Generate a single-species record table with individual identification from camera trap images

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Description

The function generates a single-species record table containing individual IDs, e.g. for (spatial) capture-recapture analyses. It prepares input for the function spatialDetectionHistory.

Usage

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recordTableIndividual(inDir,
  hasStationFolders,
  IDfrom,
  cameraID,
  camerasIndependent,
  minDeltaTime = 0,
  deltaTimeComparedTo,
  timeZone,
  stationCol,
  writecsv = FALSE,
  outDir,
  metadataHierarchyDelimitor = "|",
  metadataIDTag,
  additionalMetadataTags,
  removeDuplicateRecords = TRUE
)

Arguments

inDir

character. Directory containing images of individuals. Must end with species name (e.g. ".../speciesImages/Clouded Leopard")

hasStationFolders

logical. Does inDir have station subdirectories? If TRUE, station IDs will be taken from directory names. If FALSE, they will be taken from image filenames (requires images renamed with imageRename).

IDfrom

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

cameraID

character. Should the function look for camera IDs in the image file names? If so, set to 'filename'. Requires images renamed with imageRename. If missing, no camera ID will be assigned and it will be assumed there was 1 camera only per station.

camerasIndependent

logical. If TRUE, cameras at a station are assumed to record individuals independently. If FALSE, cameras are assumed to be non-independent (e.g. in pairs). Takes effect only if there was more than 1 camera per station and cameraID = "filename".

minDeltaTime

numeric. time difference between observation of the same individual at the same station/camera to be considered independent (in minutes)

deltaTimeComparedTo

character. For two records to be considered independent, must the second one be at least minDeltaTime minutes after the last independent record of the same individual ("lastIndependentRecord"), or minDeltaTime minutes after the last record ("lastRecord")?

timeZone

character. timeZone must be an argument of OlsonNames

stationCol

character. Name of the camera trap station column in the output table.

writecsv

logical. Should the individual record table be saved as a .csv file?

outDir

character. Directory to save csv file to. If NULL and writecsv = TRUE, the output csv will be written to inDir.

metadataHierarchyDelimitor

character. The character delimiting hierarchy levels in image metadata tags in field "HierarchicalSubject". Either "|" or ":".

metadataIDTag

character. In custom image metadata, the individual ID tag name.

additionalMetadataTags

character. additional camera model-specific metadata tags to be extracted.

removeDuplicateRecords

logical. If there are several records of the same individual at the same station (also same camera if cameraID is defined) at exactly the same time, show only one?

Details

The function can handle a number of different ways of storing images. In every case, images need to be stored in a species directory first (e.g. using function getSpeciesImages). Station subdirectories are optional. Camera subdirectories are not allowed. This directory structure can be created easily with function getSpeciesImages.

As with species identification, individuals can be identified in 2 different ways: by moving images into individual directories ("Species/Station/Individual/XY.JPG" or "Species/Individual/XY.JPG") or by metadata tagging (without the need for individual directories: "Species/XY.JPG" or "Species/Station/XY.JPG").

minDeltaTime is a criterion for temporal independence of records of an individual at the same station/location. Setting it to 0 will make the function return all records. camerasIndependent defines if the cameras at a station are to be considered independent (e.g. FALSE if both cameras face each other and possibly TRUE if they face different trails). stationCol is the station column name to be used in the resulting table. Station IDs are read from the station directory names if hasStationFolders = TRUE. Otherwise, the function will try to extract station IDs from the image filenames (requires images renamed with imageRename.

If individual IDs were assigned with image metadata tags, metadataIDTag must be set to the name of the metadata tag group used for individual identification. metadataHierarchyDelimitor is "|" for images tagged in DigiKam and images tagged in Adobe Bridge/ Lightroom with the default settings. Manufacturer-specific Exif metadata tags such as "AmbientTemperature" or "MoonPhase" can be extracted if specified in additionalMetadataTags. Multiple names can be specified as a character vector as: c(Tag1, Tag2, ...). Because they are not standardized, function exifTagNames provides a vector of all available tag names. The metadata tags thus extracted may be used as individual covariates in spatial capture-recapture models.

Value

A data frame containing species records with individual IDs and additional information about stations, date, time and (optionally) further metadata.

Warning

Be sure to read the section on individual identification in the package vignette (https://CRAN.R-project.org/package=camtrapR/vignettes/SpeciesIndividualIdentification.html).

Af you use image metadata tags for identification, the tags must be written to the image metadata. The function cannot read tags from .xmp sidecar files. Make sure you set the preferences of your image management software accordingly. In DigiKam, go to Settings/Configure digiKam/Metadata. There, make sure "Write to sidecar files" is unchecked.

Author(s)

Juergen Niedballa

References

Phil Harvey's ExifTool http://www.sno.phy.queensu.ca/~phil/exiftool/

Examples

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 wd_images_ID <- system.file("pictures/sample_images_tagged/LeopardCat", package = "camtrapR")
 # missing space in species = "LeopardCat" is because of CRAN package policies

 if (Sys.which("exiftool") != ""){        # only run these examples if ExifTool is available

 rec.db.pbe <- recordTableIndividual(inDir                     = wd_images_ID,
                                        minDeltaTime           = 60,
                                        deltaTimeComparedTo    = "lastRecord",
                                        hasStationFolders      = FALSE,
                                        IDfrom                 = "metadata",
                                        camerasIndependent     = FALSE,
                                        writecsv               = FALSE,
                                        metadataIDTag          = "individual",
                                        additionalMetadataTags = c("Model", "Make"),
                                        timeZone               = "Asia/Kuala_Lumpur"
 )

 } else {                                # show function output if ExifTool is not available
 message("ExifTool is not available. Cannot test function")
 data(recordTableIndividualSample)
 }

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