R: Create an object of class unmarkedFramePCO that contains data...

unmarkedFramePCO {unmarked} | R Documentation

## Create an object of class unmarkedFramePCO that contains data used by pcountOpen.

### Description

Organizes repeated count data along with the covariates and possibly the dates on which each survey was conducted. This S4 class is required by the data argument of `pcountOpen`

### Usage

    unmarkedFramePCO(y, siteCovs=NULL, obsCovs=NULL, yearlySiteCovs, mapInfo,
        numPrimary, primaryPeriod)

### Arguments

`y` | An MxJT matrix of the repeated count data, where M is the number of sites, J is the maximum number of secondary sampling periods per site and T is the maximum number of primary 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 MxJT rows in site-major order.
`yearlySiteCovs` | Either a named list of MxT `data.frame`s, or a site-major `data.frame` with MT rows and 1 column per covariate.
`mapInfo` | Currently ignored
`numPrimary` | Maximum number of observed primary periods for each site
`primaryPeriod` | matrix of integers indicating the primary period of each survey.

### Details

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

The unmarkedFramePCO class is similar to the unmarkedFramePCount class except that it contains the dates for each survey, which needs to be supplied .

### Value

an object of class unmarkedFramePCO

### See Also

`unmarkedFrame-class`, `unmarkedFrame`, `pcountOpen`

### Examples

    # Repeated count data with 5 primary periods and
    # no secondary sampling periods (ie J==1)
    y1 <- matrix(c(
        0, 2, 3, 2, 0,
        2, 2, 3, 1, 1,
        1, 1, 0, 0, 3,
        0, 0, 0, 0, 0), nrow=4, ncol=5, byrow=TRUE)

    # Site-specific covariates
    sc1 <- data.frame(x1 = 1:4, x2 = c('A','A','B','B'))

    # Observation-specific covariates
    oc1 <- list(
        x3 = matrix(1:5, nrow=4, ncol=5, byrow=TRUE),
        x4 = matrix(letters[1:5], nrow=4, ncol=5, byrow=TRUE))

    # Primary periods of surveys
    primaryPeriod1 <- matrix(as.integer(c(
        1, 2, 5, 7, 8,
        1, 2, 3, 4, 5,
        1, 2, 4, 5, 6,
        1, 3, 5, 6, 7)), nrow=4, ncol=5, byrow=TRUE)

    # Create the unmarkedFrame
    umf1 <- unmarkedFramePCO(y=y1, siteCovs=sc1, obsCovs=oc1, numPrimary=5,
        primaryPeriod=primaryPeriod1)

    # Take a look
    umf1
    summary(umf1)

    # Repeated count data with 4 primary periods and
    # no 2 secondary sampling periods (ie J=2)
    y2 <- matrix(c(
        0,0,  2,2,  3,2,  2,2,
        2,2,  2,1,  3,2,  1,1,
        1,0,  1,1,  0,0,  0,0,
        0,0,  0,0,  0,0,  0,0), nrow=4, ncol=8, byrow=TRUE)

    # Site-specific covariates
    sc2 <- data.frame(x1 = 1:4, x2 = c('A','A','B','B'))

    # Observation-specific covariates
    oc2 <- list(
        x3 = matrix(1:8, nrow=4, ncol=8, byrow=TRUE),
        x4 = matrix(letters[1:8], nrow=4, ncol=8, byrow=TRUE))

    # Yearly-site covariates
    ysc <- list(
        x5 = matrix(c(
            1,2,3,4,
            1,2,3,4,
            1,2,3,4,
            1,2,3,4), nrow=4, ncol=4, byrow=TRUE))

    # Primary periods of surveys
    primaryPeriod2 <- matrix(as.integer(c(
        1,2,5,7,
        1,2,3,4,
        1,2,4,5,
        1,3,5,6)), nrow=4, ncol=4, byrow=TRUE)

    # Create the unmarkedFrame
    umf2 <- unmarkedFramePCO(y=y2, siteCovs=sc2, obsCovs=oc2,
        yearlySiteCovs=ysc,
        numPrimary=4, primaryPeriod=primaryPeriod2)

    # Take a look
    umf2
    summary(umf2)

[Package unmarked version 1.0.0 Index]