Function reference • seabORD

Functions to run the model

seabord(): SeabORD main function

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_medianprey(): Set the median prey value across the region

set_initialbirdtype(): Create individual seabirds for the simulation

set_initialchickstate(): Set initial values for individual chicks

set_initialbirdstate(): Set initial values for individual birds

Datasets available

example_1_lists: example_1_lists

example_lists_calibration: example_lists_calibration

example_scenario_output: example_scenario_output

specieslist: Species List Dataset

spalist: SPA Site List Dataset

CEF_colsize_table: CEF Size Table

energeticsandpreydata: Energetics and Prey Data

BrdData_example: BrdData_example

frgcompdata_example: frgcompdata_example

cef_coast_4326: cef_coast_4326

cef_coast_3035: cef_coast_3035

seamask_3035_example: seamask_3035_example

spacoordinates: Spatial Coordinates of Sites

UK9004171_bysea_3035: UK9004171_bysea_3035

FlightGridcorrection_3035: FlightGridcorrection_3035: TransitionLayer Object

offshorerenewabledevelopmentnames: offshorerenewabledevelopmentnames

ORDpoly_example: ORDpoly_example

ORDpoly_example_wfold: ORDpoly_example_wfold

example_calibration_output: example_calibration_output

DBS_map_example: DBS_map_example.R

DBS_withORDs_example: DBS_withORDs_example.R

example_lists_calibration_dd: example_lists_calibration_dd

frgcompdata_example_dd: frgcompdata_example_dd

BrdData_example_dd: BrdData_example_dd

UK9002491_bysea_3035: UK9002491_bysea_3035

example_lists_dd: example_lists_dd

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