secrfunc (version 1.0.0)

polygonhistoriescpp: Probability of Polygon Capture Histories

Description

polygonhistoriescpp is the core function for the contribution of individual histories to likelihood. It is called by internal secr function generalsecrloglik().

polygonfxicpp is the core code for 'fxi' calculations in secr when the detector type is polygon or transect based. It is called by the internal secr function allhistpolygonfxi.

Usage

polygonhistoriescpp(nc, detectfn, grain, ncores, minp, binomN, w, xy, start, 
    group, hk, H, gsbval, pID, mask, density, PIA, Tsk, h, hindex, debug)
    
polygonfxicpp(nc, detectfn, grain, ncores, minp, binomN, w, xy, start, 
    group, hk, H, gsbval, pID, mask, density, PIA, Tsk, h, hindex)

Value

For polygonhistoriescpp -- Numeric vector of probabilities, one per individual.

For polygonfxicpp -- Numeric matrix with probability density for each individual (rows) at each mask point (columns).

Arguments

nc

integer number of individuals

detectfn

integer detector code (see secr)

grain

integer grain argument of RcppParallel::parallelFor

ncores

integer number of threads

minp

double minimum probability

binomN

integer vector binomial code

w

3-D integer array of capture histories (individual x occasion x detector)

xy

2-column matrix of detection location coordinates

start

integer vector of index of row in xy for each first detection

group

integer vector; code for group of each individual (zero-based)

hk

numeric array of detection hazards from makegkPolygoncpp

H

numeric unbounded integrated hazard from radial function from makegkPolygoncpp

gsbval

matrix of real parameter values, one row per combination

pID

numeric matrix occasions x nmix. NOT USED?

mask

2-column matrix of mask coordinates

density

matrix relative density at each mask point (row) for each group? (column)

PIA

integer vector for the slice of the parameter index array for a given mixture component and session

Tsk

detector usage (numeric matrix detectors x occasions)

h

for exclusive detectors, pre-computed hazard; otherwise -1

hindex

for exclusive detectors, index to precomputed hazard; otherwise -1

debug

logical; if TRUE...

Details

The capture history 'w' merely records detection/nondetection on a particular occasion. 'xy' records the location of each positive detection.

See Also

makegkPolygoncpp

Examples

datafilename <- system.file("extdata/testdata.RData", package = "secrfunc")
load(datafilename)  # loads w, dimw, xy, start, traps, mask, gsbval, cumk, binomN

detectfn <- 14   # hazard half-normal
dim <- 2
convex <- TRUE
grain <- 1
ncores <- 2

gkhk <- makegkPolygoncpp(detectfn, dim, convex, grain, ncores, gsbval, cumk, traps, mask)
# see tests for expected result

nc      <- dimw[1]  # individuals
S       <- dimw[2]  # occasions
K       <- dimw[3]  # single polygon
minp    <- 1e-200
group   <- rep(0,nc)
pID     <- matrix(1, nrow = S, ncol = 1)
density <- matrix(1/nrow(mask), nrow(mask), 1)
PIA     <- as.integer(array (1, dim = c(nc, S, K)))
Tsk     <- matrix(1, nrow = K, ncol = S)
h       <- matrix(-1)
hindex  <- matrix(-1)
debug   <- FALSE

prw <- polygonhistoriescpp(nc, detectfn, grain, ncores, minp, binomN, w, xy, start, 
    group, gkhk$hk, gkhk$H, gsbval, pID, mask, density, PIA, Tsk, h, hindex, debug)
# see tests for expected result

fxi <- polygonfxicpp(nc, detectfn, grain, ncores, minp, binomN, w, xy, start, 
    group, gkhk$hk, gkhk$H, gsbval, pID, mask, density, PIA, Tsk, h, hindex)
# see tests for expected result