RMark 1.7.1

[jlaake]

A new version of RMark has been put on the Cornell MARK website. The main reason for the update was the inclusion of the 13 Occupancy models in MARK. You should update and use MARK.EXE from MARK 5.0 because it fixes a couple of minor bugs with some of the occupancy models. Note that you can probably use that MARK.EXE with the interface from 4.3. Examples from Nichols et al(2007), the occupancy book by McKenzie et al and from Exercise 7 & 8 from the Occupancy web site are included.

Below is an additional example for an occupancy model that was inspired by a posting on species richness in the Presence list.

Imagine a scenario in which you wanted to model species-habitat dependent occupancy with detection probability dependent on effort which varied by occasion and site. An example run in RMark would be as follows:

# Input data set shown below
CovOccup=import.chdata("CovariateOccupancyExample.txt",field.types=c("n","f","f","n","n","n","n","n"))

# fit an additive Species+Habitat Psi model and Effort model for p
mark(CovOccup,model="Occupancy",group=c("Species","Habitat"),
model.parameters=list(Psi=list(formula=~Species+Habitat),p=list(formula=~Effort)))


Snippet of the Data set

ch freq Species Habitat Effort1 Effort2 Effort3 Effort4 Effort5
00111 1 LGB Forest 5 2 14 2 5
00111 1 LGB Forest 5 3 16 3 5
10011 1 LGB Forest 4 2 11 2 4
10110 1 LGB Forest 5 3 15 3 5
00000 1 LBB Forest 5 3 16 3 5
00000 1 LBB Forest 6 3 19 3 6
00010 1 LBB Forest 3 1 8 1 3
00000 1 LBB Forest 5 3 16 3 5
00000 1 LBB Forest 4 2 13 2 4
00111 1 LBB Forest 4 2 12 2 4
00000 1 LBB Forest 5 2 14 2 5
00111 1 LBB Forest 3 2 10 2 3
00000 1 LBB Grassland 4 2 11 2 4
00000 1 LBB Grassland 3 2 10 2 3
00000 1 LBB Grassland 4 2 12 2 4
00000 1 LBB Grassland 2 1 6 1 2
00100 1 LGB Grassland 5 2 15 2 5
00100 1 LGB Grassland 4 2 13 2 4