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

In unmarked: Models for Data from Unmarked Animals

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.frames 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)

unmarked documentation built on Sept. 11, 2024, 8:28 p.m.