Circuit connectivity operators

`circuit.advanced`#

Currents and voltages of a raster circuit with sources and grounds, Circuitscape 6.1's advanced mode through landschaft's C++: each cell with a conductance a node joined to its 8 neighbours (4 asked) by the average conductance; current injected at the sources, drawn at the grounds (a conductance to ground, or a direct ground: inf); every component with both solved exactly. The node current is the larger of a cell's inflow and outflow.

Input	Type	What it is
`conductance`required	map	the conductance of each cell (no value: no node)
`source`required	map	the current injected at each cell, amps
`ground`required	map	the conductance to ground of each cell (inf: direct)

Output	Type	What it is
`current`	map	the node current of each cell
`voltage`	map	the voltage of each cell

Setting	Type	What it is
`four_neighbors`	bool	the four orthogonal neighbours only

`circuit.circuitscape_ini`#

Run a Circuitscape INI file on rasters, as Circuitscape.compute(path) does (landschaft's circuitscape_ini): advanced, pairwise, one-to-all and all-to-one, with its polygons, mask, reclassification, included pairs and variable source strengths; the inputs read as Circuitscape reads them (ASCII grids in double, GeoTIFFs, text lists; paths from the working directory or next to the INI), the outputs written as it names them next to output_file (ASCII grids, or GeoTIFF with write_as_tif). solver, precision and parallelize have no effect: every solve is exact in double.

Output	Type	What it is
`resistances`	table	pairwise: a row per point and its resistances; one-to-all: id, value
`voltage`	map	advanced: the voltages
`current`	map	advanced: the currents
`cum`	map	the cumulative current
`max`	map	the largest current
`maps`	stack	the pairs' (or points') voltage and current maps

Setting	Type	What it is
`path`required	text	the INI file
`write_outputs`	bool	write the output files as Circuitscape (default true)
`batch`	integer	one-to-all problems solved together (default 4 x the threads)

`circuit.network_advanced`#

Circuitscape's advanced mode on a network (data_type = network; landschaft's circuitscape_network_advanced): currents injected at nodes and grounds (a resistance of 0 a direct ground) on a graph of edges numbered from 1 (or 0, then every number shifted, as Circuitscape.jl). Duplicate edges add up. Every component with a source and a ground is solved.

Input	Type	What it is
`graph`	table	the edges: node, node, resistance (or conductance)
`sources`	table	node, current
`grounds`	table	node, resistance (or conductance) to ground

Output	Type	What it is
`voltages`	table	node, voltage (0 where not solved)
`node_currents`	table	node, current
`branch_currents`	table	from, to, current

Setting	Type	What it is
`graph_file`	text	or Circuitscape's edge list file
`graph_is_resistance`	bool	the edge values are resistances (default true)
`sources_file`	text	or Circuitscape's source file
`grounds_file`	text	or Circuitscape's ground file
`ground_is_resistance`	bool	the ground values are resistances (default true)
`remove_src_or_gnd`	text	nodes that are both: keepall (default)...

`circuit.network_pairwise`#

Circuitscape's pairwise mode on a network (landschaft's circuitscape_network_pairwise): the effective resistance between every pair of focal nodes (-1: not connected), every component factorised once; included or excluded pairs from Circuitscape's file; with the map options every pair's node voltages, node and branch currents (JSON), and the currents summed over the pairs.

Input	Type	What it is
`graph`	table	the edges: node, node, resistance (or conductance)

Output	Type	What it is
`resistances`	table	a row per focal node: its id, then its resistances
`cum_node_currents`	table	with current_maps: node, current summed over the pairs
`cum_branch_currents`	table	with current_maps: from, to, current
`maps`	any	with the map options: each pair's values (JSON)

Setting	Type	What it is
`graph_file`	text	or Circuitscape's edge list file
`graph_is_resistance`	bool	the edge values are resistances (default true)
`focal_nodes`required	any	the focal node numbers, or the path of Circuitscape's file
`included_pairs`	text	Circuitscape's include / exclude pairs file
`voltage_maps`	bool	every pair's node voltages
`current_maps`	bool	every pair's currents, and their sums

`circuit.omniscape`#

Omnidirectional connectivity with Omniscape's moving-window circuits (Omniscape 0.7 through landschaft's C++): a target every block_size cells injects its block's source strength into the sources within radius, grounded at the target; the node currents of every window add up into the cumulative current. The flow potential (the same on a conductance of 1) and the current normalised by it (above 1: channelled; below: impeded) when asked. Sources from the resistance (its conductance) unless given; conditions keep the sources whose values match the target's.

Input	Type	What it is
`resistance`required	map	the resistance (or conductance), > 0; no value: no data
`source`	map	the source strengths (default: from the resistance)
`condition1`	map	conditional connectivity: the first condition
`condition1_future`	map	its future values (compare_to_future)
`condition2`	map	a second condition
`condition2_future`	map	its future values

Output	Type	What it is
`current`	map	the cumulative current (cum_currmap)
`flow_potential`	map	the flow potential (flow_potential: true)
`normalized`	map	the current over the flow potential (normalized_current)

Setting	Type	What it is
`radius`required	number	the window's radius, in cells
`block_size`	number	targets every this many cells, odd (1)
`buffer`	number	cells beyond the radius in each window (0)
`source_threshold`	number	sources given: below this none (0)
`r_cutoff`	number	sources from the resistance: none above it (inf)
`resistance_is_conductance`	bool	the map holds conductances
`four_neighbors`	bool	the four orthogonal neighbours only
`flow_potential`	bool	the flow potential too
`normalized_current`	bool	the normalised current too
`correct_artifacts`	bool	undo the blocks' artifacts (true)
`mask_nodata`	bool	no value where the resistance has none (true)
`reclass_table`	any	[[value, new value], ...] (null: no data)
`compare_to_future`	text	none (default), 1, 2 or both
`comparison1`	text	within (default) or equal
`comparison2`	text	within (default) or equal
`condition1_lower`	number	within: the least difference (0)
`condition1_upper`	number	within: the largest difference (0)
`condition2_lower`	number	within: the least difference (0)
`condition2_upper`	number	within: the largest difference (0)
`precision`	text	double (default) or single

`circuit.omniscape_ini`#

Run an Omniscape INI file, as run_omniscape(path) does (landschaft's omniscape_ini): every option of Omniscape 0.7 with its defaults (radius, resistance_file and project_name required), paths from the working directory or next to the INI; the outputs written to project_name (_1, _2... when it exists) as Omniscape writes them: config.ini, cum_currmap, flow_potential, normalized_cum_currmap, classified_resistance (GeoTIFF or ASCII grids, no data -9999).

Output	Type	What it is
`current`	map	the cumulative current (cum_currmap)
`flow_potential`	map	with calc_flow_potential
`normalized`	map	with calc_normalized_current
`classified_resistance`	map	with reclassify_resistance

Setting	Type	What it is
`path`required	text	the INI file
`write_outputs`	bool	write the outputs to the project folder (default true)

`circuit.one_to_all`#

Circuitscape's one-to-all (or all-to-one) mode on rasters (landschaft's circuitscape_one_to_all): for every focal point in turn, 1 A (or its strength) injected there with every other point a direct ground (one-to-all), or the point grounded and the others injecting (all-to-one); the voltage over the strength at each point (one-to-all), the cumulative and largest current maps when asked. Circuitscape's quirks kept (strengths by position); all-to-one measures no resistances, so its table's value column is 0, as Circuitscape's: read its current maps.

Input	Type	What it is
`habitat`required	map	the resistance (or conductance); no value: no node
`points`required	map	the focal points' ids (0 or no value elsewhere; cells of one id: a region)
`polygons`	map	short-circuit regions: ids > 0, their cells one node
`mask`	map	cells where it is not positive (or has no value) removed

Output	Type	What it is
`resistances`	table	the effective resistances
`cum`	map	the cumulative current (cum_map)
`max`	map	the largest current of the pairs (max_map)

Setting	Type	What it is
`habitat_is_resistance`	bool	resistances (default) or conductances
`four_neighbors`	bool	the four orthogonal neighbours only
`avg_resistances`	bool	neighbours joined by their resistances' average
`cum_map`	bool	the cumulative current
`max_map`	bool	the largest current
`focal_zero`	bool	current 0 on the focal nodes in the maps
`reclass_table`	any	[[value, new value], ...] applied to the habitat first
`all_to_one`	bool	all-to-one instead of one-to-all
`strengths`	any	[[id, strength], ...], by position as Circuitscape
`batch`	integer	the problems solved together (default 4 x the threads; the last bits depend on it)

`circuit.pairwise`#

Circuitscape's pairwise mode on rasters (landschaft's circuitscape_pairwise): the effective resistance between every pair of focal points (-1: not connected), every component factorised once and its pairs solved together; the cumulative and the largest current maps when asked.

Input	Type	What it is
`habitat`required	map	the resistance (or conductance); no value: no node
`points`required	map	the focal points' ids (0 or no value elsewhere; cells of one id: a region)
`polygons`	map	short-circuit regions: ids > 0, their cells one node
`mask`	map	cells where it is not positive (or has no value) removed

Output	Type	What it is
`resistances`	table	the effective resistances
`cum`	map	the cumulative current (cum_map)
`max`	map	the largest current of the pairs (max_map)

Setting	Type	What it is
`habitat_is_resistance`	bool	resistances (default) or conductances
`four_neighbors`	bool	the four orthogonal neighbours only
`avg_resistances`	bool	neighbours joined by their resistances' average
`cum_map`	bool	the cumulative current
`max_map`	bool	the largest current
`focal_zero`	bool	current 0 on the focal nodes in the maps
`reclass_table`	any	[[value, new value], ...] applied to the habitat first
`null_currents`	bool	no value instead of 0 where no current (in the maps)
`log_transform`	bool	log10 of the current maps

circuit.advanced#

circuit.circuitscape_ini#

circuit.network_advanced#

circuit.network_pairwise#

circuit.omniscape#

circuit.omniscape_ini#

circuit.one_to_all#

circuit.pairwise#