snip: Slice Transect Into Shorter Sections

In secr: Spatially Explicit Capture-Recapture

Slice Transect Into Shorter Sections

Description

This function splits the transects in a ‘transect’ or ‘transectX’ traps object into multiple shorter sections. The function may also be applied directly to a capthist object based on transect data. This makes it easy to convert detection data collected along linear transects to point detection data (see Example).

Usage

snip(object, from = 0, by = 1000, length.out = NULL, keep.incomplete = TRUE, tol = 0.01)

Arguments

object	secr ‘traps’ or ‘capthist’ object based on transects
from	numeric starting posiiton (m)
by	numeric length of new transects (m)
length.out	numeric number of new transects, as alternative to ‘by’
keep.incomplete	logical; if TRUE then initial or terminal sections of each original transect that are less than ‘by’ will be retained in the output
tol	numeric tolerance for xyontransect (capthist only)

Details

If a positive length.out is specified, by will be computed as (transectlength(object) - from) / length.out.

Value

A ‘traps’ or ‘capthist’ object, according to the input. If keep.incomplete == FALSE animals and detections from the

Warning

snip does not work for mark–resight data.

See Also

transectlength, discretize

Examples

x <- seq(0, 4*pi, length = 41)
temptrans <- make.transect(x = x*100, y = sin(x)*300)
plot (snip(temptrans, by = 200), markvertices = 1)

## Not run: 

## simulate some captures
tempcapt <- sim.capthist(temptrans, popn = list(D = 2,
   buffer = 300), detectfn = 'HHN', binomN = 0,
   detectpar = list(lambda0 = 0.5, sigma = 50))

## snip capture histories
tempCH <- snip(tempcapt, by = 20)

## collapse from 'transect' to 'count', discarding location within transects
tempCH <- reduce(tempCH, outputdetector = "count")

## fit secr model and examine H-T estimates of density
## fails with detectfn = 'HN'
fit <- secr.fit(tempCH, buffer = 300, CL = TRUE, detectfn = 'HHN', trace = FALSE)
derived(fit)

## also, may split an existing transect into equal lengths
## same result:
plot(snip(temptrans, by = transectlength(temptrans)/10),
    markvertices = 1)
plot(snip(temptrans, length.out = 10), markvertices = 1)


## End(Not run)

secr documentation built on Nov. 4, 2024, 9:06 a.m.