array3d2SCR.fn: utility function to convert 3-d encounter history array to...
In jaroyle/SCRbayes: Bayesian analysis of spatial capture-recapture models

Description Usage Arguments Details Value Author(s) Examples

individuals x sampling occasion x traps into a 2 dimensional matrix where column 1=traps, column 2=individuals and column 3=sample occasion which can passed into the function SCRf.fn~~

1	array3d2SCR.fn(y = object)

`y`	i=number of individuals, k=number of sampling occasion, and j=number of traps ~~

A typical object is constructed of an array containing zero and 1 variables indicating if individual i was observed on sampling occasion k in trap j

matrix of nrows and 3 columns is returned where columns contain trap number, individual, and sampling occasions of observed animals. Object can be used as a input for the function SCRf.fn

Andy Royle aroyle@usgs.gov

##---- test.data<-array(dim=c(200,3,50)) 
##-- for(i in 1:200)
	{
	for(j in 1:3)
	{
	for(k in 1:50)
	{
	test.data[i,j,k]<-rbinom(1,1,0.2)
	}
	}
	}
SCR.data<-array3d2SCR.fn(test.data)

##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (y = tiger.data3d) 
{
    dd <- dim(y)
    nind <- dd[1]
    nrep <- dd[2]
    ntrap <- dd[3]
    indid <- repid <- trapid <- NULL
    for (i in 1:nind) {
        yi <- y[i, , ]
        indid <- c(indid, rep(i, sum(yi > 0, na.rm = TRUE)))
        repid <- c(repid, row(yi)[!is.na(yi) & yi > 0])
        trapid <- c(trapid, col(yi)[!is.na(yi) & yi > 0])
    }
    o <- cbind(trapid, indid, repid)
    dimnames(o) <- list(NULL, c("trapid", "individual", "sample"))
    o <- o[order(o[, 1]), ]
    o
  }