Description Usage Arguments Details Value See Also Examples
Constructor for unmarkedFrames.
1 |
y |
A matrix of the observed measured data. |
siteCovs |
|
obsCovs |
list of |
obsToY |
optional matrix specifying relationship between observation-level covariates and response matrix |
mapInfo |
geographic coordinate information |
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.
an unmarkedFrame object
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | # 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)
# Set up data for colext()
frogUMF <- formatMult(masspcru)
summary(frogUMF)
|
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