Simulate individual trajectory

Simulate the trajectory of a free ranging individual, over a given time period. The function works similarly as simulate_trajectory_CPF but the individual is not restrained around a colony and does not perform homing bout. Here, potential_position_func() considers the initial position as the colony, so that the dist_col field in the output corresponds to the distance to this starting point. The individual starts selecting its next positions based on environmental conditions (checking for residence time) at the third step (against 5th step for central-place foragers).

Usage

simulate_trajectory_FR(
  initial_position,
  resource_layer,
  starting_hour,
  starting_bearing = c(90, 10),
  starting_step = c(4.5, 3),
  travel_bearing = c(0, 20),
  travel_step = c(3, 3),
  foraging_bearing = c(0, 0.5),
  foraging_step = c(1, 3),
  minx = 0,
  maxx = 90,
  miny = 0,
  maxy = 90,
  step_duration = 1,
  activity_threshold = 0.5,
  max_duration = 720,
  residence_radius = NULL,
  residence_time = NULL
)

Arguments

initial_position

data.frame containing the coordinates of the point the individual starts from (Lon, Lat fields)

resource_layer

SpatRaster of the resource layer

starting_hour

Starting hour

starting_bearing

Bearing when departing the colony (mu, kappa)

starting_step

Step length when departing the colony (mu, kappa)

travel_bearing

Bearing from previous step when traveling (mu, kappa)

travel_step

Distance from previous step when traveling (scale, rate)

foraging_bearing

Bearing from previous step when foraging/searching (mu, kappa)

foraging_step

Distance from previous step when foraging (scale, rate)

minx

Minimum longitude of the bounding box to simulate trajectory within

maxx

Maximum longitude of the bounding box to simulate trajectory within

miny

Minimum latitude of the bounding box to simulate trajectory within

maxy

Maximum latitude of the bounding box to simulate trajectory within

step_duration

Duration of a step length, in minutes (defaults 1), defines the sampling interval

activity_threshold

Threshold environmental value defining when an individual switches from travelling to foraging movement

max_duration

Total duration of a full trip, in minutes (defaults to 720, 12h)

residence_radius

The distance at which testing for residence time (in system unit). This value is used to draw a radius around each position to evaluate the residence time. If one of residence_radius and residence_time is NULL (both, by default), no residence time constraint is applied.

residence_time

The time an animal is allowed to spend in a same area (residence time). Expressed in number of steps (take care to provide a number of step consistent with step_duration). If one of residence_radius and residence_time is NULL (both, by default), no residence time constraint is applied.

Value

a data.frame

See also

Other individual movement functions: potential_position_func(), randomdir(), randomdist(), simulate_trajectory_CPF()

Examples

library(ggplot2)
library(viridis)
library(tidyterra)
library(lubridate)
colony_location <- data.frame(Lon = 50, Lat = 50)
cdt <- generate_env_layer(grid = create_grid(), n = 1, seed = 4)
#> [using unconditional Gaussian simulation]
    
single_traj <- simulate_trajectory_FR(initial_position = colony_location, 
                    resource_layer = cdt$rasters, 
                    starting_hour = ymd_hms("2022-08-02 06:00:00"),
                    starting_bearing = c(90,10), 
                    starting_step = c(4.5, 3),
                    travel_bearing = c(0, 20), 
                    travel_step = c(3, 3), 
                    foraging_bearing = c(0, 0.5), 
                    foraging_step = c(1, 3),
                    minx = 0, maxx = 90, 
                    miny = 0, maxy = 90,
                    step_duration = 1,
                    activity_threshold = 0.7,
                    max_duration = 2000,
                    residence_radius = 1,
                    residence_time = 20)

# view the trajectory
ggplot(single_traj) +
  geom_spatraster(data = cdt$rasters, alpha = 0.5) + 
  geom_point(aes(x = Lon, y = Lat, color = activity)) +
  geom_point(data = colony_location, aes(x = Lon, y = Lat), col = "red") +
  scale_fill_viridis(option = "H") 


# look at the density distribution of distance to colony and movement parameters
ggplot(single_traj) + geom_density(aes(x = dist_col))

ggplot(single_traj |> subset(activity %in% c("forage", "travel"))) + 
  geom_density(aes(x = angle)) + facet_wrap("activity")

ggplot(single_traj |> subset(activity %in% c("forage", "travel"))) + 
  geom_density(aes(x = step)) + facet_wrap("activity")