Package: animl 3.3.1

Kyra Swanson

animl: A Collection of ML Tools for Species Detection and Classification in Camera Trap Images and Videos

Functions required to classify subjects within camera trap field data. The package can handle both images and videos. The authors recommend a two-step approach using Microsoft's 'MegaDector' model and then a second model trained on the classes of interest.

Authors:Kyra Swanson [aut, cre], Mathias Tobler [aut]

animl_3.3.1.tar.gz
animl_3.3.1.tar.gz(r-4.7-any)animl_3.3.1.tar.gz(r-4.6-any)
animl_3.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
animl/json (API)

# Install 'animl' in R:
install.packages('animl', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.18 score 9 scripts 490 downloads 53 exports 13 dependencies

Last updated from:e089767928. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK134
source / vignettesOK190
linux-release-x86_64OK136
wasm-releaseOK107

Exports:active_timesaniml_installaniml_install_instructionsbuild_file_manifestcheck_animl_pycheck_pythonclassifycompute_batched_distance_matrixcompute_distance_matrixcosine_distancecreate_pyenvdelete_pyenvdetectdownload_modeleuclidean_squared_distanceexport_camptrapdpexport_camtrapRexport_cocoexport_foldersexport_megadetectorexport_timelapseexport_train_val_testexport_yoloextract_framesextract_miew_embeddingsget_animalsget_emptyget_frame_as_imagelist_modelsload_animlload_class_listload_classifierload_dataload_detectorload_jsonload_miewload_yamlparse_detectionsplot_all_bounding_boxesplot_boxremove_diagonalremove_linksave_classifiersave_jsonsave_yamlsequence_calculationsequence_classificationsingle_classificationtest_classifiertrain_classifierupdate_animl_pyupdate_labels_from_foldersWorkingDirectory

Dependencies:herejsonlitelatticeMatrixpbapplypngrappdirsRcppRcppTOMLreticulaterlangrprojrootwithr

Readme and manuals

Help Manual

Help pageTopics
Get start and stop dates for each camera folder.active_times
Load animl-py if availableaniml_install
Installation Instructions for animl-r Python dependenciesaniml_install_instructions
File Management Modulebuild_file_manifest
Check if animl-py can connect to exiftool and CUDAcheck_animl_py
Check for files existence and prompt user if they want to loadcheck_file
Check that the python version is compatible with the current version of animl-pycheck_python
Infer Species for Given Detectionsclassify
Computes the distance matrix in a batched manner to save memory.compute_batched_distance_matrix
A wrapper function for computing distance matrix.compute_distance_matrix
Computes cosine distance of two sets of matricescosine_distance
Install python if necessary and create the environment animl_envcreate_pyenv
Delete the animl_env environmentdelete_pyenv
Apply MegaDetector to a Given Batch of Imagesdetect
Download specified model to the given directory.download_model
Computes euclidean squared distance of two sets of matriceseuclidean_squared_distance
Export a manifest to camtrapdp formatexport_camptrapdp
Export data into sorted folders organized by stationexport_camtrapR
Converts the .csv file to a COCO-formatted .json file.export_coco
Create SymLink Directories and Sort Classified Imagesexport_folders
Converts the .csv file to the MD-formatted .json file.export_megadetector
Converts the Manifests to a csv file that contains columns needed for TimeLapse conversion in later stepexport_timelapse
Splits the manifest into training validation and test datasets for trainingexport_train_val_test
Export a manifest to YOLO format for model trainingexport_yolo
Extract frames from video for classificationextract_frames
Compare to Animl-Py version, ignoring patch numberextract_major_minor
Extract Embeddings from MiewIDextract_miew_embeddings
Return a dataframe of only MD animalsget_animals
Return MD empty, vehicle and human images in a dataframeget_empty
Given a video path, return a specific frame as an RGB imageget_frame_as_image
List available models for download.list_models
Load animl-py if availableload_animl
Load class list .csv fileload_class_list
Load a Classifier Model and Class_listload_classifier
Load .csv or .Rdata fileload_data
Load an Object Detectorload_detector
Load data from a JSON file.load_json
Load MiewID modelload_miew
Load data from a YAML file.load_yaml
Parse MD results into a simple dataframeparse_detections
Plot all bounding boxes in a manifestplot_all_bounding_boxes
Plot bounding boxes on image from md resultsplot_box
Removes the diagonal elements from a square matrix.remove_diagonal
Remove Sorted Linksremove_link
Save model state weightssave_classifier
Save Data to Given Filesave_data
Save data to a JSON file.save_json
Save data to a YAML filesave_yaml
Calculate sequence from timestampssequence_calculation
Leverage sequences to classify imagessequence_classification
Get Maximum likelihood label for each Detectionsingle_classification
Test a model with a Config filetest_classifier
Model Trainingtrain_classifier
Update animl-py version for the given environmentupdate_animl_py
Udate Results from File Browserupdate_labels_from_folders
Set Working Directory and Save File Global VariablesWorkingDirectory