Matt’s compositional analysis

This file is to play with ways to compare proportion of habitat used v available.

There are two matrices: one for availability (Habitat Availability.csv) and one for use (Habitat Use.csv). They are in Gondek, Matt -> Data _ Gondek

hu7 = read.csv("Habitat Use_007.csv", header=T)
ha = read.csv("Habitat Availability.csv", header=T)
hu3 = read.csv("Habitat Use_003.csv", header=T)
hu1 = read.csv("Habitat Use_001.csv", header=T)

## Loading required package: sp

## Loading required package: ade4

## Loading required package: adehabitatMA

## Registered S3 methods overwritten by 'adehabitatMA':
##   method                       from
##   print.SpatialPixelsDataFrame sp  
##   print.SpatialPixels          sp

## Loading required package: adehabitatHR

## Loading required package: deldir

## deldir 0.1-25

## Loading required package: adehabitatLT

## Loading required package: CircStats

## Loading required package: MASS

## Loading required package: boot

Analysis with 0s represented as 0.007

compana(hu7, ha, test = c("randomisation", "parametric"),
        rnv = 0.01, nrep = 500, alpha = 0.1)

## ************ Compositional analysis of habitat use ***************
## 
## The analysis was carried out with 7 animals and 7 habitat types
## 1. Test of the habitat selection:
##    randomisation test
##      Lambda           P 
## 0.005747109 0.194000000 
## 
## 2. Ranking of habitats (profile):
##                                                                             
## habitat      Herb.wet  Ag  Shrub.Scrub  Wood.wet  Open.water  Forest  Grass 
## Herb.wet    ---------------------------          ------------               
## Ag          ---------------------------          ------------               
## Shrub.Scrub ---------------------------          ------------               
## Wood.wet                               ------------------------------       
## Open.water  ----------------------------------------------------------------
## Forest                                 -------------------------------------
## Grass                                            ---------------------------

Analysis with 0s represented as 0.003

compana(hu3, ha, test = c("randomisation", "parametric"),
        rnv = 0.01, nrep = 500, alpha = 0.1)

## ************ Compositional analysis of habitat use ***************
## 
## The analysis was carried out with 7 animals and 7 habitat types
## 1. Test of the habitat selection:
##    randomisation test
##      Lambda           P 
## 0.004760556 0.110000000 
## 
## 2. Ranking of habitats (profile):
##                                                                             
## habitat      Herb.wet  Ag  Shrub.Scrub  Wood.wet  Open.water  Forest  Grass 
## Herb.wet    ---------------------------          ------------               
## Ag          ---------------------------          ------------               
## Shrub.Scrub ---------------------------          ------------               
## Wood.wet                               ------------------------------       
## Open.water  ----------------------------------------------------------------
## Forest                                 -------------------------------------
## Grass                                            ---------------------------

Analysis with 0s represented as 0.001

compana(hu1, ha, test = c("randomisation", "parametric"),
        rnv = 0.01, nrep = 500, alpha = 0.1)

## ************ Compositional analysis of habitat use ***************
## 
## The analysis was carried out with 7 animals and 7 habitat types
## 1. Test of the habitat selection:
##    randomisation test
##      Lambda           P 
## 0.004760556 0.132000000 
## 
## 2. Ranking of habitats (profile):
##                                                                             
## habitat      Herb.wet  Ag  Shrub.Scrub  Wood.wet  Open.water  Forest  Grass 
## Herb.wet    ---------------------------          ------------               
## Ag          ---------------------------          ------------               
## Shrub.Scrub ---------------------------          ------------               
## Wood.wet                               ------------------------------       
## Open.water  ----------------------------------------------------------------
## Forest                                 -------------------------------------
## Grass                                            ---------------------------