Function reference • seabORD

Functions to run the model

seabord(): Run a SeabORD simulation

Main functions behind the seabORD model

calc_adultbmchange(): Update adult body mass

calc_adultdee(): Calculate Daily Energy Requirement

calc_pSurvival(): Probability of winter survival (mass-survival)

calc_puffinmortality(): Puffin chick mortality from predation due to hunger

calc_chickcare(): Parenting the chicks

calc_othermortality(): Chick mortality as a result of other causes

calc_unattendmortality(): Chick mortality as a result of adults not attending the nest

calc_strategy(): Calculate the foraging strategy for the timestep

calc_foragecapture(): Calculate the time taken to forage required amount

memoised_calc_foragecapture(): Memoized Version of calc_foragecapture

Other functions behind seabORD

set_seedvalues(): Set the seeds needed for reproducibility

set_initialbirdtype(): Create individual seabirds for the simulation

set_initialchickstate(): Set initial values for individual chicks

set_initialbirdstate(): Set initial values for individual birds

seabORD distance decay

calc_birddensmap_dd_pinfr(): Calculate bird density maps

calc_birddensmap_dd_pinhalf(): Calculate bird density maps used the distance-decay function used in SeabORD, via users specifying phalf

calc_dd_phalf_from_pinfr(): Calculate 'q' from 'p' for the distance-decay model

calc_dd_pinfr_from_phalf(): Calculate 'pinfr' from 'phalf' for the distance-decay model

calc_dist_restricted(): Calculate distance restricted by obstructions

voptimise(): Use numerical optimisation to give the value of x associated with each element of a vector y, where y = fny(x) for a specified function fny

Example data

get_example_brddata(): Load example seabird-distribution raster data

get_example_DBS_map(): Load an example distance-by-sea raster

get_example_fgc_3035(): Load the example flight-grid correction object

get_example_fltdist_base(): Load example baseline flight-distance raster data

get_example_frgcompdata(): Load example foraging-competition raster data

get_example_modpar(): Load example model-control parameters

get_example_ordPar(): Load example offshore renewable development parameters

get_example_ORDpoly(): Load example offshore renewable development polygons

get_example_output(): Load example seabORD model output

get_example_par(): Load example biological and simulation parameters

get_example_seamask(): Load the example sea-mask raster

get_example_spadat1(): Load example SPA coordinate data

get_example_spadat2(): Load example SPA designation data

get_example_spdat(): Load example species parameters

get_example_switches(): Load example model switches

get_spdat(): Load species-specific data

Preparing the input

set_colony_point(): Create a colony location point

set_ORD_buffer(): Create buffer polygons around ORDs

set_prey_sequence_in_par(): Create a prey calibration sequence in Par

calc_pc_in_ORD_buffer(): Calculate the percentage of a DD map within ORD buffer zones

calc_calibration_range(): Identify prey values meeting calibration criteria

summarise_ORD_impact(): Summarise the impact of ORDs on a density decay map

check_calibration_inputs(): Check calibration input consistency

Plotting input/output

plot_adult_body_mass(): Plot adult body mass by season

plot_BirdFlightMap(): Plot a bird-flight map

plot_brddata(): Plot a bird-distribution raster

plot_calibration_outputs(): Plot calibration outputs across prey values

plot_chick_survival(): Plot chick survival by season

plot_colony_location(): Plot a colony location and surrounding coastline

plot_DBS_map(): Plot a distance-by-sea raster

plot_DD_map(): Plot a distance-decay map

plot_DD_map_with_ORDs(): Plot a distance-decay map with ORD footprints

plot_flight_distance(): Plot mean flight distance by season

plot_fltdist_base(): Plot a baseline flight-distance raster

plot_frgcompdata(): Plot a foraging-competition raster

plot_ORDpoly(): Plot offshore renewable development polygons

plot_ORD_obstruction(): Plot areas affected by ORD obstruction

plot_seamask(): Plot a sea-mask raster