wolverine: wolverine data from Audrey Magoun

In jaroyle/SCRbayes: Bayesian analysis of spatial capture-recapture models

Description

An R list with 5 components (see Section 5.9 of the SCR book):

wcaps which is the encounter data file (EDF),

wtraps is the trap deployment file (TDF) which has x,y coordinates of traps and a MASK of which trap was operating (1) or not (0) during each day of the study.

3 discrete state-space grids are provided: grid8 grid4 and grid2 which are 8x8 4x4 and 2x2 state-space grids, respectively.

Usage

data(wolverine)

Format

The format is: > str(wolverine) List of 5 $ wcaps : num [1:115, 1:4] 1 1 1 1 1 1 1 1 1 1 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:4] "year" "individual" "day" "trap" $ wtraps:'data.frame': 37 obs. of 167 variables: ..$ Easting : int [1:37] 632538 634822 638455 634649 637738 625278 631690 632631 631374 634068 ... ..$ Northing: int [1:37] 6316012 6316568 6309781 6320016 6313994 6318386 6325157 6316609 6331273 6328575 ... ..$ 1 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... ..$ 2 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... ..$ 3 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... ..$ 4 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... ..$ 5 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... ..$ 6 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... ..$ 7 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... ..$ 8 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... ..$ 9 : num [1:37] 0 1 0 0 0 0 0 0 0 0 ... .... [deleted]...... ..$ 96 : num [1:37] 1 1 0 0 1 1 1 0 1 1 ... ..$ 97 : num [1:37] 1 1 0 0 1 1 1 0 1 1 ... .. [list output truncated] $ grid8 :'data.frame': 157 obs. of 2 variables: ..$ UTMx: num [1:157] 601677 609674 617670 589840 597836 ... ..$ UTMy: num [1:157] 6425005 6425162 6425320 6416773 6416930 ... $ grid4 :'data.frame': 619 obs. of 2 variables: ..$ UTMsX: num [1:619] 607596 611594 615592 601677 605676 ... ..$ UTMsY: num [1:619] 6429121 6429200 6429279 6425005 6425084 ... $ grid2 :'data.frame': 2466 obs. of 2 variables: ..$ Xutm: num [1:2466] 612554 614553 607596 609595 611594 ... ..$ Yutm: num [1:2466] 6431219 6431258 6429121 6429161 6429200 ...

Source

Data are described in detail here:

Magoun, A. J., Long, C. D., Schwartz, M. K., Pilgrim, K. L., Lowell, R. E., and Valkenburg, P. (2011). Integrating motion-detection cameras and hair snags for wolverine identification. The Journal of Wildlife Management, 75(3), 731-739.

Royle, J. A., Magoun, A. J., Gardner, B., Valkenburg, P., and Lowell, R. E. (2011). Density estimation in a wolverine population using spatial capture-recapture models. The Journal of Wildlife Management, 75(3), 604-611.

References

SCR book, Section 5.9

Examples

data(wolverine)

## make the encounter data file (EDF)
EDF<-wolverine$wcaps
dimnames(EDF)<-list(NULL,c("session","individual","occasion","trapid"))
## grab the trap deployment file (TDF)
TDF<-wolverine$wtraps

## we will fit a model with sex-specific parameters, so grab the sex variable
wsex<-wolverine$wsex

## bundle these into an "scrdata" object along with the state-space grid
grid<-cbind(wolverine$grid2,rep(1,nrow(wolverine$grid2)))
wolv.scrdata<-scrData(TDF,EDF,grid,Xsex=wsex)

## now fit a model using the current development version of
##   the fitting function. With the 2 km grid the area per pixel is 4 km^2

test<-SCRh.fn( wolv.scrdata,ni= 1200, burn=200, skip=2,nz=100,theta=1,
               Msigma=1, Mb=0, Msex=1, Msexsigma=1, 
               coord.scale=5000, area.per.pixel=4, thinstatespace=4)

## print a summary 
print(test, digits=3)

## maybe str(wolverine) ; plot(wolverine) ...

jaroyle/SCRbayes documentation built on May 18, 2019, 4:48 p.m.