sensTime: Sensitivity of minimum trip duration on trip delineation

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

Description

This function was developped to give basic visualization tools to facilitate the selection of the minimum trip length and the effect of this variation on the number of trip generated

Usage

sensTime(
  pathF = ...,
  pathM = ...,
  nbn = c("NULL"),
  iter = 50,
  metname = NULL,
  param = NULL,
  gpst = NULL,
  FIX = NULL,
  ddep = NULL,
  drecap = NULL,
  colony = NULL,
  year = NULL,
  ring = NULL,
  tdep = NULL,
  trecap = NULL,
  timezone = NULL,
  Clong = NULL,
  Clat = NULL,
  speedTresh = NULL,
  BuffColony = NULL,
  FixInt = NULL,
  Interpolate = FALSE,
  sorc = 0.05
)

Arguments

pathF	path leading to your tracks
pathM	path leading to your metadata file
nbn	character. Vector of "names" matching your raw GPS files (i.e. which are linked by the pathF argument). See details for more details
iter	the number of bootstrapping iterations (default = 50)
metname	a character string corresponding to the metadata file's name
param	vector of time treshold to be tested. These correspond to the different scenarios to be tested. Time is in hours format
gpst	a character string corresponding to the metadata's column name containing the GPS type
FIX	a character string corresponding to the metadata's column name containing the numeric interval separating two locations in the GPS track
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)
BuffColony	numeric value indicating the buffer radius length around the colony (km)
FixInt	numeric interval that should separate two locations in GPS tracks for interpolation (minutes; e.g. 2, 10)
Interpolate	logical; if TRUE, tracks are interpolated
sorc	numeric, proportion (0:1) treshold used for the second-order-rate of change

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

a list of object containing a data frame witht the main results of the sensitivity analysis and the associated figures. Figures are also showing the "second-order-rate of change" for each scenario. For the moment, the SORC is fixed to the 5% absolute variaiton of the total magnitude of the response (i.e. max(average(nTrip))). This is seen as a measure of "stability " of the response t among scenario t-1 and t+1.

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/philip/OneDrive/NP_Kontrakt/StromTracks/files/lomvi/")
pathM <- c("C:/Users/philip/OneDrive/NP_Kontrakt/StromTracks/metadata/")
metname <- c("meta_bjorn.csv")
timezone <- c("GMT")
param <- seq(0, 100, by = 10)

st <- sensTime(pathF, pathM, metname, nbn = c("year", "colony", "ring", "recapture"),
       timezone, iter = 300, param = param, 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 = 0.15, FixInt = 2, Interpolate = T, sorc = 0.01)

## End(Not run)

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