Reformat Movebank to matrix format — reformat_movebank_to

Takes in regularly sampled GPS data in Movebank format (i.e. data frame with specified columns - see below) and converts it into the standard matrix form used by the cocomo package.

Usage

reformat_movebank_to_matrix(
  movebank_data,
  output_file_path = NULL,
  ids = NULL,
  data_chunks = NULL,
  seconds_per_time_step = 1,
  start_date = NULL,
  end_date = NULL,
  start_time = NULL,
  end_time = NULL,
  utm_zone = NULL,
  hemisphere = NULL,
  output_utm = T,
  output_latlon = T,
  use_UTC = T,
  local_timezone = NULL
)

Arguments

movebank_data: data frame that must include the columns 'timestamp (timestamp in UTC, must be character string of format YYYY-MM-DD HH:MM:SS.SSS), 'individual.local.identifier' (individual id of the tracked animals), 'location.long' (longitude coordinate), and 'location.lat (latitude coordinate). Can optionally also include the column 'study.local.timestamp' (local timestamp for each GPS fix, must be character string of format YYYY-MM-DD HH:MM:SS.SSS).
output_file_path: full path to the desired output file (must be a .RData file)
ids: optional ids data frame which if specified will determine the order of rows in matrices (code column in ids needs to match to individual.local.identifier column in movebank_data)
data_chunks: data frame with columns start and end specifying starting and ending datetimes (in POSIXct format - with time zone!) for each contiguous chunk of data. overrides other specified start and end times / dates.
seconds_per_time_step: sampling interval of GPS fixes (in seconds)
start_date: a character string specifying the starting date for data sampled in a daily basis, only used if data_chunks = NULL, format must be 'YYYY-MM-DD'
end_date: a character string specifying the end date for data sampled in a daily basis, only used if data_chunks = NULL, format must be 'YYYY-MM-DD'
start_time: a character string specifying the start time for data sampled on a daily basis, only used if data_chunks = NULL, format must be 'HH:MM:SS'
end_time: a character string specifying the end time for data sampled on a daily basis, only used if data_chunks = NULL, format must be 'HH:MM:SS'
utm_zone: numeric UTM zone (only needed if output_utm = T and if movebank_data does not have utm_easting and utm_northing columns)
hemisphere: hemisphere ('north' or 'south') for UTM calculations (only needed if output_utm = T and if movebank_data does not have utm_easting and utm_northing columns)
output_utm: whether to output xs and ys matrices (T or F)
output_latlon: whether to output lats and lons matrices (T or F)
use_UTC: if T (default) use UTC time rather than local time
local_timezone: specify local timezone string, if not using UTC (use_UTC = F)

Value

Saves a file to the location output_file_path containing the objects: timestamps (vector of timestamps in POSIXct format, of length n_times), ids (data frame containing either the original ids data or a single code column with the id from individual.local.identifier column in movebank_data), xs (n_inds x n_times matrix of UTM eastings for all individuals at each time point), ys (n_inds x n_times matrix of UTM northings for all individuals at each time point), lons (n_inds x n_times matrix of longitudes for all individuals at each time point), and lats (n_inds x n_times matrix of longitudes for all individuals at each time point). xs and ys are only saved if output_utm = T. lons and lats are only saved if output_lonlat = T

Author

Ariana Strandburg-Peshkin (primary author)

NOT YET CODE REVIEWED