pdot {secr} | R Documentation |
Net Detection Probability
Description
Compute spatially explicit net probability of detection for individual(s) at given coordinates (pdot).
Usage
pdot(X, traps, detectfn = 0, detectpar = list(g0 = 0.2,
sigma = 25, z = 1), noccasions = NULL, binomN = NULL,
userdist = NULL, ncores = NULL)
CVpdot(..., conditional = FALSE)
Arguments
X |
vector or 2-column matrix of coordinates |
traps |
|
detectfn |
integer code for detection function q.v. |
detectpar |
a named list giving a value for each parameter of detection function |
noccasions |
number of sampling intervals (occasions) |
binomN |
integer code for discrete distribution (see
|
userdist |
user-defined distance function or matrix (see userdist) |
ncores |
integer number of threads |
... |
arguments passed to |
conditional |
logical; if TRUE then computed mean and CV are conditional on detection |
Details
If traps
has a usage attribute then noccasions
is
set accordingly; otherwise it must be provided.
The probability computed is where
the product is over the detectors in
traps
, excluding any not
used on a particular occasion. The per-occasion detection function
is halfnormal (0) by default, and is assumed not to vary
over the
occasions.
For detection functions (10) and (11) the signal threshold ‘cutval’ should be
included in detectpar
, e.g., detectpar = list(beta0 = 103, beta1
= -0.11, sdS = 2, cutval = 52.5)
.
The calculation is not valid for single-catch traps because
is reduced by competition between animals.
userdist
cannot be set if ‘traps’ is any of polygon, polygonX,
transect or transectX. if userdist
is a function requiring
covariates or values of parameters ‘D’ or ‘noneuc’ then X
must
have a covariates attribute with the required columns.
Setting ncores = NULL
uses the existing value from the environment variable
RCPP_PARALLEL_NUM_THREADS (see setNumThreads
).
CVpdot
returns the expected mean and CV of pdot across the points listed in X
, assuming uniform population density. X
is usually a habitat mask. See Notes for details.
Value
For pdot
, a vector of probabilities, one for each row in X.
For CVpdot
, a named vector with elements ‘meanpdot’ and ‘CVpdot’.
Note
CVpdot
computes the mean and variance
of the location-specific overall detection probability
as follows.
For uniform density and conditional = FALSE
, is merely a scaling factor independent of
.
If conditional = TRUE
then .
The coefficient of variation is CV = .
See Also
secr
,
make.mask
,
Detection functions
,
pdot.contour
,
CV
Examples
## Not run:
temptrap <- make.grid()
## per-session detection probability for an individual centred
## at a corner trap. By default, noccasions = 5.
pdot (c(0,0), temptrap, detectpar = list(g0 = 0.2, sigma = 25),
noccasions = 5)
msk <- make.mask(temptrap, buffer = 100)
CVpdot(msk, temptrap, detectpar = list(g0 = 0.2, sigma = 25),
noccasions = 5)
## End(Not run)