Packages

• 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")

Stuff

• Habitat analysis
• Capture-recapture analysis
• Data downloads

adehabitat

• adehabitatHR - home range
• adehabitatHS - habitat suitability
• adehabitatLT - movement analysis

Home Range Estimation

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

secr - spatial capture-recapture analysis

require(secr)

## 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)

unmarked

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.

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.

• rgbif - Global Biodiversity Information Facility
• rWBclimate - world bank climate data
• Rbison - US species data
• Fishbase - fish species data and mapping
• Metadata - get assorted data sets
• rfisheries get openfisheries data