prefilter: Prepare Argos data for fitting state-space model

In foieGras: Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Movement Behaviour

Description

prefilter (1) determines Argos data type (LS or KF); (2) converts dates to POSIXt & identifies observations with duplicate dates; (3) orders observations in time; (4) removes duplicate observations; (5) removes observations occurring within 60 s of one another (keeps first); (6) shifts longitudes that straddle -180,180 to 0,360 and vice-versa; (7) projects lonlat coords to mercator x,y coords (in km); (8) adds location error multiplication factors based on Argos location class (for type LS); (9) uses a trip::sda to identify potential outlier locations. trip::sda is a fast, vectorized version of argosfilter::sdafilter see ?argosfilter::sdafilter for details on implementation

Usage

prefilter(
  data,
  vmax = 5,
  ang = c(15, 25),
  distlim = c(2500, 5000),
  spdf = TRUE,
  min.dt = 60,
  emf = NULL
)

Arguments

data	input data, must have 5 (LS), or 8 (KF) columns (see details)
vmax	max travel rate (m/s)
ang	angles of outlier location "spikes" (default is c(15,25) deg); ang = NA turns off trip::sda filter in favour of trip::speedfilter
distlim	lengths of outlier location "spikes" (default is c(2500, 5000) m); distlim = NA turns off trip::sda filter in favour of trip::speedfilter. Either ang = NA or distlim = NA are sufficient.
spdf	turn speed filter on/off (logical; default is TRUE)
min.dt	minimum allowable time difference in s between observations; dt < min.dt will be ignored by the SSM
emf	optionally supplied data.frame of error multiplication factors for Argos location quality classes. see Details

Details

called by fit_ssm.

Value

an sf object with all observations passed from data and the following appended columns

keep	logical indicating whether observation should be ignored by sfilter (FALSE)
obs.type	flag indicating whether KF or LS measurement model applies
emf_x	error multiplication factors for x direction
emf_y	error multiplication factors for y direction
geometry	sf POINT object giving x,y coordinates in km

foieGras documentation built on April 27, 2021, 1:05 a.m.