R: Organize data for the N-mixture model fit by pcount

unmarkedFramePCount {unmarked} | R Documentation

## Organize data for the N-mixture model fit by pcount

### Description

Organizes repeated count data along with the covariates. This S4 class is required by the data argument of `pcount`

### Usage

    unmarkedFramePCount(y, siteCovs=NULL, obsCovs=NULL, mapInfo)

### Arguments

`y` | An RxJ matrix of the repeated count 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 R 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

unmarkedFramePCount is the S4 class that holds data to be passed to the `pcount` model-fitting function.

### Value

an object of class unmarkedFramePCount

### See Also

`unmarkedFrame-class`, `unmarkedFrame`, `pcount`

### Examples

    # Fake data
    R <- 4 # number of sites
    J <- 3 # number of visits
    y <- matrix(c(
       1,2,0,
       0,0,0,
       1,1,1,
       2,2,1), 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 <- unmarkedFramePCount(y=y, siteCovs=site.covs,
        obsCovs=obs.covs)          # organize data
    umf                            # take a l
    summary(umf)                   # summarize data
    fm <- pcount(~1 ~1, umf, K=10) # fit a model

[Package unmarked version 1.0.0 Index]