Set network structure
set.network.structure.RdThis function sets the structure of a network object, defining its layers, columns, neuron types, and local connectivity parameters. It also generates local nodes based on the specified structure.
Usage
set.network.structure(
network,
neuron_types = c("principal"),
layer_names = c("layer"),
n_layers = 1,
n_columns = 1,
patch_depth = 1,
layer_height = 180,
column_diameter = 120,
segment_length = 20,
layer_separation_factor = 2.5,
column_separation_factor = 2.5,
patch_separation_factor = 2.5,
neurons_per_node = 10,
local_synaptic_conductance = 1e-10,
synaptic_neighborhood = 10
)Arguments
- network
Network object to configure.
- neuron_types
Character vector giving types of neurons in the network. Known types can be accessed using
print.known.celltypes(). Default is "principal", which will assign the most common neuron type for each layer, as defined inprincipal.neurons().- layer_names
Character vector giving names of layers in the network, ordered deepest to most superficial, e.g. c("L6", "L5", "L4", "L3", "L2", "L1").
- n_layers
Integer giving number of layers in the network.
- n_columns
Integer giving number of columns in the network.
- patch_depth
Integer giving the number of "patches" (n_layers x n_columns sheets) in the network.
- layer_height
Numeric giving height of each layer (in units specified at network creation, default unit is microns, default value is 180.0).
- column_diameter
Numeric giving diameter of each column (in units specified at network creation, default unit is microns, default value is 120.0).
- segment_length
Numeric giving expected length of each segment in the axonal and dendritic processes of each neuron (in units specified at network creation, default unit is microns, default value is 20.0).
- layer_separation_factor
Numeric giving mean distance between layers as a fraction of layer height (default: 2.5).
- column_separation_factor
Numeric giving mean distance between columns as a fraction of column diameter (default: 2.5).
- patch_separation_factor
Numeric giving mean distance between network patches as a fraction of column diameter (default: 2.5).
- neurons_per_node
Matrix giving number of neurons of each type per node in each layer; dimensions must match n_layers (rows) and length of neuron_types (columns).
- local_synaptic_conductance
List (one entry per layer) of matrices giving synaptic conductance in millisiemens for local connections by cell-type; each matrix must have dimensions matching length of neuron_types (rows and columns).
- synaptic_neighborhood
Numeric giving the radius (in microns) within which an axon node will trigger a synapse when near a dendrite node (default: 10.0).
- neuron_type_valences
Numeric vector giving valences of each neuron type, e.g. c(1, -1) for excitatory and inhibitory neurons.
- neuron_type_temporal_modulation
Numeric matrix giving temporal modulation time components (for modulation time in the unit_time of the network) for each neuron type: bias, step size, and count cutoff (rows as neuron types, columns as components). Will example a single value or a vector of length three.