R/data.r

In ocean-tracking-network/glatos: A package for the Great Lakes Acoustic Telemetry Observation System

#' @title [Deprecated] A SpatialPolygonDataFrame with Great Lakes coastline and some major
#'   tributaries.
#'
#' @description A SpatialPolygonDataFrame with Great Lakes coastline and some
#'   major tributaries. This is used as a default map background in several
#'   \link{glatos} functions.
#'
#' @details This dataset is deprecated and will be removed in a future version.
#'   Use \code{\link{great_lakes_polygon}} instead.
#'
#' @author Todd Hayden
"greatLakesPoly"


#' @title An sf POLYGON object with Great Lakes coastline
#'
#' @description An sf POLYGON object with Great Lakes coastline, used as default
#'   map background in several [glatos] functions.
#'
#' @details Created from [shoreline] shapefile (see
#'   'data-raw/data-great_lakes_polygon.r).
#'
#' @examples
#' \dontrun{
#' plot(sf::st_geometry(great_lakes_polygon))
#' }
#'
#' @author Todd Hayden (coerced to sf via by C. Holbrook)
"great_lakes_polygon"


#' @title A `TransitionLayer` of the Great Lakes that only prevents transition
#'   over land
#'
#' @description A TransitionLayer object that only allows transitions to occur
#'   within water (i.e., prohibits movement onto land).
#'
#' @details This dataset was developed for non-linear interpolation of fish
#'   movement paths from telemetry data and is used by default in
#'   [interpolate_path].
#'
#' @details Created from [great_lakes_polygon]; see
#'   'data-raw/data-greatLakesTrLayer.r'.
#'
#' @examples
#' \dontrun{
#' raster::plot(raster::raster(greatLakesTrLayer))
#' }
#'
#' @seealso [interpolate_path], [gdistance]
#' @author Todd Hayden (rebuilt by C. Holbrook)
"greatLakesTrLayer"


#' @title An sf POLYGON object with coastline of Higgins Lake
#'
#' @description An sf POLYGON object with coastline of Higgins Lake, Michigan.
#' Used as an example of a polygon representing a water body.
#'
#' @author Chris Holbrook
"higgins_lake_polygon"


#' @title An sf POLYGON object with coastline of Flynn Island
#'
#' @description An sf POLYGON object with coastline of Flynn Island; and
#' island within Higgins Lake, Michigan.
#' Used as an example of a polygon representing a body of land (as opposed to
#' water body).
#'
#' @author Chris Holbrook
"flynn_island_polygon"


#' Sea Lamprey positions from Lake George, St. Marys River, 2012
#'
#' Sea Lamprey positions from a positional acoustic telemetry array in Lake
#' George, North Channel of the St. Marys River during the 2012 spawning year.
#'
#' @details Data were collected as part of the GLATOS project SMRSL
#'   <http://glatos.glos.us/home/project/SMRSL>
#'
#' @details Positions were calculated using the Vemco Positioning System.
#'
#' @format A data frame with 21043 rows and 14 variables:
#' \describe{
#'   \item{DETECTEDID}{transmitter identifier (channel, frequency, code space,
#'      and ID code)}
#'   \item{DATETIME}{position timestamp, in UTC}
#'   \item{X,Y}{horizontal and vertical position on local grid, in meters}
#'   \item{D}{assumed depth at time of detection, in meters (NOT from
#'      depth/pressure sensor)}
#'   \item{LAT,LON}{position latitude and longitude, decimal degrees (west
#'      is negative); CRS: WGS84}
#'   \item{n}{?}
#'   \item{HPE}{horizontal position error; calculated by VEMCO}
#'   \item{HPEm}{horizontal position error, in meters; calculated by VEMCO}
#'   \item{TEMP}{temperature at time of detection (from temperature sensor)}
#'   \item{DEPTH}{depth at time of detection (from pressure sensor)}
#'   \item{ACCEL}{acceleration at time of detection (from accelerometer)}
#'   \item{DRX}{receivers that detected the associated transmission}
#' }
#'
#' @source Chris Holbrook, US Geological Survey (cholbrook@usgs.gov)
#'
"lamprey_tracks"

#' Detection range data set
#'
#' Sample detection range data set from Lake Superior.
#'
#' @details Data from a stationary detection range test conducted in 2018. Data
#'   are in standard GLATOS detection export format and are intened to
#'   accompany detecton range analysis vignette.
#'
#' @format A data frame with 58309 rows and 30 variables
#'
#' @source F. Zomer, T. Hayden
#'
"range_detection"

#' A schema for Innovasea Fathom (VDAT) CSV files
#'
#' A schema for Innovasea Fathom (VDAT) CSV files, produced by 'vdat.exe'
#' (Fathom Connect) or [vdat_convert()].
#'
#' @details A list of lists of data frames that define record types (e.g.,
#'   `DIAG`, `DET`, `EVENT_OFFLOAD`), columm names (e.g. `Device Time (UTC)`,
#'   `Time`), and data types (e.g., `character`, `POSIXct`) for
#'   comma-separated-values text file containing data produced by Innovasea's
#'   `vdat.exe` (packaged with Fathom Connect software).
#'
#' @details This is used to enforce column names and data types in
#'   [read_vdat_csv()].
#'
#' @author C. Holbrook
#'
"vdat_csv_schema"

#' Detection Efficiency data set
#'
#' Sample detection efficiency data set from Lake Papineau, Quebec, Canada.
#'
#' @details Data is from a preliminary range test, where tags were deployed at
#' set distances away from a VR2W receiver for 24 hours. Once downloaded the vrl
#' files were used in Vemco's Range Testing Software to produced this dataset.
#'
#' @format A data frame with 7 rows and 5 variables
#' \describe{
#'   \item{distance_m}{distance away from the receiver in meters}
#'   \item{avg_percent}{average detection efficiency}
#'   \item{std_dev}{standard deviation of detection efficiency}
#'   \item{avg_percent_d}{average detection efficiency in decimal form needs
#'   to be created by dividing \code{avg_percent} by 100}
#'   \item{intercept}{y-intercept used for third order polynomial, set at 100.
#'   Needs to be added to the original dataframe}
#'   }
#'
#' @source B.L. Hlina
#'
"sample_detection_efficiency"