unmarkedFrame {unmarked} | R Documentation

## Create an unmarkedFrame, or one of its child classes.

### Description

Constructor for unmarkedFrames.

### Usage

    unmarkedFrame(y, siteCovs=NULL, obsCovs=NULL, mapInfo, obsToY)

### Arguments

`y` | An MxJ matrix of the observed measured data, where M is the number of sites and J is the maximum number of observations 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 MxJ rows in site-major order.
`obsToY` | optional matrix specifying relationship between observation-level covariates and response matrix
`mapInfo` | geographic coordinate information. Currently ignored.

### Details

unmarkedFrame is the S4 class that holds data structures to be passed to the model-fitting functions in unmarked.

An unmarkedFrame contains the observations (`y`), covariates measured at the observation level (`obsCovs`), and covariates measured at the site level (`siteCovs`). For a data set with M sites and J observations at each site, y is an M x J matrix. `obsCovs` and `siteCovs` are both data frames (see data.frame). `siteCovs` has M rows so that each row contains the covariates for the corresponding sites. `obsCovs` has M*obsNum rows so that each covariates is ordered by site first, then observation number. Missing values are coded with `NA` in any of y, siteCovs, or obsCovs.

Additionally, unmarkedFrames contain metadata: obsToY, mapInfo. obsToY is a matrix describing relationship between response matrix and observation-level covariates. Generally this does not need to be supplied by the user; however, it may be needed when using `multinomPois`. For example, double observer sampling, y has 3 columns corresponding the observer 1, observer 2, and both, but there were only two independent observations. In this situation, y has 3 columns, but obsToY must be specified.

Several child classes of `unmarkedFrame` require addional metadata. For example, `unmarkedFrameDS` is used to organize distsance sampling data for the `distsamp` function, and it has arguments dist.breaks, tlength, survey, and unitsIn, which specify the distance interval cut points, transect lengths, "line" or "point" transect, and units of measure, respectively.

All site-level covariates are automatically copied to obsCovs so that site level covariates are available at the observation level.

### Value

an unmarkedFrame object

### See Also

`unmarkedFrame-class`, `unmarkedFrameOccu`, `unmarkedFramePCount`, `unmarkedFrameDS`

### Examples

    # Set up data for pcount()
    data(mallard)
    mallardUMF <- unmarkedFramePCount(mallard.y, siteCovs = mallard.site,
    	obsCovs = mallard.obs)
    summary(mallardUMF)

    # Set up data for occu()
    data(frogs)
    pferUMF <- unmarkedFrameOccu(pfer.bin)

    # Set up data for distsamp()
    data(linetran)
    ltUMF <- with(linetran, {
    	unmarkedFrameDS(y = cbind(dc1, dc2, dc3, dc4),
    	siteCovs = data.frame(Length, area, habitat),
    	dist.breaks = c(0, 5, 10, 15, 20),
    	tlength = linetran$Length * 1000, survey = "line", unitsIn = "m")
    	})
    summary(ltUMF)

    # Set up data for multinomPois()
    data(ovendata)
    ovenFrame <- unmarkedFrameMPois(ovendata.list$data,
    	siteCovs=as.data.frame(scale(ovendata.list$covariates[,-1])),
    	type = "removal")
    summary(ovenFrame)

    ## Not run:
    # Set up data for colext()
    frogUMF <- formatMult(masspcru)
    summary(frogUMF)

    ## End(Not run)

[Package unmarked version 0.12-3 Index]