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R for biodiversity research

Books on R

Resources for R

User interface/IDEs for R

  • R studio - A great new interface/IDE for R that works on Windows, Mac and Linux.
  • R commander - A cross-platform solution, it also provides an interface with drop-down menus to perform common analyses in a user-friendly way.
  • Tinn-R - A good, but Windows only graphical user interface for R.
  • Rkward - This is a nice, clean interface for R. It works on Linux and Windows but the Windows version has some known issues.

R packages for graphics

  • ggplot2 - A very elaborate and powerful graphics package based on the system described in “A Grammar of Graphics” by Leland Wilkinson.
  • Lattice - Another powerful graphics package that allows for many types of plots with sophisticated layouts.

R Packages for General Ecology

  • ADE4 - Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences.
  • primer - A support package for Stevens 'A Primer of Ecology with R, Springer'. Provides functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices.

R Packages for Community Ecology and Biodiversity

  • vegan - Very extensive R package for community ecology
  • BiodiversityR - Graphical user interface for biodiversity and community ecology analysis.
  • vegetarian - Jost Diversity Measures for Community Data.
  • FD - Measuring functional diversity (FD) from multiple traits, and other tools for functional ecology.
  • untb - A collection of utilities for biodiversity data. Includes the simulation of ecological drift under Hubbell's Unified Neutral Theory of Biodiversity.

R Packages for Spatial Analysis

  • ads - Spatial point patterns analysis.
  • raster - Geographic analysis and modeling with raster data.
  • gdistance - : distances and routes on geographical grids.
  • GeoXp - Interactive exploratory spatial data analysis.
  • spatial - Functions for Kriging (geostatistical method of interpolation) and Point Pattern Analysis.
  • spatstat - Spatial Point Pattern analysis, model-fitting, simulation, tests.
  • spatgraphs - Graphs for spatial point patterns.
  • MarkedPointProcess - Analysis of marks of marked point processes.
  • spatgraphs - Spatial Point Pattern analysis, model-fitting, simulation, tests.
  • geodist - Calculates a geographic distance matrix from a table of latitude and longitude information using the law of cosines. Written by Simon Joly.

R Packages for Studies on Animals

  • adehabitat - Analysis of habitat selection by animals.

R Packages for Multivariate Analysis

  • labdsv - Ordination and Multivariate Analysis for Ecology.
  • cluster - Cluster analysis extended.
  • amap - Another Multidimensional Analysis Package, tools for Clustering and Principal Component Analysis.

R Packages for Genetics and Sequence Analyses

  • adegenet - Classes and methods for the multivariate analysis of genetic markers.
  • adephylo - Exploratory analyses for the phylogenetic comparative method.
  • hierfstat - Exploratory analyses for the phylogenetic comparative method. - hierarchical F-statistics from genetic data (e.g. Fst value)
  • ape - Reading, writing, plotting, and manipulating phylogenetic trees. Analyses of comparative data in a phylogenetic framework in general.
  • edgeR - A Bioconductor package for differential expression analysis of digital gene expression data.
  • DESeq - Another Bioconductor package for differential expression analysis of digital gene expression data, based on the negative binomial distribution.
  • DEGseq - Yet another Bioconductor package to identify differentially expressed genes from RNA-seq data.
resources_for_r.txt · Last modified: 2014/11/04 11:09 by sebastien.renaut