R/CameraTrapDataAccess.R

In DenaJGibbon/behaviouR: An R Package for Online Teaching of Fundamental Concepts in Behavior and Ecology

#' @title Snapshot Serengeti camera trap access
#' @description Function to access Snapshot Serengeti camera trap photos on the Labeled Information Library of Alexandria: Biology and Conservation http://lila.science/datasets/snapshot-serengeti
#'
#' @param urlpath location of Snapshot Serengeti database
#' @param season which season to query; options are 1-4, 6-8,10,11
#' @param AnimalID which animal photos to download
#' @param NumPhotos the number of photos to download
#' @param create.dir logical; create a new directory (TRUE) or save to current temp directory (FALSE); to see temp directory use tempdir()
#' @importFrom utils download.file
#' @return a dataframe with image metadata and downloaded images
#' @export
#'
#' @examples
#' \donttest{CombinedAnimalDF <- CameraTrapDataAccess(urlpath=
#' 'https://lilablobssc.blob.core.windows.net/snapshotserengeti-unzipped/',
#' season= list(1,2,3),AnimalID='leopard', NumPhotos= 50,create.dir=TRUE)}


CameraTrapDataAccess <-
  function(urlpath = 'https://lilablobssc.blob.core.windows.net/snapshotserengeti-unzipped/',
           season = list(1, 2),
           AnimalID = 'leopard',
           NumPhotos = 5,
           create.dir = '') {

    if (create.dir == '') {
      stop('Value for create.dir missing; user must specify where to store images')
    }

    if (season== 5 | season== 9) {
      # print('Value for create.dir missing; user must specify where to store images')
      stop('The specified season is not available; please choose a different season')
    }

    if (create.dir == TRUE) {
      dir.create(file.path(paste('CameraTrapPhotos', AnimalID, sep = '')), showWarnings = FALSE)
      FilePathPhotos <-
        paste('CameraTrapPhotos', AnimalID, .Platform$file.sep, sep = '')
    }

    if (create.dir == FALSE) {
      FilePathPhotos <- getwd()
    }

    UpdatedCameraTrapDF <- data.frame()
    for (a in 1:length(season)) {
      dataSet <- paste('season', season[a], 'df', '.rda', sep = '')

      githubURL <-
        paste(
          'https://github.com/DenaJGibbon/behaviouRdata/raw/master/data/',
          dataSet,
          sep = ''
        )
      CameraTrapDf <- get(load(url(githubURL)))
      CameraTrapDf

      # Loop to download camera trap photos for the first animal
      file.index <- which(CameraTrapDf$category_id == AnimalID)

      if (length(file.index) > NumPhotos) {
        file.index <-  sample(file.index, NumPhotos, replace = FALSE)
      }


      for (b in 1:length(file.index)) {
        tryCatch({
          filepath <-
            paste(CameraTrapDf$image_id[file.index[[b]]], '.JPG', sep = '')
          whichseason <- CameraTrapDf$season[file.index[[b]]]
          location <- CameraTrapDf$location[file.index[[b]]]
          filename <-
            paste(FilePathPhotos,
                  AnimalID,
                  '_',
                  whichseason,
                  '_',
                  location,
                  '.JPG',
                  sep = '')
          download.file(url = paste(urlpath, filepath, sep = ''),
                        destfile = filename)
          TempRow <-
            cbind.data.frame(CameraTrapDf[file.index[[b]],], filename)
          UpdatedCameraTrapDF <-
            rbind.data.frame(UpdatedCameraTrapDF, TempRow)
        }, error = function(e) {
          cat("ERROR :", conditionMessage(e), "\n")
        })
      }
    }

    return(UpdatedCameraTrapDF)
  }