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Convert Routes to BirdFlowRoutes

Source: R/as_BirdFlowRoutes.R
as_BirdFlowRoutes.Rd

Convert Routes objects to BirdFlowRoutes, adding BirdFlow-specific spatiotemporal coordinates. This may require aggregating multiple observations within the same timestep (week) which is controlled with the aggregate argument. Note the coordinates and dates in the result will be snapped to the cell and timestep (week) centers of the BirdFlow model (bf).

Usage

as_BirdFlowRoutes(
  routes,
  bf,
  aggregate = "random",
  valid_only = TRUE,
  sort_id_and_dates = TRUE,
  reset_index = FALSE
)

Arguments

routes

A Routes object.

bf

A BirdFlow object for spatial and temporal reference.

aggregate

The aggregation method if more than one timestep is presented in a route. Options include mean, median, midweek, random. Default to random. See snap_to_birdflow for a description of each aggregation method.

valid_only

Logical. Should only valid points be included? Defaults to TRUE.

sort_id_and_dates

Logical. Should data be sorted by route ID and date? Defaults to TRUE.

reset_index

Logical. Should indices be reset after sorting? Defaults to FALSE.

Value

A BirdFlowRoutes object.

See also

  • route() for creating synthetic routes from a BirdFlow model.

  • Routes() for converting observational data into a formal Routes object suitable for use with this function.

  • plot_routes() for plotting arguments used when calling plot() on Routes and BirdFlowRoutes objects.

  • snap_to_birdflow() to align observational data with a BirdFlow model without making a formal Routes object. This function also provides more details when errors arise - usually due to the data not overlapping the modeled states as defined by the mask and dynamic mask within bf.

  • as_BirdFlowIntervals() for making intervals from the BirdFlowModels BirdFlowIntervals define movements between pair of locations. Typically they are used to evaluate model performance.

Examples

route_data <- data.frame(
  route_id = c("001", "001", "001", "001", "001",
  "003", "003", "003", "004"),
  date = as.Date(c("2025-01-01", "2025-01-08", "2025-01-15", "2025-01-21",
  "2025-02-10", "2025-03-01", "2025-05-01", "2025-06-01", "2025-05-01")),
  lon = c(-75.0060, -75.0060, -74.0060, -87.6298, -87.6298, -87.6298,
  -89.6298, -85.6298, -95.3698),
  lat = c(39.7128, 39.7128, 40.7128, 41.8781, 41.8781, 41.8781,
  42.8781, 40.8781, 29.7604),
  route_type = c("tracking", "tracking", "tracking", "tracking",
  "tracking", "motus", "motus", "motus", "motus")
)
bf <- BirdFlowModels::amewoo
routes <- Routes(route_data, species = species(bf), source = "Pkg. example")

bf_routes <- as_BirdFlowRoutes(routes, bf)