ct_fit_rest: Fit the Random Encounter and Staying Time (REST / RAD-REST)...

In ct: Camera Trap Data Management and Multi-Method Ecological Analysis

Fit the Random Encounter and Staying Time (REST / RAD-REST) model

Description

Estimates animal density from camera-trap data without individual recognition using the Random Encounter and Staying Time (REST) model of Nakashima, Fukasawa & Samejima (2018) and its RAD-REST extension (Nakashima et al. 2026). Parameters are estimated in a Bayesian framework by MCMC sampling with nimble.

Usage

ct_fit_rest(
  stay_data,
  station_data,
  activity_data,
  species,
  focal_area,
  model = c("REST", "RAD-REST"),
  stay_formula = Stay ~ 1,
  density_formula = ~1,
  passes_formula = ~1,
  stay_random_effect = NULL,
  stay_distribution = c("lognormal", "gamma", "weibull", "exponential"),
  activity_method = c("kernel", "mixture"),
  bandwidth_adjust = 1,
  mixture_components = 10,
  compare_models = FALSE,
  iterations = 5000,
  burnin = 1000,
  thin = 2,
  chains = 3,
  cores = 3,
  quiet = FALSE
)

Arguments

stay_data	Staying-time data, e.g. the output of ct_rest_stay(), with columns Station, Species, Stay (seconds) and Cens (1 = censored, 0 = fully observed).
station_data	Per-station encounter and effort data, e.g. the output of ct_rest_effort(). For model = "REST" it must contain Station, Species, Effort (days) and Y (passes). For model = "RAD-REST" it must instead contain N (videos) and the y_0, y_1, ... pass-count columns.
activity_data	Detection times in radians, e.g. the output of ct_rest_activity(), with columns Species and time.
species	Single species name to analyse (must appear in the data).
focal_area	Focal-area size in square metres. Either a single number (the same area at every camera) or the name of a column in station_data giving a camera-specific focal area per station.
model	Either "REST" or "RAD-REST".
stay_formula	Model formula for staying time. The left-hand side names the staying-time column, e.g. Stay ~ 1 or Stay ~ 1 + habitat.
density_formula	One-sided formula for density covariates, e.g. ~ 1 or ~ habitat. Density is latent, so the left-hand side is omitted.
passes_formula	One-sided formula for the number of passes. Used only when model = "RAD-REST"; ignored otherwise.
stay_random_effect	Optional column in stay_data giving a random effect on staying time. Default NULL (no random effect).
stay_distribution	Distribution for staying time: one of "lognormal", "gamma", "weibull" or "exponential". Ideally chosen with ct_rest_select_stay().
activity_method	How to estimate the activity proportion: "kernel" (fixed kernel density) or "mixture" (Bayesian von Mises mixture).
bandwidth_adjust	Bandwidth multiplier for activity_method = "kernel".
mixture_components	Maximum number of von Mises components for activity_method = "mixture".
compare_models	If TRUE, fit every combination of the density covariates and rank them by WAIC. If FALSE, fit only density_formula.
iterations, burnin, thin, chains, cores	MCMC settings: total iterations per chain, burn-in length, thinning interval, number of chains and CPU cores for parallel sampling.
quiet	If TRUE, suppress progress messages.

Details

The idea behind REST

A camera watches a small focal area of known size in front of the lens. If we know (i) how often animals pass through that area, (ii) how long they stay in it on average, and (iii) the fraction of the day they are active, density follows from a simple flow argument. Intuitively, the expected number of detected passes is

E[Y] = D \times S \times T \times p_{act} / \bar{t}

where D is density, S the focal-area size, T the survey duration, p_{act} the activity proportion and \bar{t} the mean staying time. Re-arranging gives the density estimator D = Y\,\bar{t} / (S\,T\,p_{act}). ct_fit_rest() fits every piece of this equation jointly so that uncertainty propagates into the density estimate.

Three sub-models are combined:

• Staying time (stay_data): a survival model. Animals still in the focal area when the video ends are right-censored; the chosen stay_distribution (lognormal/gamma/weibull/exponential) handles this.

• Encounters (station_data): the number of passes Y per station is modelled as negative-binomial (REST), or, for RAD-REST, the number of videos showing 0,1,2,... passes is modelled with a Dirichlet-multinomial so that miscounting of passes is accounted for.

• Activity (activity_data): the active fraction of the day, estimated either by kernel density (Rowcliffe et al. 2014) or a Bayesian von Mises mixture (Nakashima et al. 2026).

Value

An object of class ct_rest (a list) with:

waic

A tibble ranking the candidate density models by WAIC.

summary

A tibble of posterior summaries for density (individuals per km^2), mean staying time and, for RAD-REST, the mean number of passes.

samples

A coda::mcmc.list of posterior draws for the best model.

activity_curve

(mixture only) the estimated activity density curve.

References

Nakashima, Y., Fukasawa, K. & Samejima, H. (2018) Estimating animal density without individual recognition using information derived from camera traps. Journal of Applied Ecology, 55, 735-744.

Nakashima, Y. et al. (2026) Reducing data-processing effort in camera-trap density estimation: extending the REST model. Methods in Ecology and Evolution.

See Also

ct_rest_stay(), ct_rest_effort(), ct_rest_activity(), ct_rest_select_stay()

Examples

data(rest_detection)
data(rest_station)

# 1. Build the three inputs from raw detections (these steps run quickly)
stay <- ct_rest_stay(rest_detection, rest_station)
stations <- ct_rest_passes(rest_detection, rest_station, model = "REST")
stations <- ct_rest_effort(rest_detection, stations)
activity <- ct_rest_activity(rest_detection)

## Not run: 
# 2. Fit REST for the focal species (requires the 'nimble' package)
fit <- ct_fit_rest(
  stay_data = stay,
  station_data  = stations,
  activity_data = activity,
  species = "Red duiker",
  focal_area = 3.0, # focal-area size in m^2
  model = "REST",
  stay_distribution = "lognormal",
  iterations = 3000, burnin = 1000, chains = 2, cores = 2
)
fit
fit$summary   # density (individuals per km^2) and mean staying time

# RAD-REST instead: use pass-classified station data
stations_rad <- ct_rest_effort(
  detection_data = rest_detection,
  station_data = ct_rest_passes(rest_detection, rest_station, model = "RAD-REST")
)

fit_rad <- ct_fit_rest(
  stay_data = stay,
  station_data  = stations_rad,
  activity_data = activity,
  species = "Red duiker",
  focal_area = 3.0,
  model = "RAD-REST"
)

## End(Not run)

ct documentation built on Oct. 22, 2026, 1:07 a.m.