Workflow for GeoPressureR

The geopressuretemplate() function manages the complete workflow for modelling bird trajectories using geolocator data. It includes the creation tag object, the construction of the likelihood maps (pressure and/or light), the creation of the graph model construction, and, finally, the estimation of the trajectory products and the pressure path computation. Read the Workflow chapter in the GeoPressureManual for more information.

To be able to run successfully these function, you will need to have correctly set-up the data and configuration files according following the GeoPressureTemplate standard .

Usage

geopressuretemplate(
  id,
  config = config::get(config = id),
  quiet = FALSE,
  file = glue::glue("./data/interim/{id}.RData"),
  ...
)

geopressuretemplate_config(
  id,
  config = config::get(config = id),
  assert_graph = FALSE,
  ...
)

geopressuretemplate_graph(
  id,
  config = config::get(config = id),
  quiet = FALSE,
  file = glue::glue("./data/interim/{id}.RData"),
  ...
)

geopressuretemplate_pressurepath(
  id,
  config = config::get(config = id),
  quiet = FALSE,
  file = glue::glue("./data/interim/{id}.RData"),
  ...
)

geopressuretemplate_tag(
  id,
  config = config::get(config = id),
  quiet = FALSE,
  file = glue::glue("./data/interim/{id}.RData"),
  assert_graph = FALSE,
  ...
)

Arguments

id

unique identifier of a tag.

config

configuration object specifying workflow parameters, which is loaded by default using config::get(config = id).

quiet

Logical. If TRUE, suppresses informational messages during execution. The default value is FALSE.

file

A file path to save the intermediate results (e.g., tag, graph, and pressure paths). Default is ./data/interim/{id}.RData.

...

Additional parameters to overwrite default or config values. Always prefer to modify config.yml if possible.

assert_graph

Logical. If TRUE, check that the config is compatible for the creation of a graph. The default value is TRUE. Set to FALSE only if you don't want to create a graph model

Value

The function returns nothing. Instead, it saves the processed outputs (tag, graph, pressure paths, etc.) to the specified file.

Details

The geopressuretemplate function is a high-level entry point that coordinates multiple steps for processing the geolocator data and produce trajectories. It relies on underlying child functions for each step:

• Tag Creation geopressuretemplate_tag(): Initializes and labels the tag object. It also generates light and pressure likelihood maps:

1. tag_create(): Initializes the tag object.

2. tag_label(): Adds labels.

3. tag_set_map(): Sets the spatial and temporal parameters.

4. If "map_pressure" is in the config$geopressuretemplate$likelihood:

   • geopressure_map(): Computes the pressure likelihood.

5. If "map_light" is in the config$geopressuretemplate$likelihood:

   • twilight_create() |> twilight_read() |> geolight_map(): Computes the light likelihood.

• Graph Creation geopressuretemplate_graph(): Builds a movement model graph based tag data, and can include wind effects if specified. Outputs such as marginal distributions, most likely paths, and simulation paths can be computed.

1. graph_create(): Creates the graph based on tag.

2. If config$graph_set_movement$type == "gs" (i.e., no wind):

   • graph_set_movement(): Sets the movement model without wind.

3. If config$graph_set_movement$type == "as" (i.e., with wind):

   • graph_add_wind(): Adds wind data to the graph.

   • graph_set_movement(): Sets the movement model with wind.

4. If "marginal" is in config$geopressuretemplate$outputs:

   • graph_marginal(): Computes the marginal distribution map.

5. If "most_likely" is in config$geopressuretemplate$outputs:

   • graph_most_likely(): Computes the most likely path based on the movement model.

6. If "simulation" is in config$geopressuretemplate$outputs:

   • graph_simulation(): Runs simulations to model multiple possible paths.

7. save(): Saves the computed graph and associated objects in data/interim/{id}.Rdata

• Pressure Path Processing geopressuretemplate_pressurepath(): Computes pressurepaths (pressurepath_create) using the content of the Rdata file and appending the pressurepath data.frame to the same file.

1. If "most_likely" is in config$geopressuretemplate$pressurepath, computes the pressure path for path_most_likely.

2. If "geopressureviz" is in config$geopressuretemplate$pressurepath computes the pressure path for path_geopressureviz

Each of these child functions can be called individually or automatically as part of the geopressuretemplate workflow.

See also

GeoPressureManual

Examples

if (FALSE) { # \dontrun{
# Run the complete geopressuretemplate workflow
geopressuretemplate("18LX")

# Or run step-by-step
# you can check that all the parameters are correctly set in the config file
geopressuretemplate_config(id)
# 1. creation of the tag
tag <- geopressuretemplate_tag("18LX")
# 2. creation of the graph
geopressuretemplate_graph("18LX")
# 3. Computation of the pressurepath
geopressuretemplate_pressurepath("18LX")
} # }