ct_fit_encounter_response: Fit a conditional encounter-response model for camera-trap...

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

Fit a conditional encounter-response model for camera-trap events

Description

Estimates whether encounters of a response species become more or less likely in the minutes to hours after encounters of a trigger species at the same camera. Unlike a diel overlap coefficient – which only compares two species' marginal activity curves – this is a directed, time-lagged association: it contrasts the response encounter rate in successive windows after a trigger with that camera's expected rate at the same time of day and month. It quantifies association, not causation.

Usage

ct_fit_encounter_response(
  data,
  deployment,
  trigger,
  response,
  species_column,
  cam_column,
  datetime_column,
  start_column,
  end_column,
  interval = 15 * 60,
  lag_breaks = c(0, 30 * 60, 2 * 3600, 6 * 3600),
  independence = 2 * 60,
  engine = c("glm", "glmm"),
  n_boot = NULL,
  interval_sensitivity = NULL,
  seed = NULL
)

Arguments

data	A data frame with one row per camera-trap record (the observation data).
deployment	A data frame of actual camera deployment intervals. It must contain the camera ID, start, and end columns. Intervals for the same camera may not overlap.
trigger	Character scalar naming the species whose event initiates a response window.
response	Character scalar naming the species whose encounter rate is modelled.
species_column	Unquoted column in data giving the species name.
cam_column	Unquoted column giving the camera ID. This column must be present, with the same name, in both data and deployment so that records can be matched to their deployment intervals.
datetime_column	Unquoted column in data giving the event date-time.
start_column, end_column	Unquoted columns in deployment giving the deployment interval start and end date-times respectively.
interval	Width of analysis intervals in seconds. It must not exceed the narrowest response-lag window.
lag_breaks	Numeric vector of lag boundaries in seconds. The default estimates associations for 0–30 minutes, 30 minutes–2 hours, and 2–6 hours after a trigger. Time after the final boundary is the reference.
independence	Minimum number of seconds between retained records of the same species at the same camera. Defaults to 2 minutes; set to 0 to retain every record. See Details for why this default is smaller than the value used for activity-level estimation.
engine	Fitting engine. "glm" (default) fits a camera-stratified quasi-Poisson GLM with camera fixed effects and a camera-block bootstrap. "glmm" fits a Poisson/negative-binomial mixed model with camera (and, where present, deployment) random intercepts, using glmmTMB if installed and otherwise lme4.
n_boot	Number of camera-block bootstrap replicates used for percentile confidence intervals. If NULL (default) it is set to 199 for engine = "glm" and to 0 for engine = "glmm". Set to 0 to return model-based intervals only.
interval_sensitivity	Optional numeric vector of alternative interval widths (seconds). When supplied, the lag-specific rate ratios are refitted at each width and returned in ⁠$sensitivity⁠, so the reader can judge how far the conclusion depends on the binning choice. Each value must not exceed the narrowest lag window.
seed	Optional integer seed for the bootstrap.

Details

What is being approximated. The quantity of interest – "does an encounter of species A raise or lower the short-term encounter intensity of species B?" – is formally a mutually exciting (Hawkes-type) point process. Fitting such a process directly is data-hungry and fragile with sparse camera-trap detections, so this function uses a transparent discrete-time approximation: camera uptime is sliced into short intervals, the number of response detections per interval is modelled as a count, and time-since-last-trigger is entered as a step function (lag_breaks). Because it is an approximation, the interval width matters – always inspect interval_sensitivity before interpreting an effect.

How confounders are handled. Camera uptime enters as an offset so unequal effort is accounted for; circular (harmonic) terms hold the shared diel activity curve constant; a month factor absorbs broad seasonal variation; and each camera contributes only within-camera temporal contrasts, so time-invariant differences in habitat, placement and baseline abundance are differenced out. With engine = "glm" cameras are fixed effects; with engine = "glmm" they are random intercepts (partial pooling), which is more efficient with many sparse cameras and avoids the incidental-parameter problem of many fixed effects.

Inference. Successive intervals at one camera are serially correlated and response detections cluster in time. A quasi-Poisson dispersion correction rescales for overdispersion but not for this autocorrelation, so model-based intervals from engine = "glm" are optimistic. The default inference is therefore a camera-block bootstrap (n_boot), which resamples whole cameras and so respects within-camera dependence; treat those intervals as the primary uncertainty. With engine = "glmm" the camera random effect already propagates between-camera variance, so the bootstrap is skipped.

The dominant limitation – shared transient drivers. The controls above remove stable and diel/seasonal confounding, but they cannot remove episodic shared drivers: a fruiting tree, a waterhole, a prey pulse, moonlight or a weather front can draw both species independently within the same hours and manufacture an apparent "response" with no behavioural interaction whatsoever. Detection is also a thinned, imperfect observation of presence, so a shift in detection rate need not reflect a shift in true site use. For these reasons the result is an association conditional on the fitted baseline, never evidence of a direct behavioural or causal effect. Corroborate with randomization or simulation checks, and never treat deployments reconstructed from first/last detections as camera uptime.

Independence filtering. independence collapses repeat detections of the same species at the same camera that fall within a short window – these are usually one animal lingering in front of the sensor, i.e. one biological event. Note the tension with this model: unlike activity-level estimation (where 30 min is conventional), a long filter here would erase exactly the rapid successive detections that a short-term response would produce. The default is therefore deliberately small (2 minutes): long enough to merge a single pass into one event, short enough to preserve genuine reactivity in the first lag window. Set independence = 0 to keep every record.

Value

An object of class ct_encounter_response containing the fitted model, lag-specific rate ratios, analysis-interval data, an optional bin-width sensitivity table, and settings. A rate ratio below one indicates fewer response encounters than expected after a trigger, conditional on the fitted baseline terms.

References

Hawkes, A. G. (1971). Spectra of some self-exciting and mutually exciting point processes. Biometrika, 58(1), 83–90. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/biomet/58.1.83")}

Ridout, M. S., & Linkie, M. (2009). Estimating overlap of daily activity patterns from camera trap data. Journal of Agricultural, Biological, and Environmental Statistics, 14(3), 322–337. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1198/jabes.2009.08038")}

Examples

## Not run: 
data(ACBR)
fit <- ct_fit_encounter_response(
  data = ACBR$acbr_data,
  deployment = ACBR$deployment,
  trigger = "Cercopithecus mona", response = "Tragelaphus spekii",
  species_column = species, cam_column = cam, datetime_column = datetime,
  start_column = start, end_column = end
)
summary(fit)

# Random-effects engine plus a bin-width sensitivity check
fit_glmm <- ct_fit_encounter_response(
  data = ACBR$acbr_data,
  deployment = ACBR$deployment,
  trigger = "Cercopithecus mona", response = "Tragelaphus spekii",
  species_column = species, cam_column = cam, datetime_column = datetime,
  start_column = start, end_column = end,
  engine = "glmm",
  interval_sensitivity = c(5 * 60, 10 * 60, 30 * 60)
)
fit_glmm$sensitivity

## End(Not run)

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