Package index • sheepdog

Stage 1 - Validation data

Read BirdNET selection tables, select clips for manual review, and cut and pack them.

Classify the reviewed clips and summarise precision, thresholds, presence and retraining clips.

Split the clips among reviewers, measure their agreement and combine their verdicts.

Calibrate confidence scores into probabilities of true detection and build nightly detection histories.

calibrate(): Calibrate confidence scores and build detection histories
read_validations(): Read the validation tables for calibration
calibration_models(): Candidate calibration models
calibration_folds(): Assign cross-validation folds for calibration
compare_calibration_models(): Compare calibration models by cross-validation
select_calibration_model(): Select the calibration model
fit_calibration(): Fit the calibration model
calibration_effort(): Effort curve of the calibration
score_detections(): Score every detection with the calibration model
detection_history(): Nightly detection history
summarise_history(): Summarise the detection history by site and species
plot_calibration(): Plot the calibration curves

Fit the calibration with brms, check the prior and the fit, and propagate the uncertainty to the histories and the matrices.

calibration_prior(): Example prior for a Bayesian calibration model
prior_predictive_calibration(): Prior predictive calibration curves
calibration_diagnostics(): Convergence diagnostics of a Bayesian calibration model
calibration_sensitivity(): Prior and likelihood sensitivity of a Bayesian calibration model
plot_calibration_draws(): Calibration curves of posterior (or prior) draws
history_draws(): Nightly detection histories over posterior draws
community_matrices_draws(): Community matrices over posterior draws

Effort-standardised site x month matrices from calibrated histories.

build_community_matrices(): Write the community matrices
community_matrices(): Community matrices from the detection history
cell_status(): Status of each site x species cell for the community matrices
suggest_core_species(): Suggest the core species of the community matrices

sheepdog sheepdog-package: sheepdog: Sample, Validate and Calibrate 'BirdNET' Detections