sim: simulate animal tracks

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

simulate from the rw, crw of mpm process models to generate a set of x,y (or lon,lat) coordinates with or without error from supplied input parameters.

Usage

sim(
  N = 100,
  start = list(c(0, 0), as.POSIXct(format(Sys.time(), tz = "UTC", usetz = TRUE))),
  model = c("rw", "crw", "mpm"),
  vmax = 4,
  sigma = c(4, 4),
  rho_p = 0,
  D = 0.05,
  sigma_g = 1.25,
  error = c("ls", "kf"),
  tau = c(1.5, 0.75),
  rho_o = 0,
  tdist = c("reg", "gamma"),
  ts = 3,
  tpar = c(0.23, 1),
  alpha = c(0.9, 0.8)
)

Arguments

N	number of time steps to simulate
start	coordinates and datetime of start location for simulated track
model	simulate from the rw, crw or mpm process models
vmax	maximum travel rate (m/s) of simulated animal
sigma	a vector of process error sd's for the rw model (ignored if model != "rw")
rho_p	correlation parameter for rw model process covariance matrix (ignored if model != "rw")
D	diffusion coefficient for crw model process covariance matrix (ignored if model != "crw")
sigma_g	random walk sd for time-varying move persistence parameter (ignored if model != "mpm")
error	indicates whether measurement error should mimic Argos Least-Squares ("ls") or Argos Kalman Filter ("kf")
tau	vector of LS measurement error sd's (ignored if error = "kf")
rho_o	correlation parameter for LS covariance matrix (ignored if error = "kf")
tdist	distribution for simulating location times ("reg" generates locations at regular ts intervals, in h; "gamma" uses a gamma distribution to generate random time intervals)
ts	time interval in h (ignored if tdist = "gamma")
tpar	shape and scale parameters for the gamma distributed times (ignored if tdist = "reg")
alpha	transition probabilities switching model versions of rw or crw models. Probabilities are the transition matrix diagonals (ignored if sigma has length 2 or D has length 1)

Value

a tibble is returned with columns that can include some or all of the following, depending on the arguments used

date	time as POSIXct tz = UTC (default)
lc	Argos location class
lon	longitude with error
lat	latitude with error
x	x in km from arbitrary origin without error
y	y in km from arbitrary origin without error
x.err	a random deviate drawn from Argos LS or KF error distribution
y.err	a random deviate drawn from Argos LS or KF error distribution
smaj	Argos error ellipse semi-major axis in m (if error = "kf")
smin	Argos error ellipse semi-minor axis in m (if error = "kf")
eor	Argos error ellipse orientation in degrees (if error = "kf")
u	velocity in x direction (if model = "crw")
v	velocity in y direction (if model = "crw")
b	behavioural state (if model = "rw" or "crw" and multiple process variances given, see examples)
g	movement persistence - the autocorrelation between successive movements on the interval 0,1 (if model = "mpm")

Examples

tr <- sim(N = 200, model = "crw", D = 0.1, error = "kf", tdist = "reg", ts=12)
plot(tr, error = TRUE)

tr <- sim(N = 200, model = "rw", sigma = c(4,4,0.5,0.5), error = "ls", tdist = "reg")
plot(tr)

tr <- sim(N = 200, model = "crw", D = c(0.1, 0.05), error = "kf", tdist="reg")
plot(tr)

tr <- sim(N = 200, model = "mpm", sigma_g = 1.2, error = "ls", tau = c(2, 1.5), 
tdist = "gamma", tpar = c(1, 4))
plot(tr, error = TRUE, pal = "Cividis")

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