subset.capthist: Subset or Split capthist Object

In secr: Spatially Explicit Capture-Recapture

Subset or Split capthist Object

Description

Create a new capthist object or list of objects by selecting rows (individuals), columns (occasions) and traps from an existing capthist object.

Usage

## S3 method for class 'capthist'
subset(x, subset = NULL, occasions = NULL, traps = NULL,
    sessions = NULL, cutval = NULL, dropnullCH = TRUE, dropnullocc = FALSE,
    dropunused = TRUE, droplowsignals = TRUE, dropNAsignals = FALSE,
    cutabssignal = TRUE, renumber = FALSE, ...)

## S3 method for class 'capthist'
split(x, f, drop = FALSE, prefix = "S", bytrap = FALSE, 
 byoccasion = FALSE, bysession = FALSE, ...)

Arguments

x	object of class capthist
subset	vector of subscripts to select rows (individuals) (see Details for variations)
occasions	vector of subscripts to select columns (occasions)
traps	vector of subscripts to select detectors (traps)
sessions	vector of subscripts to select sessions
cutval	new threshold for signal strength
dropnullCH	logical for whether null (all-zero) capture histories should be dropped
dropnullocc	logical for whether occasions with no detections should be dropped
dropunused	logical for whether never-used detectors should be dropped
droplowsignals	logical for whether cutval should be applied at each microphone rather than to sound as a whole
dropNAsignals	logical for whether detections with missing signal should be dropped
cutabssignal	logical for whether to apply cutval to absolute signal strength or the difference between signal and noise
renumber	logical for whether row.names should be replaced with sequence number in new capthist
f	factor or object that may be coerced to a factor
drop	logical indicating if levels that do not occur should be dropped (if f is a factor)
prefix	a character prefix to be used for component names when values of f are numeric
bytrap	logical; if TRUE then each level of f identifies traps to include
byoccasion	logical; if TRUE then each level of f identifies occasions to include
bysession	logical; if TRUE then each level of f identifies sessions of a multisession capthist to include
...	other arguments passed to subset.capthist (split.capthist) or to optional subset function (subset.capthist)

Details

Subscript vectors may be either logical- (length equal to the relevant dimension of x), character- or integer-valued. Subsetting is applied to attributes (e.g. covariates, traps) as appropriate. The default action is to include all animals, occasions, and detectors if the relevant argument is omitted.

When traps is provided, detections at other detectors are set to zero, as if the detector had not been used, and the corresponding rows are removed from traps. If the detector type is ‘proximity’ then selecting traps also reduces the third dimension of the capthist array.

split generates a list in which each component is a capthist object. Each component corresponds to a level of f. Multi-session capthists are accepted in secr >= 4.4.0; f should then be a list of factors with one component per session and the same levels in all.

To combine (pool) occasions use reduce.capthist. There is no equivalent of unlist for lists of capthist objects.

The effect of droplowsignals = FALSE is to retain below-threshold measurements of signal strength on all channels (microphones) as long as the signal is above cutval on at least one. In this case all retained sounds are treated as detected on all microphones. This fails when signals are already missing on some channels.

Subsetting is awkward with multi-session input when the criterion is an individual covariate. See the Examples for one way this can be tackled.

Value

capthist object with the requested subset of observations, or a list of such objects (i.e., a multi-session capthist object). List input results in list output, except when a single session is selected.

Warning

split.capthist does not work for mark–resight data.

See Also

capthist, rbind.capthist, reduce.capthist

Examples

tempcapt <- sim.capthist (make.grid(nx = 6, ny = 6), noccasions = 6)
summary(subset(tempcapt, occasions = c(1,3,5)))

## Consider `proximity' detections at a random subset of detectors
## This would not make sense for `multi' detectors, as the 
## excluded detectors influence detection probabilities in 
## sim.capthist.

tempcapt2 <- sim.capthist (make.grid(nx = 6, ny = 6, 
    detector = "proximity"), noccasions = 6)
tempcapt3 <- subset(tempcapt2, traps = sample(1:36, 18, 
    replace = FALSE))
summary(tempcapt3)
plot(tempcapt3)

tempcapt4 <- split (tempcapt2, f = sample (c("A","B"), 
    nrow(tempcapt2), replace = TRUE))
summary(tempcapt4)

## Split out captures on alternate rows of a grid
tempcapt5 <- split(captdata, f = rep(1:2, 50), bytrap = TRUE)
summary(tempcapt5)

## Divide one session into two by occasion
tempcapt6 <- split(captdata, f = factor(c(1,1,2,2,2)), byoccasion = TRUE)
summary(tempcapt6)

## Applying a covariate criterion across all sessions of a
## multi-session capthist object e.g. selecting male ovenbirds from the
## 2005--2009 ovenCH dataset. We include a restriction on occasions
## to demonstrate the use of 'MoreArgs'. Note that mapply() creates a
## list, and the class of the output must be restored manually.

ovenCH.males <- mapply(subset, ovenCH,
    subset = lapply(ovenCH, function(x) covariates(x)$Sex == "M"),
    MoreArgs = list(occasions = 1:5))
class(ovenCH.males) <- class(ovenCH)
summary(ovenCH.males, terse = TRUE)

## A simpler approach using a function to define subset
subsetfn <- function(x, sex) covariates(x)$Sex == sex
ovenCH.males <- subset(ovenCH, subset = subsetfn, sex = "M")
summary(ovenCH.males, terse = TRUE)

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