R: Organize data for the single season occupancy models fit by...

unmarkedFrameOccuFP {unmarked} | R Documentation

## 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.frame`s 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

### Details

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

### Value

an object of class unmarkedFrameOccuFP

### See Also

`unmarkedFrame-class`, `unmarkedFrame`, `occuFP`

### Examples

    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)

[Package unmarked version 1.0.0 Index]