animl 3.3.1

New Functions for 3.3

• active_times(): Get start and stop dates for each camera folder from a manifest or directory.
• export_yolo(): Export a manifest to YOLO format for model training, including train/val/test splits.
• export_camptrapdp(): Export a manifest to Camera Trap Data Package (camtrapdp) format.
• export_camtrapR(): Export data into sorted folders organized by station in camtrapR format.

API Changes

Detection

• load_detector(): Expanded supported model_type values to include "mdv5", "mdv6", "mdv1000-cedar", "mdv1000-larch", "mdv1000-sorrel", "mdv1000-redwood", "mdv1000-spruce", "yolov5", "yolo", and "onnx".
• Detection category mapping (MD_LABELS): numeric categories in the category column now follow the MegaDetector convention — 0 = empty, 1 = animal, 2 = human, 3 = vehicle. This mapping is used consistently by get_empty(), get_animals(), and the visualization functions.
• get_empty(): Returns all non-animal frames (category != 1), including empty (0), human (2), and vehicle (3) detections. NA categories are treated as empty (0). Adds prediction and confidence columns to the result.
• get_animals(): Returns only frames where category == 1 (animal detections).

Classification

• load_classifier(): Changed default architecture from "CTL" to "efficientnet_v2_m".
• classify(): Now automatically unpacks a model if it is passed as a list.
• single_classification(): Renamed parameter predictions_raw to predictions_output; added file_col and failed_files parameters.

Visualization

• plot_box() and plot_all_bounding_boxes(): Replaced label_col parameter with classifier_label_col and added detector_category_col parameter (default "category") for more granular control over bounding box display. The detector_category_col column is used to color-code and label boxes by detection category (0=empty, 1=animal, 2=human, 3=vehicle).

File Management

• sequence_calculation(): Renamed parameter datetime_col to timestamp_col; added sort_columns and file_col parameters.

Export

• export_folders(): Added timestamp_col and station_col parameters.
• remove_link(): Fixed bug where pbapply was used instead of pbsapply.
• export_megadetector(): Output JSON now includes a detection_categories field with the standard category mapping (0=empty, 1=animal, 2=human, 3=vehicle).

Re-ID

Distance metric functions (remove_diagonal(), euclidean_squared_distance(), cosine_distance(), compute_distance_matrix(), compute_batched_distance_matrix()) are now implemented natively in R, removing the dependency on the Python back-end for these calculations.

Other Changes

• video_processing: Increased default num_workers to 4 for faster video processing.
• install_animl(): Added conda environment handling for more flexible Python environment management.
• Added comprehensive testthat unit tests for all core functions.
• not loading conda env correctly (returning Null read as error)
• update classifier and detector docs to reflect named object output
• build_file_manifest() now returns posixct for datetime, createdate, filemodifydate
• fix interactive messaging for .onLoad and .onAttach