Packages for Ecology


  • Most packages are found on CRAN
  • Install with install.packages("foo")
  • Check for vignettes
> vignette(package="sp")

Vignettes in package ‘sp’:

intro_sp  sp: classes and methods for spatial data  
over      sp: overlay and aggregation 

> vignette("intro_sp")


  • Habitat analysis
  • Capture-recapture analysis
  • Data downloads


Home Range Estimation

data(puechabonsp)  # boar data
cp <- mcp(puechabonsp$relocs[, 1], percent = 95)
palette(brewer.pal(4, "Set1"))
plot(puechabonsp$relocs[, 1], add = TRUE, col = puechabonsp$relocs$Name)
plot of chunk hremaps

secr - spatial capture-recapture analysis

## Loading required package: secr
## Loading required package: abind
## This is secr 2.6.1. For overview type ?secr
## Attaching package: 'secr'
## The following object(s) are masked from 'package:boot':
## logit
## The following object(s) are masked from 'package:adehabitatMA':
## join
plot(housemouse, title = paste("Coulombe (1965), Mus musculus,", "California salt marsh"), 
    border = 5, rad = 0.5, gridlines = FALSE)
plot of chunk unnamed-chunk-1


Description: Unmarked fits hierarchical models of animal abundance and
        occurrence to data collected using survey methods such as point
        counts, site occupancy sampling, distance sampling, removal
        sampling, and double observer sampling. Parameters governing
        the state and observation processes can be modeled as functions
        of covariates.

Data Interfaces

There are now many R packages to get data from internet repositories

A number of these are developed by the rOpenSci people. These are not on CRAN, and install intructions are on their web pages.