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

unmarkedFrameDSO {unmarked} | R Documentation

## Create an object of class unmarkedFrameDSO that contains data used by distsampOpen.

### Description

Organizes distance sampling data and experimental design information from multiple primary periods along with associated covariates. This S4 class is required by the data argument of `distsampOpen`

### Usage

    unmarkedFrameDSO(y, siteCovs=NULL, yearlySiteCovs=NULL, numPrimary,
           primaryPeriod, dist.breaks, tlength, survey, unitsIn)

### Arguments

`y` | An MxJT matrix of the repeated count data, where M is the number of sites (i.e., points or transects), J is the number of distance classes 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
`yearlySiteCovs` | Either a named list of MxT `data.frame`s, or a site-major `data.frame` with MT rows and 1 column per covariate
`numPrimary` | Maximum number of observed primary periods for each site
`primaryPeriod` | An MxJT matrix of integers indicating the primary period of each observation
`dist.breaks` | vector of distance cut-points delimiting the distance classes. It must be of length J+1
`tlength` | A vector of length R containing the transect lengths. This is ignored when survey="point"
`survey` | Either "point" or "line" for point- and line-transects
`unitsIn` | Either "m" or "km" defining the measurement units for both `dist.breaks` and `tlength`

### Details

`unmarkedFrameDSO` is the S4 class that holds data to be passed to the `distsampOpen` model-fitting function. Unlike most unmarked functions, `obsCovs` cannot be supplied.

If you have continuous distance data, they must be "binned" into discrete distance classes, which are delimited by dist.breaks.

When gamma or omega are modeled using year-specific covariates, the covariate data for the final year will be ignored; however, they must be supplied.

If the time gap between primary periods is not constant, an M by T matrix of integers should be supplied using the `primaryPeriod` argument.

### Value

an object of class unmarkedFrameDSO

### See Also

`unmarkedFrame-class`, `unmarkedFrame`, `distsampOpen`

### Examples

    # Fake data
    M <- 4 # number of sites
    J <- 3 # number of distance classes
    T <- 2 # number of primary periods

    db <- c(0, 10, 20, 30) # distance break points

    y <- matrix(c(
       5,4,3, 6,2,1, # In bin 1: 5 detections in primary period 1, 6 in period 2
       0,0,0, 0,1,0,
       2,1,1, 0,0,0,
       1,1,0, 1,1,1), nrow=M, ncol=J*T, byrow=TRUE)
    y

    # Primary periods of observations
    # In this case there are no gaps
    primPer <- matrix(as.integer(c(
        1,2,
        1,2,
        1,2,
        1,2)), nrow=M, ncol=T, byrow=TRUE)

    #Site covs: M rows and 1 column per covariate
    site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
    site.covs

    #Yearly site covs on gamma/omega
    ysc <- list(
        x3 = matrix(c(
            1,2,
            1,2,
            1,2,
            1,2), nrow=M, ncol=T, byrow=TRUE))

    umf <- unmarkedFrameDSO(y=y, siteCovs=site.covs, yearlySiteCovs=ysc,
                            numPrimary=T, primaryPeriod=primPer,
                            dist.breaks=db, survey="point", unitsIn="m")

    umf                         # look at data
    summary(umf)                # summarize

[Package unmarked version 1.0.0 Index]