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Temporal availability adjustment

Source: R/CTDS.R
ct_availability.Rd

Calculates availability correction factors by accounting for temporal variation in animal activity patterns and camera deployment effort. The availability rate represents the proportion of time animals are available for detection (Rowcliffe, et al., 2014; Howe et al., 2017) given their activity patterns and camera sampling effort.

Usage

ct_availability(
  times,
  format = NULL,
  sample = c("data", "model"),
  n_bootstrap = 1000,
  cam_daily_effort = 24,
  ...
)

Arguments

times

Vector of detection times, either in radians (0 - \(2*pi\)) or formatted times (see format parameter).

format

Time format string (e.g., "%H:%M:%S", "%H:%M") if times need conversion to radians. Set to NULL if times are already in radians.

sample

Character string defining sampling method for bootstrapping errors (see details).

n_bootstrap

Number of bootstrap iterations to perform. Ignored if sample=="none"

cam_daily_effort

Daily operational hours of cameras (default = 24 for continuous operation).

...

Arguments passed on to ct_fit_activity

weights

A numeric vector of weights for each dat value.

bandwidth

Numeric value for kernel bandwidth. If NULL, calculated internally.

adjustment

Numeric bandwidth adjustment multiplier.

bounds

A two-element vector defining radian bounds at which to truncate.

show

Logical whether or not to show a progress bar while bootstrapping.

Value

A list containing data frame with:

  • rate: Estimated availability rate (0-1)

  • SE: Standard error of the availability rate

References

Howe, E. J., Buckland, S. T., Després-Einspenner, M. L., & Kühl, H. S. (2017). Distance sampling with camera traps. Methods in Ecology and Evolution, 8(11), 1558-1565. doi:10.1111/2041-210X.12790

Rowcliffe, J. M., Kays, R., Kranstauber, B., Carbone, C., & Jansen, P. A. (2014). Quantifying levels of animal activity using camera trap data. Methods in Ecology and Evolution, 5(11), 1170-1179. doi:10.1111/2041-210X.12278

See also

ct_fit_activity()

Examples

# \donttest{
# Example with times already in radians
radian_times <- c(1.2, 3.4, 5.1, 0.5, 2.8)
ct_availability(radian_times, sample = "data")
#> Warning: max(dat) < 1, expecting radian data
#> Warning: max(dat) < 1, expecting radian data
#> $creation
#>        rate         SE
#> 1 0.4614052 0.08683349
#> 

# Example with formatted times
time_strings <- c("06:30", "18:15", "12:00", "23:45")
ct_availability(time_strings, sample = "data", format = "%H:%M")
#> $creation
#>        rate        SE
#> 1 0.9499413 0.2171634
#> 

# With bootstrap resampling
ct_availability(radian_times, sample = "data", n_bootstrap = 100)
#> $creation
#>        rate         SE
#> 1 0.4614052 0.07927602
#> 
# }