camtrapR (version 0.99.0)

getSpeciesImages: Collect all images of a species

Description

This function will fetch all images of a particular species from all camera trap stations and copies these images to a new location. Species IDs can be read from species directories or from metadata. Earlier in the workflow, images should have been renamed (with imageRename) to give images unique file names based on station ID and date/time.

Usage

getSpeciesImages(species, 
  inDir, 
  outDir, 
  createStationSubfolders = FALSE,
  IDfrom,
  metadataSpeciesTag,
  metadataHierarchyDelimitor = "|"
  )

Arguments

species

character. Species whose images are to be fetched

inDir

character. Directory containing identified (species level) camera trap images sorted into station subdirectories (e.g. inDir/StationA/)

outDir

character. Directory in which to save species images (in a species subdirectory)

createStationSubfolders

logical. Save images in station directories within the newly created species directory in outDir?

IDfrom

character. Read species ID from image metadata ("metadata") of from species directory names ("directory")?

metadataSpeciesTag

character. The species ID tag name in image metadata (if IDfrom = "metadata").

metadataHierarchyDelimitor

character. The character delimiting hierarchy levels in image metadata tags in field "HierarchicalSubject". Either "|" or ":" (if IDfrom = "metadata").

Value

• A data.frame with old and new file locations and the copy status (copy_ok; TRUE if copying was successful).

Details

The function can derive species IDs both from a directory structure like this > inDir/Station/Species or > inDir/Station/Camera/Species, or from species metadata tags. In the latter case, only station directories are needed. In any case, the argument species must match species IDs (either directory names or species metadata tags). Before running the function, first rename the images using function imageRename to provide unique file names and prevent several images from having the same name (if generic names like "IMGP0001.jpg" are used). The function will not copy images if there are duplicate filenames to prevent overwriting images unintentionally.

Examples

# define image directory
wd_images_ID <- system.file("pictures/sample_images", package = "camtrapR")
wd_images_ID_copy <- file.path(tempdir(), "sample_species_images")

species_to_copy <- "VTA"    # = Viverra tangalunga, Malay Civet

specImagecopy <- getSpeciesImages(species                 = species_to_copy,
                                  inDir                   = wd_images_ID,
                                  outDir                  = wd_images_ID_copy,
                                  createStationSubfolders = FALSE,
                                  IDfrom                  = "directory"
                                  )