manual (420 kb)
spstat: Spatial Point Pattern data analysis for modeling and simulation using multi type point data sets.
tripack package manual (420 kb)
tripack: triangulation and Voronoi mosaic creation and analysis.