Package index • BirdFlowR

All functions

Routes(): Routes() is used to convert data frames containing bird movement data into a formal Routes object with the same data.

add_dynamic_mask(): Convert a BirdFlow object without a dynamic mask into one with a dynamic mask

add_stay_id(): Add Stay IDs

add_stay_id_with_varied_intervals(): Add Stay IDs with Temporal Thresholds

animate_distr(): Animate distributions

animate_flux(): Animate flux

animate_movement_vectors(): Animate movement vectors

animate_routes(): Animate routes

as_BirdFlowIntervals(): Convert BirdFlowRoutes to BirdFlowIntervals

as_BirdFlowRoutes(): Convert Routes to BirdFlowRoutes

as_distr(): Convert to a BirdFlow distribution

as_transitions(): Convert a sequence of timesteps into a sequence of transition names

birdflow_options(): Set and retrieve BirdFlowR options

build_transitions() drop_transitions(): Add or drop transition matrices

calc_flux(): Estimate bird flux

calc_movement_vectors(): Calculate the average movement for cells in a BirdFlow model

calculate_interval_metrics(): Calculate interval metrics

combine_transitions(): Function to combine a sequence of transition matrices into one

compareGeom(<BirdFlow>,<BirdFlow>) compareGeom(<SpatRaster>,<BirdFlow>) compareGeom(<BirdFlow>,<SpatRaster>): BirdFlow compareGeom methods

nrow(<BirdFlow>) ncol(<BirdFlow>) dim(<BirdFlow>) n_timesteps() n_distr() n_transitions() n_active() crs(<BirdFlow>) ext(<BirdFlow>) res(<BirdFlow>) xres(<BirdFlow>) yres(<BirdFlow>) xmin(<BirdFlow>) ymin(<BirdFlow>) xmax(<BirdFlow>) ymax(<BirdFlow>) is_cyclical() n_parameters(): Dimensions of a BirdFlow object

distribution_performance(): Evaluate a BirdFlow models ability to recreate training distributions

dmi_to_i() i_to_dmi(): Convert between dynamic mask index and static location index

export_birdflow() import_birdflow(): Export and import BirdFlow models in HDF5 format

extend_birdflow(): Extend BirdFlow extent

flatten_raster(): Convert a raster bird distribution into its flattened, vector equivalent

get_dates(): Retrieve dates component of a BirdFlow model

get_distr(): Extract distributions from BirdFlow models

get_dynamic_mask(): Get the dynamic mask from a BirdFlow object

get_interval_based_validation_one_transition_pair(): Evaluate model performance using intervals (movement data)

get_loss(): Get loss values for each step in the model fitting process

get_marginal(): Return a marginal matrix from a BirdFlowR model

get_mask(): Extract mask from BirdFlow model

get_metadata(): Retrieve BirdFlow metadata

get_naturalearth() get_states() get_coastline() get_countries(): Retrieve, crop, and transform Natural Earth data

get_transition(): Return a transition matrix from a BirdFlowR model

great_circle_distance_lonlat_input(): Calculate the great circle distance based on longitude and latitude

has_marginals() has_transitions() has_distr() has_dynamic_mask(): Does a BirdFlow object have certain components

x_to_col() y_to_row() row_to_y() col_to_x() i_to_rc() i_to_row() i_to_col() i_to_x() i_to_y() i_to_xy() rc_to_i() xy_to_i() latlon_to_xy() xy_to_latlon(): Functions to convert among spatial indices

interval_log_likelihood(): Calculate log likelihoods of observed bird movements

is_location_valid() is_distr_valid(): Are locations and distributions covered by the model for the given time

load_collection_index(): Load the index to a remote model collection

load_model(): Load BirdFlow models from a collection

lookup_date(): Retrieve date associated with timesteps, transitions, or marginals

lookup_season_timesteps(): Lookup breeding, non-breeding, or migration season timesteps

lookup_timestep(): Lookup timestep

lookup_timestep_sequence(): Lookup a sequence of timesteps

validate_Routes_route_df() validate_BirdFlowRoutes_birdflow_route_df() validate_BirdFlowIntervals_birdflow_intervals() validate_Routes() validate_BirdFlowRoutes() validate_BirdFlowIntervals(): Object Validators

plot_distr(): Plot distributions

plot_flux(): Plot bird flux

plot_loss(): Plot changes in component and total loss during model fitting

plot_movement_vectors(): Plot bird movement vectors

plot_routes() plot(<BirdFlowRoutes>): Plot Routes

predict(<BirdFlow>): Predict bird distributions

preprocess_species(): Prepare eBird Status and Trends data for BirdFlow model fitting

print(<BirdFlow>): Print BirdFlow models

print(<BirdFlowIntervals>): Print a BirdFlowIntervals Object

print(<Routes>): Print Routes and BirdFlowRoutes objects

rasterize_distr() rast(<BirdFlow>): Convert a BirdFlow distribution into a raster

read_geom(): Read geom component of a BirdFlow hdf5

route(): Generate BirdFlow routes

sample_distr(): Sample locations from a distribution

shrink_birdflow(): Shrink BirdFlow extent

snap_to_birdflow(): Assign cells and timesteps to coordinates and dates

sort_by_id_and_dates(): Sort Routes by ID and Date

sparsify(): sparsify BirdFlow models

species_info() species(): Retrieve species information from a BirdFlow model

get_target_columns_Routes() get_target_columns_BirdFlowRoutes() get_target_columns_BirdFlowIntervals(): Get Target Columns for Data Frames

truncate_birdflow(): Truncate the timespan of a BirdFlow model

validate_BirdFlow(): Function to validate a BirdFlow object

validate_geom(): Validate geom component of a BirdFlow or related object