telemetry: SCR data set that contains a sample of individuals with...

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

Description

Simulated data from the sim.data() function

Usage

data(telemetry)

Format

The format is: List of 7 $ Y : int [1:53, 1:12, 1:120] 0 0 0 0 0 0 0 0 0 1 ...

$ MASK : num [1:120, 1:12] 1 1 1 1 1 1 1 1 1 1 ...

$ traplocs : num [1:120, 1:2] 125 126 125 124 125 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:120] "1" "2" "3" "4" ... .. ..$ : chr [1:2] "x" "y"

$ Xss : num [1:947, 1] -0.566 -0.292 -0.174 0.607 -0.21 ...

$ Ytel : num [1:1200, 1:3] 126 126 126 126 126 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:3] "" "" "i" ..- attr(*, "sex")= int [1:12] 0 1 0 1 0 0 1 1 1 1 ...

$ Xsex : int [1:53] 0 1 1 0 1 1 1 0 0 0 ...

$ statespace: num [1:947, 1:3] 122 122 122 123 123 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:947] "1" "2" "3" "4" ... .. ..$ : chr [1:3] "X_Coord" "Y_Coord" "tighab"

Details

This is a list having the required objects to fit a barebones SCR model that includes auxilliary data from a sample of telemetered individuals. The elements of the list Y, MASK, traplocs and statespace are standard SCR data. In addition, the following objects are provided:

Xss: a state-space covariate on "density". The data were simulated with a strong effect of Xss determining the home range centers.

Ytel: a matrix with 3 columns having telemetry observations for a sample of 12 individuals. The format is: x-coord, y-coord, individual_id. Ytel has an attribute "sex" which is the sex of the 12 telemetered individuals.

Xsex: the sex of the sample of individuals encountered by the SCR study (not including telemetered individuals).

The data set was generated such that the telemetry and SCR samples of individuals ARE NOT RECONCILED and assumed to be independent.

Source

Data come from sim.data()

References

Sollmann, R., Gardner, B., Chandler, R. B., Shindle, D. B., Onorato, D. P., Royle, J. A., & O'Connell, A. F. (2013). Using multiple data sources provides density estimates for endangered Florida panther. Journal of Applied Ecology.

Royle, J. A., Chandler, R. B., Sun, C. C., & Fuller, A. K. (2013). Integrating resource selection information with spatial capture-recapture. Methods in Ecology and Evolution.

Examples

### Here is how the data were simulated
data(tigerdata)
ssgrid<- tigerdata$grid900
ssgrid<- ssgrid/5000
ssgrid[,3]<- rep(1,nrow(ssgrid))
## Simulated a spatial covariate
## This is very inefficient and/or will crash your computer if ssgrid has 
##    a lot of rows.
set.seed(2014)
D<-e2dist(ssgrid,ssgrid)
V<- exp(-D/2)
x<-t(chol(V))%*%rnorm(nrow(ssgrid))


## Plot the covariate
par(mar=c(3,3,3,6))
spatial.plot(ssgrid,x,cx=2,add=FALSE)

traplocs<- tigerdata$tigerdata.traplocs/5000
K<- 12

## Use sim.data to simulate some data. 
telemetry<-sim.data(N = 200, sigma = c(0.35,.5), loglam0 = log(0.5), K=K, 
   statespace = ssgrid, traplocs = as.matrix(traplocs), Xss = x, alpha1 = 1, 
   coord.scale = 1,Ntel=12,nfixes=100) 

### Data can be loaded instead by doing this:
data(telemetry)

statespace<- telemetry$statespace
traplocs<-telemetry$traplocs
y<- array3d2SCR.fn(telemetry$Y)
x<- telemetry$Xss

## Reformat the "captures" data into the standard encounter data file
##    (EDF) format

edf <-cbind(session = rep(1,nrow(y)), individual=y[,2],
   occasion=y[,3],   trapid=y[,1])

## No animals were removed (dead) so "alive" is a matrix of 1's

alive=matrix(1,nrow=length(unique(edf[,"individual"])),ncol=1)

trapfile<-cbind(1:nrow(traplocs),traplocs,matrix(1,nrow=nrow(traplocs),ncol=K))

##
## Create the scrdata file:
##
scrobj<- scrData(trapfile, edf, statespace, alive = NULL, 
                 Xd = x, Ytel=telemetry$Ytel,
                 Xsex=telemetry$Xsex)

##
## Now run SCRh.fn and fit the statespace covariate on density by 
## specifying Mss=1 and indicate telemetry data is to be used by
## specifying Mtel=1. Also Msexsigma=1 says fit a model with
## sex-specific "sigma"

test<-SCRh.fn(scrobj,ni=400, burn=20, skip=1,nz=200,theta=1,
      Msigma=1, Mb=0, Msex=0, Msexsigma=1,Mss=1,Mtel=1,coord.scale=1,
      thinstatespace=1)


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

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