unmarked (version 1.0.1)

unmarkedFrameOccuFP: Organize data for the single season occupancy models fit by occuFP

Description

Organizes detection, non-detection data along with the covariates. This S4 class is required by the data argument of occu and occuRN

Usage

unmarkedFrameOccuFP(y, siteCovs=NULL, obsCovs=NULL, type, mapInfo)

Arguments

y

An RxJ matrix of the detection, non-detection data, where R is the number of sites, J is the maximum number of sampling periods per site.

siteCovs

A data.frame of covariates that vary at the site level. This should have M rows and one column per covariate

obsCovs

Either a named list of data.frames of covariates that vary within sites, or a data.frame with RxJ rows in site-major order.

type

A vector with 3 values designating the number of occassions where data is of type 1, type 2, and type 3 - see occuFP for more details about data types.

mapInfo

Currently ignored

Value

an object of class unmarkedFrameOccuFP

Details

unmarkedFrameOccuFP is the S4 class that holds data to be passed to the occu and occuRN model-fitting function.

See Also

unmarkedFrame-class, unmarkedFrame, occuFP

Examples

# NOT RUN {
n = 100
o = 10
o1 = 5
y = matrix(0,n,o)
p = .7
r = .5
fp = 0.05
y[1:(n*.5),(o-o1+1):o] <- rbinom((n*o1*.5),1,p)
y[1:(n*.5),1:(o-o1)] <- rbinom((o-o1)*n*.5,1,r)
y[(n*.5+1):n,(o-o1+1):o] <- rbinom((n*o1*.5),1,fp)
type <- c((o-o1),o1,0)  ### vector with the number of each data type
site <- c(rep(1,n*.5*.8),rep(0,n*.5*.2),rep(1,n*.5*.2),rep(0,n*.8*.5))
occ <- matrix(c(rep(0,n*(o-o1)),rep(1,n*o1)),n,o)
site <- data.frame(habitat = site)
occ <- list(METH = occ)

umf1 <- unmarkedFrameOccuFP(y,site,occ, type = type)

m1 <- occuFP(detformula = ~ METH, FPformula = ~1, stateformula = ~ habitat, data = umf1)

# }