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

unmarkedFrameOccu {unmarked} | R Documentation

## Organize data for the single season occupancy models fit by occu and occuRN

### Description

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

### Usage

    unmarkedFrameOccu(y, siteCovs=NULL, obsCovs=NULL, 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.
`mapInfo` | Currently ignored

### Details

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

### Value

an object of class unmarkedFrameOccu

### See Also

`unmarkedFrame-class`, `unmarkedFrame`, `occu`, `occuRN`

### Examples

    # Fake data
    R <- 4 # number of sites
    J <- 3 # number of visits
    y <- matrix(c(
       1,1,0,
       0,0,0,
       1,1,1,
       1,0,1), nrow=R, ncol=J, byrow=TRUE)
    y

    site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
    site.covs

    obs.covs <- list(
       x3 = matrix(c(
          -1,0,1,
          -2,0,0,
          -3,1,0,
          0,0,0), nrow=R, ncol=J, byrow=TRUE),
       x4 = matrix(c(
          'a','b','c',
          'd','b','a',
          'a','a','c',
          'a','b','a'), nrow=R, ncol=J, byrow=TRUE))
    obs.covs

    umf <- unmarkedFrameOccu(y=y, siteCovs=site.covs,
        obsCovs=obs.covs)   # organize data
    umf                     # look at data
    summary(umf)            # summarize
    fm <- occu(~1 ~1, umf)  # fit a model

[Package unmarked version 1.0.0 Index]