R: A Collection of ML Tools for Conservation Research

# A Collection of ML Tools for Conservation Research

## Documentation for package ‘animl’ version 1.1.0

- DESCRIPTION file.

## Help Pages

animl | Title
applyPredictions | Apply Classifier Predictions and Merge DataFrames
bestGuess | Select Best Classification From Multiple Frames
buildFileManifest | Extract exif Data and Create File Manifest
checkFile | Check for files existence and prompt user if they want to load
convertCoordinates | Convert bbox from Relative to Absolute Coordinates
cropImageGenerator | Tensorflow data generator that crops images to bounding box.
cropImageTrainGenerator | Tensorflow data generator for training that crops images to bounding box.
detectObject | Run MD on a Single Image
detectObjectBatch | Run MegaDetector on a batch of images
extractBoxes | Extract bounding boxes and save as new image from a batch of images
extractBoxesFromFlat | Extract crops from a single image represented by a processed dataframe
extractBoxesFromMD | Extract bounding boxes for a single image and save as new images
getAnimals | Return a dataframe of only MD animals
getEmpty | Return MD empty, vehicle and human images in a dataframe
imageAugmentationColor | Perform image augmentation through random color adjustments on an image/label pair.
imageAugmentationGeometry | Perform random geometric transformations on an image.
ImageGenerator | Tensorflow data generator that resizes images.
ImageGeneratorSize | Tensorflow data generator that resizes images and returns original image size.
imageLabel | Load image and return a tensor with an image and a corresponding label.
imageLabelCrop | Load image, crop and return a tensor with an image and a corresponding label.
imagesFromVideos | Extract frames from video for classification
loadData | Load .csv or .Rdata file
loadImage | Load an image and return the full size image as an image tensor.
loadImageResize | Load and resize an image and return an image tensor.
loadImageResizeCrop | Load, resize and crop an image and return an image tensor.
loadImageResizeSize | Load and resize an image and return an image tensor as well as a tensor with the original image size.
loadMDModel | Load MegaDetector model file from directory or file
parseMD | parse MD results into a simple dataframe
parseMDjson | converte the JSON file produced bye the Python version of MegaDetector into the format produced by detectObjectBatch
plotBoxes | Plot bounding boxes on image from md results
predictSpecies | Classifies Crops Using Specified Models
processYOLO5 | Process YOLO5 output and convert to MD format
resizePad | Resize an image with padding
saveData | Save Data to Given File
sequenceClassification | Leverage sequences to classify images
setupDirectory | Set Working Directory and Save File Global Variables
symlinkMD | Create SymLink Directories and Sort Classified Images Based on MD Results
symlinkSpecies | Create SymLink Directories and Sort Classified Images
symUnlink | Remove Symlinks
testMD | Select a Random Image and Run Through MegaDetector
updateResults | Title