filt: Delineating movement trips for central-place foraging species

In PhilBertrand/CPFMove: Delineating trips from GPS data for central-place foraging species

Description

This function was developped to conveniently delineate trips from raw GPS data for central-place foraging species. It also includes various "filtering" options to segment trips.

Usage

filt(
  pathF = ...,
  pathM = ...,
  metname = NULL,
  nbn = c("NULL"),
  gpst = NULL,
  ddep = NULL,
  drecap = NULL,
  colony = NULL,
  year = NULL,
  ring = NULL,
  tdep = NULL,
  trecap = NULL,
  timezone = NULL,
  Clong = NULL,
  Clat = NULL,
  speedTresh = NULL,
  FIX = NULL,
  FixInt = NULL,
  BuffColony = NULL,
  MinTripDur = NULL,
  Complete = FALSE,
  Interpolate = FALSE,
  filtNA = 1,
  metINFO = c(NULL),
  splt = TRUE
)

Arguments

pathF	path leading to your tracks
pathM	path leading to your metadata file
metname	a character string corresponding to the metadata file's name
nbn	character. Vector of "names" matching your raw GPS files (i.e. which are linked by the pathF argument). See details for more details
gpst	a character string corresponding to the metadata's column name containing the GPS type
ddep	a character string corresponding to the metadata's column name containing the date of departure
drecap	a character string corresponding to the metadata's column name containing the date of retrieval
colony	a character string corresponding to the metadata's column name containing individual colony attribution
year	a character string corresponding to the metadata's column name containing the year of sampling
ring	a character string corresponding to the metadata's column name containing the individual ring number
tdep	a character string corresponding to the metadata's column name containing the time of departure
trecap	a character string corresponding to the metadata's column name containing the time of retrieval
timezone	time zone in which data are recorded
speedTresh	numeric treshold used as speed cutoff for speed filtering (km/h)
FIX	a character string corresponding to the metadata's column name containing the numeric interval separating two locations in the GPS track
FixInt	numeric interval that should separate two locations in GPS tracks for interpolation (minutes; e.g. 2, 10)
BuffColony	numeric value indicating the buffer radius length around the colony (km)
MinTripDur	numeric value used for filtering trip by minimum trip duration (minutes)
Complete	logical; if TRUE, only complete trip will be kept
Interpolate	logical; if TRUE, tracks are interpolated
filtNA	numeric value which correspond of the filtering treshold for number of NAs generated along the interpolation. Between 0 and 1, whereas 1 correspond to no filtration at all (filtering only trips that are 100% full of NAs)
metINFO	character string(s). Used as a vector of name for the additional information you want to add to the final data frame for facilitating the subsequent analyses. However, names should fit the column name occuring in the metadata file (i.e. pathM)
splt	logical; if TRUE, the final trips are ordered as a list instead of an unique data frame. Default FALSE

Details

Raw GPS data (located via pathF) should be as .csv format. This version only include 4 types of GPS format 1) Catlog, 2) IGotU, 3) PathTracks and 4) Ecotone. If your file doesn't have any specific format, the gpst could be specified as IGotU (one line header, and the raw data in the second lines. However, one should make sure that the Latitude, Longitude, Date and Time are specified. Date could be supplied as character, as YYYY-MM-DD or MM/DD/YYYY and Time also as character as HH:MM:SS). Raw GPS data are expected to be in lat long coordinate system Distance between points are calculated via the Great Circle distance, computed via sp package

Value

the function return either a data frame (splt = FALSE) or a list (splt = TRUE) containing each bird trip as component Metrics for each trip are also computed, as;

• track_ID: is the unique track ID, should be named following each GPS raw file

• nbNA: indicating if the relative point is precise or if is was NA after the interpolation process

• ColonyDist: is the distance (km) separating the relative point and the colony

• PointDist: is the distance (km) separating two consecutive points (zi - zi-1)

• tripID: trip number in the trackID group

• birdTrip: unique bird trip identifyer

• TripLength: Total time length of the trip (min)

• TripDist: Cumulative distance flew by the bird for the specific trip

• Speed: Speed between t-1 and t in m/s

• nPoints: number of points composing the trip

• maxDist: maximum distance that the bird went in its trip, relative to the colony

• propNA: proportion of NAs in the trip. Convenient for filtering for reliability of the statistics

• BegPoint: colony or trip. Specify if the first point was at the colony or outside (i.e. trip). Convenient for filtering for completness

• EndPoint: colony or trip. Specify if the last point was at the colony or outside (i.e. trip). Convenient for filtering for completness

References

• Freitas, C., Lydersen, C., Ims, R.A., Fedak, M.A. and Kovacs, K.M. (2008) A simple new algorithm to filter marine mammal Argos locations Marine Mammal Science 24:315-325.

• McConnell, B.J., Chambers, C. and Fedak, M.A. (1992) Foraging ecology of southern elephant seals in relation to the bathymetry and productivity of the Southern Ocean. Antarctic Science 4:393-398.

Examples

## Not run: 
pathF <- c("C:/Users/User/files/allspecies/")
pathM <- c("C:/Users/User/files/metadata/")
metname <- c("meta.csv")
timezone <- c("GMT")

f <- filt(pathF, pathM, metname, nbn = c("year", "colony", "ring", "recapture"),
timezone, speedTresh = 90, gpst = "GPSType",
ddep = "deployment", drecap = "recapture", colony = "colony", year = "year",
ring = "ring", FIX = "FIX", tdep = "utc_deployment", trecap = "utc_retrieval",
Clong = "Clongitude", Clat = "Clatitude", BuffColony = 0.5, MinTripDur = 30, Complete = T, FixInt = 2,
Interpolate = T, filtNA = 0.9, metINFO = c("ring", "year", "species", "colony"), splt = F)

## End(Not run)

PhilBertrand/CPFMove documentation built on Nov. 22, 2020, 4:45 a.m.