Package index

IBM setup

High-level IBM controls and definitions

IBM-class

<IBM>

IBM()

Create a <IBM> object

ModelConfig-class

Class <ModelConfig>

ModelConfig()

Create a <ModelConfig> object

Species definitions

Species/simulated population level functions

ArgSpec-class

Class <ArgSpec>

ArgSpec()

Create a <ArgSpec> object

Species-class

<Species>

Species()

Create <Species> objects

Environment definitions

Functions relating to the driver definitions

Driver-class

Class <Driver>

Driver()

Create a <Driver> object

DriverResponse-class

Class <DriverResponse>

DriverResponse()

Create a <DriverResponse> object

Classes

Class definitions

Agent-class

<Agent>

AgentCondition-class

<AgentCondition>

AgentProperties-class

<AgentProperties>

ArgSpec-class

Class <ArgSpec>

Driver-class

Class <Driver>

DriverResponse-class

Class <DriverResponse>

IBM-class

<IBM>

ModelConfig-class

Class <ModelConfig>

MoveInfluence-class

<MoveInfluence>

Species-class

<Species>

State-class

Class <State>

StateInfluence-class

<StateInfluence>

VarDist-class

Class <VarDist>

VarFn-class

Class <VarFn>

check_class()

Validate Object Class

Alphabetical

Complete list of user-facing functions

Agent-class

<Agent>

Agent()

Create <Agent> objects

AgentCondition-class

<AgentCondition>

AgentCondition()

Create <AgentCondition> objects

AgentProperties-class

<AgentProperties>

AgentProperties()

Create <AgentProperties> objects

ArgSpec-class

Class <ArgSpec>

ArgSpec()

Create a <ArgSpec> object

Driver-class

Class <Driver>

Driver()

Create a <Driver> object

DriverResponse-class

Class <DriverResponse>

DriverResponse()

Create a <DriverResponse> object

IBM-class

<IBM>

IBM()

Create a <IBM> object

ModelConfig-class

Class <ModelConfig>

ModelConfig()

Create a <ModelConfig> object

MoveInfluence-class

<MoveInfluence>

MoveInfluence()

Create a <MoveInfluence> object

Species-class

<Species>

Species()

Create <Species> objects

State-class

Class <State>

State()

Create a <State> object

StateInfluence-class

<StateInfluence>

VarDist-class

Class <VarDist>

distr(<VarDist>) units(<VarDist>) generate(<VarDist>) parameters(<VarDist>)

Utility functions for <VarDist> objects

VarDist()

Create a <VarDist> object

VarFn-class

Class <VarFn>

VarFn()

Create a <VarFn> object

as_vardist()

Cast numeric, distributional and unit objects as VarDist

bm_smooth_opts()

Set options for body mass smoother

build_cost_fn()

State cost function factory

calculate_track()

Shortest path calc

check_class()

Validate Object Class

check_dist()

helper to check validity of probability distribution names

check_units_contextual()

Check if units of an object are those expected under a specific context

compute_vector_fields()

Compute vector field of a stars raster

create_dnbs_config()

Helper to extract data and info required for configuring DisNBS's agent simulation model

derive_night_cube()

Derive rasters of night-time proportion per day

estimate_costs()

Estimate energy costs for each state in the profile, given agents condition (e.g. location, bodymass, etc)

extract_dns_layer()

wrapper on slice_strs() to slice density surface with appropriate indices. Slice construction relies on cfg to define the available non-raster dimensions to evaluate

get_slope_aspect()

Calculates slope and aspect of one attribute in the stars object and binds them to the original stars object as attributes

init_check_consistency()

Initialization object's consistency check

introspect_stars()

Introspects <stars> objects from the stars_obj argument of Driver()

is_empty(<VarDist>)

Empty assertion

is_empty(<VarFn>)

Empty assertion

is_empty_function()

Assertion for empty <function> objects

is_stars_empty()

Assertion for empty <stars> objects

pluck_s4()

Get element of list of S4 objects

rebalance_states()

Rebalance activity states

rmr_initiate()

Initialize the Individual Based Model

rover

A mock Species object

run_disnbs()

Run the DisNBS individual-based model

sample_cell()

Sampling a density map as PDF

save_rng()

Store and Restore RNGs

set_fn_env()

Set function environment, binding locally defined functions

simulate_agent_disnbs()

Run Agent-level simulation under the DisNBS model

slice_strs()

Slicer

smooth_body_mass()

Title Energy to mass conversion

update_agent()

Update agent's condition

velocity_ou()

Find 2D velocity vector of an Ornstein-Uhlenbeck process