The cl-ctrnn Reference Manual

Table of Contents

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The cl-ctrnn Reference Manual

This is the cl-ctrnn Reference Manual, version 1.0, generated automatically by Declt version 2.3 "Robert April" on Wed Mar 14 03:11:37 2018 GMT+0.


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1 Systems

The main system appears first, followed by any subsystem dependency.


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1.1 cl-ctrnn

Author

Øyvin Halfdan Thuv

Version

1.0

Source

cl-ctrnn.asd (file)

Components

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2 Files

Files are sorted by type and then listed depth-first from the systems components trees.


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2.1 Lisp


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2.1.1 cl-ctrnn.asd

Location

cl-ctrnn.asd

Systems

cl-ctrnn (system)


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2.1.2 cl-ctrnn/defpackage.lisp

Parent

cl-ctrnn (system)

Location

defpackage.lisp

Packages

continous-time-recurrent-neural-network

Exported Definitions

*timestep* (special variable)


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2.1.3 cl-ctrnn/cl-ctrnn.lisp

Dependencies
Parent

cl-ctrnn (system)

Location

cl-ctrnn.lisp

Exported Definitions

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2.1.4 cl-ctrnn/neuron-and-synapse-methods.lisp

Dependencies
Parent

cl-ctrnn (system)

Location

neuron-and-synapse-methods.lisp

Exported Definitions

add-dendrite! (method)


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2.1.5 cl-ctrnn/neurons.lisp

Dependency

defpackage.lisp (file)

Parent

cl-ctrnn (system)

Location

neurons.lisp

Exported Definitions
Internal Definitions

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2.1.6 cl-ctrnn/synapses.lisp

Dependency

defpackage.lisp (file)

Parent

cl-ctrnn (system)

Location

synapses.lisp

Exported Definitions
Internal Definitions

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3 Packages

Packages are listed by definition order.


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3.1 continous-time-recurrent-neural-network

Source

defpackage.lisp (file)

Nickname

ctrnn

Use List

common-lisp

Exported Definitions
Internal Definitions

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4 Definitions

Definitions are sorted by export status, category, package, and then by lexicographic order.


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4.1 Exported definitions


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4.1.1 Special variables

Special Variable: *timestep*
Package

continous-time-recurrent-neural-network

Source

defpackage.lisp (file)


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4.1.2 Generic functions

Generic Function: add-dendrite! NEURON SYNAPSE
Package

continous-time-recurrent-neural-network

Methods
Method: add-dendrite! (NEURON neuron) (SYNAPSE synapse)

(Destructively) add a new dendrite to a neuron, and connect a synapse to it.

Source

neuron-and-synapse-methods.lisp (file)

Generic Function: add-neuron! NETWORK NEURON
Package

continous-time-recurrent-neural-network

Methods
Method: add-neuron! (NETWORK neural-network) (NEURON neuron)

Destructively modify (add to) the neurons in a network.

Source

cl-ctrnn.lisp (file)

Generic Function: firing-frequency NEURON
Package

continous-time-recurrent-neural-network

Methods
Method: firing-frequency (NEURON neuron)

Return firing frequency based on membrane potential.

Source

neurons.lisp (file)

Generic Function: motor-neuron-motor-function OBJECT
Generic Function: (setf motor-neuron-motor-function) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: motor-neuron-motor-function (MOTOR-NEURON motor-neuron)
Method: (setf motor-neuron-motor-function) NEW-VALUE (MOTOR-NEURON motor-neuron)

A one arg. function mapping firing freq. -> motor force.

Source

neurons.lisp (file)

Generic Function: neural-network-neurons OBJECT
Generic Function: (setf neural-network-neurons) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neural-network-neurons (NEURAL-NETWORK neural-network)

automatically generated reader method

Source

cl-ctrnn.lisp (file)

Method: (setf neural-network-neurons) NEW-VALUE (NEURAL-NETWORK neural-network)

automatically generated writer method

Source

cl-ctrnn.lisp (file)

Generic Function: neuron-bias OBJECT
Generic Function: (setf neuron-bias) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neuron-bias (NEURON neuron)
Method: (setf neuron-bias) NEW-VALUE (NEURON neuron)
Source

neurons.lisp (file)

Generic Function: neuron-dendrites OBJECT
Generic Function: (setf neuron-dendrites) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neuron-dendrites (NEURON neuron)
Method: (setf neuron-dendrites) NEW-VALUE (NEURON neuron)

Contains a pointer to a synapse object.

Source

neurons.lisp (file)

Generic Function: neuron-external-current OBJECT
Generic Function: (setf neuron-external-current) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neuron-external-current (NEURON neuron)
Method: (setf neuron-external-current) NEW-VALUE (NEURON neuron)

External current, e.g. sensory input.

Source

neurons.lisp (file)

Generic Function: neuron-external-current-magnitude OBJECT
Generic Function: (setf neuron-external-current-magnitude) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neuron-external-current-magnitude (NEURON neuron)
Method: (setf neuron-external-current-magnitude) NEW-VALUE (NEURON neuron)

The value to set the ext.-cur. to for f.ex. sensor neurons.

Source

neurons.lisp (file)

Generic Function: neuron-membrane-potential OBJECT
Generic Function: (setf neuron-membrane-potential) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neuron-membrane-potential (NEURON neuron)
Method: (setf neuron-membrane-potential) NEW-VALUE (NEURON neuron)

The neurons membrane potential as it was last calculated.

Source

neurons.lisp (file)

Generic Function: neuron-time-constant OBJECT
Generic Function: (setf neuron-time-constant) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neuron-time-constant (NEURON neuron)
Method: (setf neuron-time-constant) NEW-VALUE (NEURON neuron)

(> 0) How responsive the neuron is (’time constant’).

Source

neurons.lisp (file)

Generic Function: sensor-neuron-sensor-function OBJECT
Generic Function: (setf sensor-neuron-sensor-function) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: sensor-neuron-sensor-function (SENSOR-NEURON sensor-neuron)
Method: (setf sensor-neuron-sensor-function) NEW-VALUE (SENSOR-NEURON sensor-neuron)

A one-arg. func. setting the ext. current of the neuron.

Source

neurons.lisp (file)

Generic Function: synapse-from-neuron OBJECT
Generic Function: (setf synapse-from-neuron) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: synapse-from-neuron (SYNAPSE synapse)
Method: (setf synapse-from-neuron) NEW-VALUE (SYNAPSE synapse)

The neuron that this synapse comes from.

Source

synapses.lisp (file)

Generic Function: synchronously-update-membrane-potentials! NEURAL-NETWORK
Package

continous-time-recurrent-neural-network

Methods
Method: synchronously-update-membrane-potentials! (NEURAL-NETWORK neural-network)

(Destructively) update membrane potentials in the network.

Source

cl-ctrnn.lisp (file)

Generic Function: update-membrane-potential! NEURON
Package

continous-time-recurrent-neural-network

Methods
Method: update-membrane-potential! (NEURON sensor-neuron) before
Source

neurons.lisp (file)

Method: update-membrane-potential! (NEURON neuron)

Calculate and modify neuron current membrane potential. Return energy used.

Source

neurons.lisp (file)

Method: update-membrane-potential! (NEURON motor-neuron) around

Call the associated motor function. Return energy consumed.

Source

neurons.lisp (file)


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4.1.3 Classes

Class: motor-neuron ()

A neuron mapping it’s firing frequency into motor force.

Package

continous-time-recurrent-neural-network

Source

neurons.lisp (file)

Direct superclasses

neuron (class)

Direct methods
Direct slots
Slot: motor-function

A one arg. function mapping firing freq. -> motor force.

Initargs

:motor-function

Initform

(function (lambda (continous-time-recurrent-neural-network::self) (declare (ignore continous-time-recurrent-neural-network::self))))

Readers

motor-neuron-motor-function (generic function)

Writers

(setf motor-neuron-motor-function) (generic function)

Class: neural-network ()

A network containing a bunch of neurons.

Package

continous-time-recurrent-neural-network

Source

cl-ctrnn.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: neurons
Initargs

:neurons

Readers

neural-network-neurons (generic function)

Writers

(setf neural-network-neurons) (generic function)

Class: neuron ()

Parent of all neuron types.

Package

continous-time-recurrent-neural-network

Source

neurons.lisp (file)

Direct superclasses

standard-object (class)

Direct subclasses
Direct methods
Direct slots
Slot: bias
Initargs

:bias

Initform

0.0

Readers

neuron-bias (generic function)

Writers

(setf neuron-bias) (generic function)

Slot: dendrites

Contains a pointer to a synapse object.

Initargs

:dendrites

Readers

neuron-dendrites (generic function)

Writers

(setf neuron-dendrites) (generic function)

Slot: external-current

External current, e.g. sensory input.

Initargs

:external-current

Initform

0.0

Readers

neuron-external-current (generic function)

Writers

(setf neuron-external-current) (generic function)

Slot: external-current-magnitude

The value to set the ext.-cur. to for f.ex. sensor neurons.

Initargs

:external-current-magnitude

Initform

20.0

Readers

neuron-external-current-magnitude (generic function)

Writers

(setf neuron-external-current-magnitude) (generic function)

Slot: maximum-membrane-potential

An upper limit of how much the cell membrane can store.

Initargs

:maximum-membrane-potential

Initform

1000

Readers

neuron-maximum-membrane-potential (generic function)

Writers

(setf neuron-maximum-membrane-potential) (generic function)

Slot: membrane-potential

The neurons membrane potential as it was last calculated.

Initargs

:membrane-potential

Initform

0.0

Readers

neuron-membrane-potential (generic function)

Writers

(setf neuron-membrane-potential) (generic function)

Slot: snapshot-firing-frequency

A place to store the firing frequency at a given time.

Initargs

:snapshot-firing-frequency

Initform

0.0

Readers

neuron-snapshot-firing-frequency (generic function)

Writers

(setf neuron-snapshot-firing-frequency) (generic function)

Slot: time-constant

(> 0) How responsive the neuron is (’time constant’).

Initargs

:time-constant

Initform

1.0

Readers

neuron-time-constant (generic function)

Writers

(setf neuron-time-constant) (generic function)

Class: sensor-neuron ()
Package

continous-time-recurrent-neural-network

Source

neurons.lisp (file)

Direct superclasses

neuron (class)

Direct methods
Direct slots
Slot: sensor-function

A one-arg. func. setting the ext. current of the neuron.

Initargs

:sensor-function

Initform

(function (lambda (continous-time-recurrent-neural-network::self) (declare (ignore continous-time-recurrent-neural-network::self))))

Readers

sensor-neuron-sensor-function (generic function)

Writers

(setf sensor-neuron-sensor-function) (generic function)

Class: synapse ()

Weighted onnection between two neurons.

Package

continous-time-recurrent-neural-network

Source

synapses.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: from-neuron

The neuron that this synapse comes from.

Initargs

:from-neuron

Readers

synapse-from-neuron (generic function)

Writers

(setf synapse-from-neuron) (generic function)

Slot: strength

The weight of this synapse.

Initargs

:strength

Initform

1.0

Readers

synapse-strength (generic function)

Writers

(setf synapse-strength) (generic function)


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4.2 Internal definitions


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4.2.1 Generic functions

Generic Function: neuron-maximum-membrane-potential OBJECT
Generic Function: (setf neuron-maximum-membrane-potential) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neuron-maximum-membrane-potential (NEURON neuron)
Method: (setf neuron-maximum-membrane-potential) NEW-VALUE (NEURON neuron)

An upper limit of how much the cell membrane can store.

Source

neurons.lisp (file)

Generic Function: neuron-snapshot-firing-frequency OBJECT
Generic Function: (setf neuron-snapshot-firing-frequency) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: neuron-snapshot-firing-frequency (NEURON neuron)
Method: (setf neuron-snapshot-firing-frequency) NEW-VALUE (NEURON neuron)

A place to store the firing frequency at a given time.

Source

neurons.lisp (file)

Generic Function: synapse-strength OBJECT
Generic Function: (setf synapse-strength) NEW-VALUE OBJECT
Package

continous-time-recurrent-neural-network

Methods
Method: synapse-strength (SYNAPSE synapse)
Method: (setf synapse-strength) NEW-VALUE (SYNAPSE synapse)

The weight of this synapse.

Source

synapses.lisp (file)


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Appendix A Indexes


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A.1 Concepts

Jump to:   C   F   L  
Index Entry  Section

C
cl-ctrnn.asd: The cl-ctrnn<dot>asd file
cl-ctrnn/cl-ctrnn.lisp: The cl-ctrnn/cl-ctrnn<dot>lisp file
cl-ctrnn/defpackage.lisp: The cl-ctrnn/defpackage<dot>lisp file
cl-ctrnn/neuron-and-synapse-methods.lisp: The cl-ctrnn/neuron-and-synapse-methods<dot>lisp file
cl-ctrnn/neurons.lisp: The cl-ctrnn/neurons<dot>lisp file
cl-ctrnn/synapses.lisp: The cl-ctrnn/synapses<dot>lisp file

F
File, Lisp, cl-ctrnn.asd: The cl-ctrnn<dot>asd file
File, Lisp, cl-ctrnn/cl-ctrnn.lisp: The cl-ctrnn/cl-ctrnn<dot>lisp file
File, Lisp, cl-ctrnn/defpackage.lisp: The cl-ctrnn/defpackage<dot>lisp file
File, Lisp, cl-ctrnn/neuron-and-synapse-methods.lisp: The cl-ctrnn/neuron-and-synapse-methods<dot>lisp file
File, Lisp, cl-ctrnn/neurons.lisp: The cl-ctrnn/neurons<dot>lisp file
File, Lisp, cl-ctrnn/synapses.lisp: The cl-ctrnn/synapses<dot>lisp file

L
Lisp File, cl-ctrnn.asd: The cl-ctrnn<dot>asd file
Lisp File, cl-ctrnn/cl-ctrnn.lisp: The cl-ctrnn/cl-ctrnn<dot>lisp file
Lisp File, cl-ctrnn/defpackage.lisp: The cl-ctrnn/defpackage<dot>lisp file
Lisp File, cl-ctrnn/neuron-and-synapse-methods.lisp: The cl-ctrnn/neuron-and-synapse-methods<dot>lisp file
Lisp File, cl-ctrnn/neurons.lisp: The cl-ctrnn/neurons<dot>lisp file
Lisp File, cl-ctrnn/synapses.lisp: The cl-ctrnn/synapses<dot>lisp file

Jump to:   C   F   L  

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A.2 Functions

Jump to:   (  
A   F   G   M   N   S   U  
Index Entry  Section

(
(setf motor-neuron-motor-function): Exported generic functions
(setf motor-neuron-motor-function): Exported generic functions
(setf neural-network-neurons): Exported generic functions
(setf neural-network-neurons): Exported generic functions
(setf neuron-bias): Exported generic functions
(setf neuron-bias): Exported generic functions
(setf neuron-dendrites): Exported generic functions
(setf neuron-dendrites): Exported generic functions
(setf neuron-external-current): Exported generic functions
(setf neuron-external-current): Exported generic functions
(setf neuron-external-current-magnitude): Exported generic functions
(setf neuron-external-current-magnitude): Exported generic functions
(setf neuron-maximum-membrane-potential): Internal generic functions
(setf neuron-maximum-membrane-potential): Internal generic functions
(setf neuron-membrane-potential): Exported generic functions
(setf neuron-membrane-potential): Exported generic functions
(setf neuron-snapshot-firing-frequency): Internal generic functions
(setf neuron-snapshot-firing-frequency): Internal generic functions
(setf neuron-time-constant): Exported generic functions
(setf neuron-time-constant): Exported generic functions
(setf sensor-neuron-sensor-function): Exported generic functions
(setf sensor-neuron-sensor-function): Exported generic functions
(setf synapse-from-neuron): Exported generic functions
(setf synapse-from-neuron): Exported generic functions
(setf synapse-strength): Internal generic functions
(setf synapse-strength): Internal generic functions

A
add-dendrite!: Exported generic functions
add-dendrite!: Exported generic functions
add-neuron!: Exported generic functions
add-neuron!: Exported generic functions

F
firing-frequency: Exported generic functions
firing-frequency: Exported generic functions

G
Generic Function, (setf motor-neuron-motor-function): Exported generic functions
Generic Function, (setf neural-network-neurons): Exported generic functions
Generic Function, (setf neuron-bias): Exported generic functions
Generic Function, (setf neuron-dendrites): Exported generic functions
Generic Function, (setf neuron-external-current): Exported generic functions
Generic Function, (setf neuron-external-current-magnitude): Exported generic functions
Generic Function, (setf neuron-maximum-membrane-potential): Internal generic functions
Generic Function, (setf neuron-membrane-potential): Exported generic functions
Generic Function, (setf neuron-snapshot-firing-frequency): Internal generic functions
Generic Function, (setf neuron-time-constant): Exported generic functions
Generic Function, (setf sensor-neuron-sensor-function): Exported generic functions
Generic Function, (setf synapse-from-neuron): Exported generic functions
Generic Function, (setf synapse-strength): Internal generic functions
Generic Function, add-dendrite!: Exported generic functions
Generic Function, add-neuron!: Exported generic functions
Generic Function, firing-frequency: Exported generic functions
Generic Function, motor-neuron-motor-function: Exported generic functions
Generic Function, neural-network-neurons: Exported generic functions
Generic Function, neuron-bias: Exported generic functions
Generic Function, neuron-dendrites: Exported generic functions
Generic Function, neuron-external-current: Exported generic functions
Generic Function, neuron-external-current-magnitude: Exported generic functions
Generic Function, neuron-maximum-membrane-potential: Internal generic functions
Generic Function, neuron-membrane-potential: Exported generic functions
Generic Function, neuron-snapshot-firing-frequency: Internal generic functions
Generic Function, neuron-time-constant: Exported generic functions
Generic Function, sensor-neuron-sensor-function: Exported generic functions
Generic Function, synapse-from-neuron: Exported generic functions
Generic Function, synapse-strength: Internal generic functions
Generic Function, synchronously-update-membrane-potentials!: Exported generic functions
Generic Function, update-membrane-potential!: Exported generic functions

M
Method, (setf motor-neuron-motor-function): Exported generic functions
Method, (setf neural-network-neurons): Exported generic functions
Method, (setf neuron-bias): Exported generic functions
Method, (setf neuron-dendrites): Exported generic functions
Method, (setf neuron-external-current): Exported generic functions
Method, (setf neuron-external-current-magnitude): Exported generic functions
Method, (setf neuron-maximum-membrane-potential): Internal generic functions
Method, (setf neuron-membrane-potential): Exported generic functions
Method, (setf neuron-snapshot-firing-frequency): Internal generic functions
Method, (setf neuron-time-constant): Exported generic functions
Method, (setf sensor-neuron-sensor-function): Exported generic functions
Method, (setf synapse-from-neuron): Exported generic functions
Method, (setf synapse-strength): Internal generic functions
Method, add-dendrite!: Exported generic functions
Method, add-neuron!: Exported generic functions
Method, firing-frequency: Exported generic functions
Method, motor-neuron-motor-function: Exported generic functions
Method, neural-network-neurons: Exported generic functions
Method, neuron-bias: Exported generic functions
Method, neuron-dendrites: Exported generic functions
Method, neuron-external-current: Exported generic functions
Method, neuron-external-current-magnitude: Exported generic functions
Method, neuron-maximum-membrane-potential: Internal generic functions
Method, neuron-membrane-potential: Exported generic functions
Method, neuron-snapshot-firing-frequency: Internal generic functions
Method, neuron-time-constant: Exported generic functions
Method, sensor-neuron-sensor-function: Exported generic functions
Method, synapse-from-neuron: Exported generic functions
Method, synapse-strength: Internal generic functions
Method, synchronously-update-membrane-potentials!: Exported generic functions
Method, update-membrane-potential!: Exported generic functions
Method, update-membrane-potential!: Exported generic functions
Method, update-membrane-potential!: Exported generic functions
motor-neuron-motor-function: Exported generic functions
motor-neuron-motor-function: Exported generic functions

N
neural-network-neurons: Exported generic functions
neural-network-neurons: Exported generic functions
neuron-bias: Exported generic functions
neuron-bias: Exported generic functions
neuron-dendrites: Exported generic functions
neuron-dendrites: Exported generic functions
neuron-external-current: Exported generic functions
neuron-external-current: Exported generic functions
neuron-external-current-magnitude: Exported generic functions
neuron-external-current-magnitude: Exported generic functions
neuron-maximum-membrane-potential: Internal generic functions
neuron-maximum-membrane-potential: Internal generic functions
neuron-membrane-potential: Exported generic functions
neuron-membrane-potential: Exported generic functions
neuron-snapshot-firing-frequency: Internal generic functions
neuron-snapshot-firing-frequency: Internal generic functions
neuron-time-constant: Exported generic functions
neuron-time-constant: Exported generic functions

S
sensor-neuron-sensor-function: Exported generic functions
sensor-neuron-sensor-function: Exported generic functions
synapse-from-neuron: Exported generic functions
synapse-from-neuron: Exported generic functions
synapse-strength: Internal generic functions
synapse-strength: Internal generic functions
synchronously-update-membrane-potentials!: Exported generic functions
synchronously-update-membrane-potentials!: Exported generic functions

U
update-membrane-potential!: Exported generic functions
update-membrane-potential!: Exported generic functions
update-membrane-potential!: Exported generic functions
update-membrane-potential!: Exported generic functions

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A   F   G   M   N   S   U  

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A.3 Variables

Jump to:   *  
B   D   E   F   M   N   S   T  
Index Entry  Section

*
*timestep*: Exported special variables

B
bias: Exported classes

D
dendrites: Exported classes

E
external-current: Exported classes
external-current-magnitude: Exported classes

F
from-neuron: Exported classes

M
maximum-membrane-potential: Exported classes
membrane-potential: Exported classes
motor-function: Exported classes

N
neurons: Exported classes

S
sensor-function: Exported classes
Slot, bias: Exported classes
Slot, dendrites: Exported classes
Slot, external-current: Exported classes
Slot, external-current-magnitude: Exported classes
Slot, from-neuron: Exported classes
Slot, maximum-membrane-potential: Exported classes
Slot, membrane-potential: Exported classes
Slot, motor-function: Exported classes
Slot, neurons: Exported classes
Slot, sensor-function: Exported classes
Slot, snapshot-firing-frequency: Exported classes
Slot, strength: Exported classes
Slot, time-constant: Exported classes
snapshot-firing-frequency: Exported classes
Special Variable, *timestep*: Exported special variables
strength: Exported classes

T
time-constant: Exported classes

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B   D   E   F   M   N   S   T  

Previous: , Up: Indexes   [Contents][Index]

A.4 Data types

Jump to:   C   M   N   P   S  
Index Entry  Section

C
cl-ctrnn: The cl-ctrnn system
Class, motor-neuron: Exported classes
Class, neural-network: Exported classes
Class, neuron: Exported classes
Class, sensor-neuron: Exported classes
Class, synapse: Exported classes
continous-time-recurrent-neural-network: The continous-time-recurrent-neural-network package

M
motor-neuron: Exported classes

N
neural-network: Exported classes
neuron: Exported classes

P
Package, continous-time-recurrent-neural-network: The continous-time-recurrent-neural-network package

S
sensor-neuron: Exported classes
synapse: Exported classes
System, cl-ctrnn: The cl-ctrnn system

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