R/move2KBA.r

In steffenoppel/track2iba: Identifying Important Areas from Animal Tracking Data

## move2kba   ##################################################################

#' Import Movebank data sets for track2KBA analysis
#'
#' \code{move2KBA} imports data from Movebank repository and re-formats them to
#' fit track2KBA functions.
#'
#' This is a wrapper function for functions in \code{move} package to import and
#'  format tracking data from Movebank. It also attains study site location data
#'   (lat/lons).
#'
#' @param movebankID character or numeric. Character: full name of the study, as
#' stored on Movebank. Numeric: Movebank ID of the study. Both can be obtained
#'  on the Study Details page on Movebank (\url{https://www.movebank.org}) or with
#'  \code{\link[move]{getMovebankID}}.
#' @param user Username associated with your Movebank account.
#' @param password password associated with your Movebank username.
#' @param filename character. File path to .csv downloaded
#' from \url{https://www.movebank.org}.
#'
#' @return Returns a list object of length two, containing tracking data
#' (accessed using: \code{dataset$data}) and study site location information
#' (accessed using: \code{dataset$site}) .
#'
#' @seealso \code{\link[move]{getMovebankData}} for data download,
#' \code{\link[move]{getMovebank}} for study metadata,
#' \code{\link[move]{getMovebankID}} for getting study ID number
#'
#' @examples
#' \dontrun{
#'
#' dataset <- move2KBA(movebankID=xxx, user="myusername", password="mypassword")
#'
#' tracks <- dataset$data  ## access tracking data
#' site   <- dataset$site    ## access study site coordinates
#'}
#'
#' @export
#' @importFrom move movebankLogin getMovebankID getMovebankData getMovebank
#' @importFrom magrittr %>%
#' @importFrom dplyr select rename arrange

move2KBA <- function(movebankID=NULL, user=NULL, password=NULL, filename=NULL) {

  ### IMPORT FROM MOVEBANK IF CREDENTIALS SUPPLIED ----------------------------
  if (any(!is.null(movebankID), !is.null(user), !is.null(password))) {
    loginStored <- move::movebankLogin(username = user, password = password)

    if (is.character(movebankID)) {# convert study name to numeric movebankID
    movebankID <- move::getMovebankID(movebankID, loginStored)
    }

    ### IMPORT FROM MOVEBANK
    input <- move::getMovebankData(study = movebankID, login = loginStored)
    try(
      study <- move::getMovebank(entity_type = "study",
      login = loginStored, study_id = movebankID),
      silent = FALSE
      )

    ### EXTRACT THE IMPORTANT COLUMNS AND RENAME ------------------------------
    tracks <- input@data %>%
      dplyr::select(
        .data$deployment_id, .data$timestamp,
        .data$location_lat, .data$location_long) %>%
      rename(ID = .data$deployment_id, DateTime = .data$timestamp,
        Latitude = .data$location_lat, Longitude = .data$location_long) %>%
      arrange(.data$ID, .data$DateTime)

    ### IMPORT FROM FILE IF NO LOGIN IS PROVIDED ------------------------------
  } else {
    if (is.null(filename)) stop (
    "No filename provided, credentials for Movebank login are missing. Please
    provide a numeric Movebank ID, user and password")
    input <- utils::read.csv(filename, stringsAsFactors = FALSE)

    ### EXTRACT THE IMPORTANT COLUMNS AND RENAME
    tracks <- input %>%
      dplyr::select(
        .data$`individual.local.identifier`,
        .data$timestamp,
        .data$`location.lat`, .data$`location.long`) %>%
      rename(
        ID = .data$`individual.local.identifier`,
        DateTime = .data$timestamp,
        Latitude = .data$`location.lat`, Longitude = .data$`location.long`) %>%
      arrange(.data$ID, .data$DateTime)

  }

  ### EXTRACT COLONY INFORMATION FROM EITHER TRACKS OR FIRST LINE IN TRACKS ---
  if ("study" %in% ls()) {
    Colony <- study %>%
      dplyr::select(.data$main_location_long, .data$main_location_lat) %>%
      rename(
        Longitude = .data$main_location_long, Latitude = .data$main_location_lat
        )
  } else {
    Colony <- tracks[1, ] %>% dplyr::select(.data$Longitude, .data$Latitude)
    message(
    "Study had no information on colony location. Used first locations as colony
    location. If a different location desired, please manually specify.")}

  tracks_list <- list(data = tracks, site = Colony)

  return(tracks_list)
}