The cl-bayesnet Reference Manual

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The cl-bayesnet Reference Manual

This is the cl-bayesnet Reference Manual, version 0.1.0, generated automatically by Declt version 2.4 "Will Decker" on Wed Jun 20 10:58:36 2018 GMT+0.


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1 Introduction

cl-bayesnet - a Common Lisp Bayesian Network Inference Engine

Overview

cl-bayesnet is a tool for the compilation and probability calculation of discrete, probabilistic Bayesian Networks.

It provides two types of compilation. The first is join-tree compilation. A join-tree is an auxiliary structure which uses message passing to calculate local probabilities given evidence in a network. Compiling a Bayesian Network to a join tree is quick, but message passing is relatively slow. The join tree's space cost should also be taken into account.

The second type of compilation compiles the Bayesian Network into an Arithmetic Circuit, which is written as a series of arithmetic instructions. These instructions can be interpreted on the fly, or written out as source code for a compiler such as gcc. The compilation process is quite slow, but the instructions are evaluated much faster than message passing (using my implementation, anyway). My tests showed approximately 70x speed up of interpreted instructions over message passing, and then the C compiled instructions executed 20x faster than interpreted instructions!

An additional advantage of the arithmetic circuit is that it compiles to a single, standalone function. That means it is perfect for embedded systems, and can be used anywhere, without dependence on any library at all! An absolutely minimal footprint.

## Scope and Goals ##

The scope of cl-bayesnet is just Bayesian Network compilation and probability calculation. There is no API for building or modifying a Bayesian Network. There are no modelling tools. There is no GUI. These tools already exist, and have done for years.

However, there are not many free, open-source Bayesian Network probability calculators. http://sourceforge.net/projects/bnj/ is the only other open-source one I know of. I know of no other project which can compile direct to machine code (through gcc) like cl-bayesnet can.

The goals of this project is to be useful to developers who want to use the results of their Bayesian Network modelling freely in any domain. If there is demand, compilation to pure Java and compilation to pure Lisp can be quickly developed.

## Highlights ##

Using cl-bayesnet

Dependencies

cl-bayesnet uses S-XML to parse xmlbif. It uses trivial-shell to call the C compiler and CFFI to load the resultant shared object file. You can disable the dependencies on CFFI and trivial-shell by adding :cl-bayesnet-no-cffi to your Lisp's features list.

All dependencies are available through quicklisp.

Installation

I suggest using quicklisp. Install that, and then grab the source (via tarball or git) and put it in ~/quicklisp/local-projects/. Symlinks work okay too.

Documentation

See the API-Documentation on github. It may not necessarily be up to date.

Or, use make-api-doc.sbcl in this directory to make the API documentation (cl-bayesnet.html). This assumes you have quicklisp and sbcl installed.

Usage

See tests/test-alarm.lisp for example usage.

Ownership and License

cl-bayesnet's contributors are listed in the AUTHORS file. The authors of cl-bayesnet grant you use of this software under the terms of the Lisp Lesser General Public License (LLGPL). For details see the files COPYING, COPYING.LESSER and COPYING.LISP in this directory.

Contributing

If you find problems with this library please take the time to report the issue. This helps you by increasing the chance the issue will be fixed. It helps motivate me by letting me know the library is being used. It helps everyone when the fixed issue creates a stronger codebase.

To report an issue, use the cl-bayesnet issue tracker at github.com.

For issue fixes and improvements, I prefer pull requests. Simple one or two liner fixes are okay over email for n


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2 Systems

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


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2.1 cl-bayesnet

Maintainer

Lucas Hope <lucas.r.hope@gmail.com>

Author

Lucas Hope <lucas.r.hope@gmail.com>

License

LLGPL

Description

A Common Lisp Bayesian Network Inference Engine

Version

0.1.0

Dependencies
Source

cl-bayesnet.asd (file)

Component

src (module)


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3 Modules

Modules are listed depth-first from the system components tree.


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3.1 cl-bayesnet/src

Parent

cl-bayesnet (system)

Location

src/

Components

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4 Files

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


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4.1 Lisp


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4.1.1 cl-bayesnet.asd

Location

cl-bayesnet.asd

Systems

cl-bayesnet (system)


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4.1.2 cl-bayesnet/src/packages.lisp

Parent

src (module)

Location

src/packages.lisp

Packages

cl-bayesnet


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4.1.3 cl-bayesnet/src/utils.lisp

Dependency

packages.lisp (file)

Parent

src (module)

Location

src/utils.lisp

Internal Definitions

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4.1.4 cl-bayesnet/src/tries.lisp

Dependency

utils.lisp (file)

Parent

src (module)

Location

src/tries.lisp

Internal Definitions

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4.1.5 cl-bayesnet/src/bn-utils.lisp

Dependency

tries.lisp (file)

Parent

src (module)

Location

src/bn-utils.lisp

Internal Definitions

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4.1.6 cl-bayesnet/src/bn.lisp

Dependency

bn-utils.lisp (file)

Parent

src (module)

Location

src/bn.lisp

Exported Definitions
Internal Definitions

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4.1.7 cl-bayesnet/src/parse-network.lisp

Dependency

bn.lisp (file)

Parent

src (module)

Location

src/parse-network.lisp

Exported Definitions
Internal Definitions

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4.1.8 cl-bayesnet/src/clique-tree.lisp

Dependency

parse-network.lisp (file)

Parent

src (module)

Location

src/clique-tree.lisp

Internal Definitions

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4.1.9 cl-bayesnet/src/message.lisp

Dependency

clique-tree.lisp (file)

Parent

src (module)

Location

src/message.lisp

Exported Definitions
Internal Definitions

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4.1.10 cl-bayesnet/src/evidence.lisp

Dependency

message.lisp (file)

Parent

src (module)

Location

src/evidence.lisp

Exported Definitions
Internal Definitions

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4.1.11 cl-bayesnet/src/compiler.lisp

Dependency

evidence.lisp (file)

Parent

src (module)

Location

src/compiler.lisp

Exported Definitions
Internal Definitions

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4.1.12 cl-bayesnet/src/emit-c.lisp

Dependency

compiler.lisp (file)

Parent

src (module)

Location

src/emit-c.lisp

Exported Definitions

use-compiled-c (function)

Internal Definitions

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4.1.13 cl-bayesnet/src/test.lisp

Dependency

emit-c.lisp (file)

Parent

src (module)

Location

src/test.lisp

Internal Definitions

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5 Packages

Packages are listed by definition order.


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5.1 cl-bayesnet

A Common Lisp Bayesian Network Inference Engine

Source

packages.lisp (file)

Nickname

bn

Use List

common-lisp

Exported Definitions
Internal Definitions

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6 Definitions

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


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6.1 Exported definitions


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6.1.1 Macros

Macro: with-evidence (NET &rest EVIDENCE) &body BODY

Saves the existing evidence in the net and sets the evidence to evidence. Restores the net to its previous state after leaving the with-evidence block.

Package

cl-bayesnet

Source

bn.lisp (file)


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6.1.2 Functions

Function: load-ace FILE

Load a file in ace file format. Returns a net.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: load-dne FILE

Load a file in Netica’s dne file format. Returns a net.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: load-xmlbif FILE

Load a file in xmlbif file format. Returns a net.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: query OBJECT &optional QUERY

Queries a net or node object.

node only - A probability vector for the states of node.

node and integer - The probability the node is in that numbered state (according to (states node)).

node and symbol - The probability the node is in that state.

node and list - A probability vector for the states of node given list, which is a plist of node-state pairs.

net only - The joint probability for the whole net.

net and vector - The joint probability for the whole net, given the vector. Vector has the num-nodes length, and contains either a state number for each node, or -1 if the node state is unknown.

net and symbol - A probability vector for the states of the node designated by symbol.

net and list - The joint probability for the whole net, given list, which is a plist of node-state pairs.

Package

cl-bayesnet

Source

bn.lisp (file)

Function: use-compiled-c NET &optional SOURCE-LOCATION

Writes out arithmetic circuit instructions to a c file, compiles it with gcc, loads the shared object, and prepares the net to use the loaded function. If source-location is specified, writes the c file there. Otherwise uses a temporary file.

Returns the closure used, the raw cffi function pointer, and the number of instructions.

Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: use-interpreted NET

Use interpreted arithmetic circuit instructions for the net. Returns the instructions object.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: use-join-tree NET

Use a join-tree to evaluate this net. Returns the join-tree object.

Package

cl-bayesnet

Source

evidence.lisp (file)


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6.1.3 Generic functions

Generic Function: add-evidence OBJECT EVIDENCE

Sets the evidence in a node via state index or symbol. For a net or join-tree, adds the evidence as a plist of node-state pairs.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: add-evidence (JT join-tree) (EVIDENCE list)
Source

evidence.lisp (file)

Method: add-evidence OBJECT EVIDENCE
Method: add-evidence (NET net) (EVIDENCE list)
Generic Function: clear-evidence OBJECT

Clear all evidence from object.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: clear-evidence (JT join-tree)
Source

evidence.lisp (file)

Method: clear-evidence (NET net)
Method: clear-evidence (NODE node)
Generic Function: evidence OBJECT

Returns the evidence in a node as its state symbol (nil if no evidence), and for nets and join-trees a plist of node-state pairs. Settable.

Package

cl-bayesnet

Source

bn.lisp (file)

Writer

(setf evidence) (generic function)

Methods
Method: evidence (NODE jt-node)
Source

evidence.lisp (file)

Method: evidence (JT join-tree)
Source

evidence.lisp (file)

Method: evidence (NET net)
Method: evidence (NODE node)
Generic Function: (setf evidence) EVIDENCE OBJECT

Sets the evidence in a node via state index or symbol. For a net or join-tree, sets the evidence as either a plist of node-state pairs, or a vector of state indices (or -1 for unobserved) corresponding to the net’s node-order.

Package

cl-bayesnet

Source

bn.lisp (file)

Reader

evidence (generic function)

Generic Function: evidence-index OBJECT

Returns the evidence in a node as a state index and nets as a vector of state indices. -1 indicates no evidence.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: evidence-index (NODE jt-node)
Source

evidence.lisp (file)

Method: evidence-index (JT join-tree)
Source

evidence.lisp (file)

Method: evidence-index (NET net)
Method: evidence-index (NODE node)
Generic Function: name NET/NODE

For a net, a string identifier and for a node, a keyword identifier.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: name (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: name (NODE node)

automatically generated reader method

Method: name (NET net)

automatically generated reader method

Generic Function: net NODE/JOIN-TREE

Returns the containing net for a node or join-tree.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: net (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Method: net (NODE node)

automatically generated reader method

Generic Function: node NAME/INDEX NET/JOIN-TREE

Retrieve the node represented by a keyword name or index from the given net or join-tree.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: node (INDEX fixnum) (JT join-tree)
Source

evidence.lisp (file)

Method: node (NAME symbol) (JT join-tree)
Source

evidence.lisp (file)

Method: node (INDEX fixnum) (NET net)
Method: node (NAME symbol) (NET net)
Generic Function: node-order NET

Returns a list of node-names as keywords. The ordering matches their index order. This is set as part of the network compilation process.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: node-order (NET net)

automatically generated reader method

Generic Function: num-nodes NET

The amount of nodes in the network.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: num-nodes (NET net)

automatically generated reader method

Generic Function: num-states NODE

The amount of states for the given node.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: num-states (NODE node)

automatically generated reader method

Generic Function: parents NODE

A vector of parent names as keywords for the given node.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: parents (NODE node)

automatically generated reader method

Generic Function: states NODE

A vector of state names as keywords for the given node.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: states (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: states (NODE node)

automatically generated reader method


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6.1.4 Classes

Class: instructions ()
Package

cl-bayesnet

Source

compiler.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: forms
Type

list

Readers

forms (generic function)

Writers

(setf forms) (generic function)

Slot: match-lookup
Readers

match-lookup (generic function)

Slot: +-lookup
Readers

+-lookup (generic function)

Slot: *-lookup
Readers

*-lookup (generic function)

Slot: form-count
Type

fixnum

Initform

0

Readers

form-count (generic function)

Writers

(setf form-count) (generic function)

Slot: assignment
Type

(simple-array fixnum *)

Readers

assignment (generic function)

Writers

(setf assignment) (generic function)

Slot: cliques
Type

simple-vector

Readers

cliques (generic function)

Writers

(setf cliques) (generic function)

Slot: tree
Type

simple-vector

Readers

tree (generic function)

Writers

(setf tree) (generic function)

Class: join-tree ()
Package

cl-bayesnet

Source

message.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: net
Initargs

:net

Readers

net (generic function)

Slot: nodes
Initargs

:nodes

Readers

nodes (generic function)

Slot: clusters
Initargs

:clusters

Readers

clusters (generic function)

Slot: links
Initargs

:links

Readers

links (generic function)

Slot: all-sep-sets
Initargs

:sep-sets

Readers

all-sep-sets (generic function)

Slot: consistent
Readers

consistent (generic function)

Writers

(setf consistent) (generic function)

Slot: assignment
Initargs

:assignment

Readers

assignment (generic function)

Slot: obs
Initargs

:obs

Readers

obs (generic function)

Writers

(setf obs) (generic function)

Slot: evidence
Initargs

:evidence

Readers

evi (generic function)

Class: net ()
Package

cl-bayesnet

Source

bn.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: name
Readers

name (generic function)

Writers

set-name (generic function)

Slot: compiled
Readers

compiled (generic function)

Writers

(setf compiled) (generic function)

Slot: node-order
Readers

node-order (generic function)

Writers

set-node-order (generic function)

Slot: num-nodes
Readers

num-nodes (generic function)

Slot: node-vec
Readers

node-vec (generic function)

Writers

(setf node-vec) (generic function)

Slot: nodes
Initform

(make-hash-table)

Readers

nodes (generic function)

Slot: properties
Initform

(make-hash-table)

Readers

properties (generic function)

Class: node ()
Package

cl-bayesnet

Source

bn.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: name
Readers

name (generic function)

Writers

set-name (generic function)

Slot: net
Initargs

:net

Readers

net (generic function)

Writers

set-net (generic function)

Slot: table
Readers

table (generic function)

Writers

(setf table) (generic function)

Slot: states
Readers

states (generic function)

Writers

set-states (generic function)

Slot: parents
Readers

parents (generic function)

Writers

set-parents (generic function)

Slot: parent-vec
Readers

parent-vec (generic function)

Writers

(setf parent-vec) (generic function)

Slot: parent-indices
Type

(simple-array fixnum *)

Readers

parent-indices (generic function)

Writers

(setf parent-indices) (generic function)

Slot: num-states
Readers

num-states (generic function)

Slot: index
Readers

index (generic function)

Writers

(setf index) (generic function)

Slot: evidence
Initform

-1

Readers

%evidence (generic function)

Writers

(setf %evidence) (generic function)

Slot: properties
Initform

(make-hash-table)

Readers

properties (generic function)


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6.2 Internal definitions


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6.2.1 Constants

Constant: +trie-hash-threshold+
Package

cl-bayesnet

Source

tries.lisp (file)


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6.2.2 Special variables

Special Variable: *calculation-context*

Used by with-calculation(-context) to define a limited caching environment.

Package

cl-bayesnet

Source

utils.lisp (file)

Special Variable: *gcc-format-string*

String to pass to format. First arg is source, second is target.

Package

cl-bayesnet

Source

emit-c.lisp (file)

Special Variable: *temporary-directory*

Temporary work directory for C-based network compilation

Package

cl-bayesnet

Source

bn-utils.lisp (file)


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6.2.3 Macros

Macro: aif TEST-FORM THEN-FORM &optional ELSE-FORM

Anaphoric if. (lexically sets ’it’ to the test-form, which can then be referenced in then-form and else-form.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: awhen TEST-FORM &body BODY

Anaphoric when. See aif.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: do-trie-branches (NEXT-TRIE TRIE &optional RESULT) &body BODY

Loop over the trie’s branches.

Package

cl-bayesnet

Source

tries.lisp (file)

Macro: do-trie-values (VALUE TRIE &optional RETVAL) &body BODY
Package

cl-bayesnet

Source

tries.lisp (file)

Macro: do-upper (I J LEN &optional RESULT) &body BODY

do for upper triangular i and j. i from 0 to len, j from i+1 to len.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: multf REF MULTIPLIER

(setf ref (* ref multiplier)). Like incf.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: multiply-floats FLOATS
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: reset-potential PLACE
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: returnit VAL &body BODY

An anaphorous macro. binds the first val to ‘it’, allows possible modifications in the body, then returns the values. A more general prog1.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: save-evidence OBJECT &body BODY
Package

cl-bayesnet

Source

bn.lisp (file)

Macro: sum-floats FLOATS
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: vlength VEC
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Macro: while EXPR &body BODY

Continue performing body until expr is false.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: with-calculation LABEL &body BODY

Unless label is nil, caches the calculation performed by body using label. If there is no calculation-context, does not evaluate label, so don’t rely on side effects.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: with-calculation-context (&optional TEST) &body BODY

Defines a calculation context within which calculations performed within with-calculation are cached according to their label.

Package

cl-bayesnet

Source

utils.lisp (file)

Macro: with-gensyms (&rest SYMBOLS) &body BODY
Package

cl-bayesnet

Source

utils.lisp (file)


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6.2.4 Functions

Function: %evidence-1 NET ARRAY
Package

cl-bayesnet

Source

bn.lisp (file)

Function: %trie-map-key-value FN KEY TRIE NEW-TRIE

Create a new trie with the same structure as trie, applying fn to the key and the old trie node.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: %trie-map-trie FN NEW-TRIE TRIE &rest TRIES

Create a new trie with the same structure as trie, applying fn to each trie-node in turn.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: add-form FORM INS &optional DEPTH
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: assign-nodes NET CLIQUES

Returns an assignment of a clique node for each net node. Since lookup within a clique is sequential, just uses an array of lists. An array of assignments from the node perspective is returned as a second value.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: best SEQ/HASH COMPARE &key KEY

Returns the best value in seq/hash, along with its position (or key for the hash), according to compare. The comparison value is returned as a third value. key extracts the value to be used for comparison.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: best-in-array ARRAY COMPARE &key KEY

return the best value in array, along with its position and its comparison value. See best.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: best-in-hash HASH COMPARE &key KEY

return the best value in hash along with its hash-key and its comparison value. See best.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: best-in-list LIST COMPARE &key KEY

return the best value in list, along with its position and its comparison value. See best.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: best-root TREE
Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: best-traversal NET INS
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: clique-tree NET

Builds a clique-tree for dag. The tree is represented by an upper triangular matrix which has lists of clique-nodes in its diagonal.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: cluster-node GRAPH NODE

Generates a list of added links (node1 . node2) which are necessary to form a cluster around node. Uses an (edge-tree).

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: collect-evidence JT CLUSTER
Package

cl-bayesnet

Source

message.lisp (file)

Function: compose &rest FNS

Create a function which is the composition of the given functions.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: connect GRAPH A B
Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: copy-array ARRAY
Package

cl-bayesnet

Source

utils.lisp (file)

Function: copy-trie INSTANCE
Package

cl-bayesnet

Source

tries.lisp (file)

Function: cpt-incf ATT-STATE ATT-MASK

Increments att-state according to att-mask; att-state and att-mask are vectors. att-mask is nil for non-included attributes and the number of values for included attributes. It takes (reduce
#’* (remove nil att-mask)) to iterate through att-state. att-state must be a positive integer below the mask’s value, wherever mask is non-nil.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: cpt-index MASK ATT-STATE

Given the mask and att-state, return an index. Used to map attribute values to a single lookup value in a table.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: cycle GRAPH A
Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: degen-prob I LENGTH

Creates a 0-vector of the given length, with the i’th argument set to 1.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: delete-node GRAPH NODE

Remove references to the node from graph. Replaces the node with t

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: dimension-list LIST

Calculates the dimensionality of the list. EG: (make-array (dimension-list list) :initial-contents list)))

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: dimension-list-but-one LIST

Calculates the dimensionality of the list, minus one. EG: (make-array (dimension-list list) :initial-contents list)))

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: distribute-evidence JT CLUSTER
Package

cl-bayesnet

Source

message.lisp (file)

Function: edge< EDGE1 EDGE2
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: edge= EDGE1 EDGE2
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: emit-c-double DOUBLE
Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: emit-c-forms FUNC-NAME NET-SPEC FORMS STREAM
Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: emit-c-net NET STREAM
Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: emit-c-preamble FUNC-NAME NET-SPEC STREAM

Write out the matching function for state and val. Returns 1.0 if state is negative (missing) or state = val. Returns 0.0 otherwise.

Package

cl-bayesnet

Source

emit-c.lisp (file)

Function: find-temporary-file PREFIX SUFFIX &optional DIRECTORY
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: float-to-fixnums FLOAT

This converts a float to a list of fixnums, useful for hashing floats using fixnum-based schemes.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: floyd-warshall GRAPH

This finds all shortest paths in graph. I could make it more efficient by using the fact that the paths are symmetric.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: gen-clique NET INS NET-STATE TRAVERSAL DEPTH
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: gen-cliques NET GRAPH

Graph is an array of (itree), where each tree contains that node’s neighbours. Returns a list of cliques obtained from triangulating the graph. The triangulation can be recovered by starting with a moral graph and ensuring each clique is completely connected. Each clique is an itree of nodes. Destroys graph.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: gen-evidence NET NET-STATE NODE-NUM
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: gen-instructions NET

Generate an arithmetic circuit for the bn represented by a
net (bn.lisp). Note that this version assumes the clique-tree is a single tree (which is correct at 15/12/2007).

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: gen-parameter NET NET-STATE NODE-NUM

Generate a parameter for the net with the given net-state and node-num.

Package

cl-bayesnet

Source

bn.lisp (file)

Function: gen-separator NET INS NET-STATE TRAVERSAL DEPTH

bn - a net object.
clique-tree - a clique-tree built from the bn’s dag. Symmetric array with node-num lists on the diagonal and t where connected. node-assignment - (aref node-assignment node-num) == node’s clique index. net-state - array of the current node states. Nil means the node hasn’t been processed.
traversal - the current traversal to operate on: (clique trav1 ... travn) depth - the current depth of the traversal.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: get-* INS VALS DEPTH
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: get-+ INS VALS DEPTH
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: get-match INS NODE-NUM VALUE
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: hash-to-trie HASH &key TRIE TRIE-KEY TRIE-VALUE BAGP

Add the elements of hash to the given trie (if no trie is given, make one with the same test as the hash table. trie-key (default #’identity) is a function to apply to the hash-key. It should convert the hash-key to a list of atoms which are compatible with the trie’s test. trie-value (default #’identity) is a function to extract the value of interest from the actual value (or the key if bagp is non-nil) held in the hash.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: interpret INS NET-SPEC
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: jt-obs JT NODE-NUM OBS

Enter the observation that node-num is obs.

Package

cl-bayesnet

Source

message.lisp (file)

Function: jt-prob JT NODE-NUM

Calculates the probability of node-num given junction tree jt.

Package

cl-bayesnet

Source

message.lisp (file)

Function: jt-propagate JT
Package

cl-bayesnet

Source

message.lisp (file)

Function: jt-retract JT
Package

cl-bayesnet

Source

message.lisp (file)

Function: junction-p CLIQUES TREE

Test whether the tree is in fact a junction tree, meaning for each pair of cliques, all cliques in between contain their intersection.

Package

cl-bayesnet

Source

test.lisp (file)

Function: keyify STRING
Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: make-join-tree NET
Package

cl-bayesnet

Source

message.lisp (file)

Function: make-potential NET CLUSTER ASSIGNMENT
Package

cl-bayesnet

Source

message.lisp (file)

Function: make-trie &key (VALUE VALUE) (COUNT COUNT) (TEST TEST) (BRANCH BRANCH)
Package

cl-bayesnet

Source

tries.lisp (file)

Function: make-trie-hash ALIST &key TEST

Converts a trie alist to a trie-specific hash.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: make-vector LEN &optional INITARG
Package

cl-bayesnet

Source

utils.lisp (file)

Function: map-int FN N

Map fn across integers from 0 below n, returning the results in an (ordered) list.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: map-pairs FN LIST

applies fn to each pair of items and returns a list of the resulting values. > (map-pairs #’cons ’(1 2 3 4))
=> ((1 . 2) (1 . 3) (1 . 4) (2 . 3) (2 . 4) (3 . 4))

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: maparray FN ARRAY

maparray applies fn to all elements in array, returning the result in an array the same dimension as the first array

Package

cl-bayesnet

Source

utils.lisp (file)

Function: marginalise SEP-SET CLUSTER

Return a new potential for sep-set to match cluster.

Package

cl-bayesnet

Source

message.lisp (file)

Function: match VAL1 VAL2

Matches evidence.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: moral NET
Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: neighbour GRAPH A B
Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: neighbours GRAPH NODE-NUM

Generates a list of neighbours of the node.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: net-graph NET

Output the net’s structure in a viewable form.

Package

cl-bayesnet

Source

test.lisp (file)

Function: net-masks NET CLIQUES TRAVERSAL

Shadowing traversal, returns (tree-node node-mask combinations) for each tree-node in traversal.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: node-combinations INITIAL NODE-MASK

Returns a vector of all node index combinations built from initial. node-mask is a vector which is nil for non-incremented nodes and numstates for included nodes. DEPRECATED for being horribly slow.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: normalize VEC &optional SMOOTHING-FACTOR

Normalize a vector. Optionally adds smoothing-factor (which should be a number) to each element first. If tot is less than or equal to 0.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: num-arcs NET
Package

cl-bayesnet

Source

bn.lisp (file)

Function: num-nodes-1 NET
Package

cl-bayesnet

Source

bn.lisp (file)

Function: num-states-1 NODE
Package

cl-bayesnet

Source

bn.lisp (file)

Function: order-vector END &optional START

Create a vector of length (end - start), filled with numbers from start...(end - 1). Start defaults to 0.

Package

cl-bayesnet

Source

utils.lisp (file)

Function: parse-ace-node NAME LIST
Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-ace-potential NET PARENTS DATA-LIST
Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-ace-stream STREAM &key NET

Idea taken from trivial-configuration-parser by Brian Mastenbrook.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-netica-net LIST &key NET
Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-netica-node NAME LIST
Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: parse-netica-stream STREAM &key NET

Idea taken from trivial-configuration-parser by Brian Mastenbrook.

Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: path GRAPH A B
Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: post-process-plus DEPTH ARGS INS

Puts the form in canonical form for insertion.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: post-process-times DEPTH ARGS INS

Puts the form in canonical form for insertion.

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: preprocess-network NET

Readies the network for efficient lookup.
Sets a node ordering for the network. Also sets node parent-vec and parent-indices.

Package

cl-bayesnet

Source

bn.lisp (file)

Function: preprocess-node NODE

Store information for efficient lookup.

Package

cl-bayesnet

Source

bn.lisp (file)

Function: push-form FORM INS &optional DEPTH

Pushes a form onto instructions, and returns an index into forms. Won’t actually add a form if a matching one exists (acts like pushnew).

Package

cl-bayesnet

Source

compiler.lisp (file)

Function: random-choose SEQ
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: random-evidence NET &optional NET-SPEC ARR
Package

cl-bayesnet

Source

test.lisp (file)

Function: random-graph NUM-NODES NUM-ARCS &key ENSURE-CONNECTED
Package

cl-bayesnet

Source

test.lisp (file)

Function: random-network MAX-STATES &rest RANDOM-GRAPH-ARGS
Package

cl-bayesnet

Source

test.lisp (file)

Function: random-prob NUM-STATES
Package

cl-bayesnet

Source

test.lisp (file)

Function: random-table NODE
Package

cl-bayesnet

Source

test.lisp (file)

Function: roots GRAPH

Returns the roots of the graph as a list.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: sep-cost A B STATES

Find prod states of x in X + prod states of y in Y. clique1 and clique2 are lists, states is a vector.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: sep-mass A B

Find |intersection| of lists clique1 and clique2

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: sep-sets CLIQUES STATES
Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: set-* INS VALS FORM-NUM DEPTH
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: set-+ INS VALS FORM-NUM DEPTH
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: set-match INS NODE-NUM VALUE FORM-NUM
Package

cl-bayesnet

Source

compiler.lisp (file)

Function: split P X
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: split-probs PROBS PROB-LENGTH
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: statep NODE STATE
Package

cl-bayesnet

Source

bn.lisp (file)

Function: symmetric ARRAY X Y

Treat 2D array as a symmetric array. Settable.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Writer

(setf symmetric) (function)

Function: (setf symmetric) VAL ARRAY X Y
Package

cl-bayesnet

Source

bn-utils.lisp (file)

Reader

symmetric (function)

Function: table-lookup TABLE INDICES
Package

cl-bayesnet

Source

bn.lisp (file)

Function: test-net-random NET &optional ITERATIONS
Package

cl-bayesnet

Source

test.lisp (file)

Function: traverse TREE &optional ROOT

Builds a traversal for the undirected tree structure tree. Structure is ;(tree-node subtraversal1 ... subtraversaln)

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: tree-depth TREE ROOT
Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: trie-bottom-p TRIE

Returns t if the given trie has no branches.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-branch INSTANCE
Function: (setf trie-branch) VALUE INSTANCE
Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-branch-count TRIE

Count the number of branches of trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-branch-values TRIE

Return (key . trie-value) for each branch of trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-clear TRIE

Empties the trie, but leaves the test as is.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-count INSTANCE
Function: (setf trie-count) VALUE INSTANCE
Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-insert VALUE TRIE KEY

Insert the value in the trie with the given key. Returns the accessed trie node.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-list-bottom TRIE

List all values at the bottom of the trie (i.e. values of all tries with no branches).

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-list-depth TRIE DEPTH

List all values at the given depth (0 is the top level).

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-list-values TRIE

Recursively list all values in the trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-b FN TRIE

Apply fn to each branch of trie. Returns the trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-branches FN TRIE

Apply fn to each branch of trie. Returns a list of the returned values.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-key-value FN TRIE

Create a new trie with the same structure as trie, applying fn to the key and the old trie node.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-trie FN TRIE &rest TRIES

Apply fn to the given trie and its children, returning the results as the values of a matching trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-map-values FN TRIE

Apply fn to the given trie’s non-nil values, returning the results as the values of a matching trie.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-p OBJECT
Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-prune TO-PRUNE EXAMPLE

Recursively remove all branches in to-prune that don’t also appear in example, thus to-prune is guaranteed to be as small as example or smaller.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-search TRIE KEY

Recursively search the trie for the given key. If key is nil, We’re at the right node, so we return it. The value (which may be nil) can then be accessed with trie-value.

Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-test INSTANCE
Function: (setf trie-test) VALUE INSTANCE
Package

cl-bayesnet

Source

tries.lisp (file)

Function: trie-value INSTANCE
Function: (setf trie-value) VALUE INSTANCE
Package

cl-bayesnet

Source

tries.lisp (file)

Function: vecfn FN NUM

Build a vector by calling fn num times.

Package

cl-bayesnet

Source

bn-utils.lisp (file)

Function: weight-cluster NET GRAPH NODE

a cluster’s weight is the product of its nodes’ states.

Package

cl-bayesnet

Source

clique-tree.lisp (file)

Function: xmlbif-add-definition NET DEF
Package

cl-bayesnet

Source

parse-network.lisp (file)

Function: xmlbif-add-variable NET NODE
Package

cl-bayesnet

Source

parse-network.lisp (file)


Next: , Previous: , Up: Internal definitions   [Contents][Index]

6.2.5 Generic functions

Generic Function: %evidence OBJECT
Generic Function: (setf %evidence) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: %evidence (NODE node)

automatically generated reader method

Source

bn.lisp (file)

Method: (setf %evidence) NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: %query NET QUERY

Query a net/node.

Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: %query (NODE jt-node) (QUERY list)

FIXME: should return a single prob for the joint distribution.

Source

evidence.lisp (file)

Method: %query (NODE jt-node) (QUERY vector)
Source

evidence.lisp (file)

Method: %query (NODE jt-node) (QUERY null)
Source

evidence.lisp (file)

Method: %query (NODE jt-node) (QUERY symbol)
Source

evidence.lisp (file)

Method: %query (NODE jt-node) (QUERY integer)
Source

evidence.lisp (file)

Method: %query (JT join-tree) (QUERY list)

FIXME: should return a single prob for the joint distribution.

Source

evidence.lisp (file)

Method: %query (JT join-tree) (QUERY vector)
Source

evidence.lisp (file)

Method: %query (JT join-tree) (QUERY null)
Source

evidence.lisp (file)

Method: %query (JT join-tree) (QUERY symbol)
Source

evidence.lisp (file)

Method: %query (JT join-tree) (QUERY fixnum)
Source

evidence.lisp (file)

Method: %query (NET net) (QUERY null)
Method: %query (NET net) (QUERY list)
Method: %query (NET net) (QUERY symbol)
Method: %query (NET net) (QUERY vector)
Method: %query (NODE node) (QUERY list)
Method: %query (NODE node) (QUERY null)
Method: %query (NODE node) (QUERY symbol)
Method: %query (NODE node) (QUERY integer)
Generic Function: *-lookup OBJECT
Package

cl-bayesnet

Methods
Method: *-lookup (INSTRUCTIONS instructions)

automatically generated reader method

Source

compiler.lisp (file)

Generic Function: +-lookup OBJECT
Package

cl-bayesnet

Methods
Method: +-lookup (INSTRUCTIONS instructions)

automatically generated reader method

Source

compiler.lisp (file)

Generic Function: all-sep-sets OBJECT
Package

cl-bayesnet

Methods
Method: all-sep-sets (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Generic Function: assignment OBJECT
Generic Function: (setf assignment) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: assignment (INSTRUCTIONS instructions)

automatically generated reader method

Source

compiler.lisp (file)

Method: (setf assignment) NEW-VALUE (INSTRUCTIONS instructions)

automatically generated writer method

Source

compiler.lisp (file)

Method: assignment (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: assignment (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Generic Function: clean-potential OBJECT
Package

cl-bayesnet

Methods
Method: clean-potential (CLUSTER cluster)

automatically generated reader method

Source

message.lisp (file)

Generic Function: cliques OBJECT
Generic Function: (setf cliques) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: cliques (INSTRUCTIONS instructions)

automatically generated reader method

Source

compiler.lisp (file)

Method: (setf cliques) NEW-VALUE (INSTRUCTIONS instructions)

automatically generated writer method

Source

compiler.lisp (file)

Generic Function: clusters OBJECT
Package

cl-bayesnet

Methods
Method: clusters (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Generic Function: compiled OBJECT
Generic Function: (setf compiled) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: compiled (NET net)

automatically generated reader method

Source

bn.lisp (file)

Method: (setf compiled) NEW-VALUE (NET net)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: consistent OBJECT
Generic Function: (setf consistent) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: consistent (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Method: (setf consistent) NEW-VALUE (JOIN-TREE join-tree)

automatically generated writer method

Source

message.lisp (file)

Generic Function: evi OBJECT
Generic Function: (setf evi) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: evi (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: (setf evi) NEW-VALUE (JT-NODE jt-node)

automatically generated writer method

Source

message.lisp (file)

Method: evi (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Generic Function: evidence-1 OBJECT
Package

cl-bayesnet

Source

bn.lisp (file)

Methods
Method: evidence-1 (JT join-tree)
Source

evidence.lisp (file)

Method: evidence-1 (NET net)
Generic Function: form-count OBJECT
Generic Function: (setf form-count) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: form-count (INSTRUCTIONS instructions)

automatically generated reader method

Source

compiler.lisp (file)

Method: (setf form-count) NEW-VALUE (INSTRUCTIONS instructions)

automatically generated writer method

Source

compiler.lisp (file)

Generic Function: forms OBJECT
Generic Function: (setf forms) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: forms (INSTRUCTIONS instructions)

automatically generated reader method

Source

compiler.lisp (file)

Method: (setf forms) NEW-VALUE (INSTRUCTIONS instructions)

automatically generated writer method

Source

compiler.lisp (file)

Generic Function: index OBJECT
Generic Function: (setf index) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: index (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: index (NODE node)

automatically generated reader method

Source

bn.lisp (file)

Method: (setf index) NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: join-tree-of OBJECT
Generic Function: (setf join-tree-of) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: join-tree-of (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: (setf join-tree-of) NEW-VALUE (JT-NODE jt-node)

automatically generated writer method

Source

message.lisp (file)

Generic Function: links OBJECT
Package

cl-bayesnet

Methods
Method: links (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Generic Function: mark OBJECT
Generic Function: (setf mark) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: mark (CLUSTER cluster)

automatically generated reader method

Source

message.lisp (file)

Method: (setf mark) NEW-VALUE (CLUSTER cluster)

automatically generated writer method

Source

message.lisp (file)

Generic Function: mask OBJECT
Package

cl-bayesnet

Methods
Method: mask (POTENTIAL-CONTAINER potential-container)

automatically generated reader method

Source

message.lisp (file)

Generic Function: match-lookup OBJECT
Package

cl-bayesnet

Methods
Method: match-lookup (INSTRUCTIONS instructions)

automatically generated reader method

Source

compiler.lisp (file)

Generic Function: message-pass JT CLIQUE1 CLIQUE2
Package

cl-bayesnet

Source

message.lisp (file)

Methods
Method: message-pass (JT join-tree) (CLIQUE1 fixnum) (CLIQUE2 fixnum)
Generic Function: node-vec OBJECT
Generic Function: (setf node-vec) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: node-vec (NET net)

automatically generated reader method

Source

bn.lisp (file)

Method: (setf node-vec) NEW-VALUE (NET net)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: nodes OBJECT
Package

cl-bayesnet

Methods
Method: nodes (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Method: nodes (NET net)

automatically generated reader method

Source

bn.lisp (file)

Generic Function: obs OBJECT
Generic Function: (setf obs) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: obs (JT-NODE jt-node)

automatically generated reader method

Source

message.lisp (file)

Method: (setf obs) NEW-VALUE (JT-NODE jt-node)

automatically generated writer method

Source

message.lisp (file)

Method: obs (JOIN-TREE join-tree)

automatically generated reader method

Source

message.lisp (file)

Method: (setf obs) NEW-VALUE (JOIN-TREE join-tree)

automatically generated writer method

Source

message.lisp (file)

Generic Function: parent-indices OBJECT
Generic Function: (setf parent-indices) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: parent-indices (NODE node)

automatically generated reader method

Source

bn.lisp (file)

Method: (setf parent-indices) NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: parent-vec OBJECT
Generic Function: (setf parent-vec) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: parent-vec (NODE node)

automatically generated reader method

Source

bn.lisp (file)

Method: (setf parent-vec) NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

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

cl-bayesnet

Methods
Method: potential (POTENTIAL-CONTAINER potential-container)

automatically generated reader method

Source

message.lisp (file)

Method: (setf potential) NEW-VALUE (POTENTIAL-CONTAINER potential-container)

automatically generated writer method

Source

message.lisp (file)

Generic Function: properties OBJECT
Package

cl-bayesnet

Methods
Method: properties (NODE node)

automatically generated reader method

Source

bn.lisp (file)

Method: properties (NET net)

automatically generated reader method

Source

bn.lisp (file)

Generic Function: set-name NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: set-name NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

Method: set-name NEW-VALUE (NET net)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: set-net NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: set-net NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: set-node-order NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: set-node-order NEW-VALUE (NET net)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: set-parents NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: set-parents NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: set-states NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: set-states NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: shuffle OBJECT

Randomise the object, which should represent a sequence.

Package

cl-bayesnet

Source

utils.lisp (file)

Methods
Method: shuffle (LENGTH integer)

Create a vector of the given length using order-vector, and shuffle it.

Method: shuffle (SEQUENCE sequence)

shuffle the items in the sequence into a random order. Converts the sequence to a vector.

Method: shuffle (VECTOR vector)

shuffle the items in vector into a random order.

Generic Function: table OBJECT
Generic Function: (setf table) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: table (NODE node)

automatically generated reader method

Source

bn.lisp (file)

Method: (setf table) NEW-VALUE (NODE node)

automatically generated writer method

Source

bn.lisp (file)

Generic Function: tree OBJECT
Generic Function: (setf tree) NEW-VALUE OBJECT
Package

cl-bayesnet

Methods
Method: tree (INSTRUCTIONS instructions)

automatically generated reader method

Source

compiler.lisp (file)

Method: (setf tree) NEW-VALUE (INSTRUCTIONS instructions)

automatically generated writer method

Source

compiler.lisp (file)


Next: , Previous: , Up: Internal definitions   [Contents][Index]

6.2.6 Structures

Structure: trie ()

A trie node.

Package

cl-bayesnet

Source

tries.lisp (file)

Direct superclasses

structure-object (structure)

Direct slots
Slot: value
Readers

trie-value (function)

Writers

(setf trie-value) (function)

Slot: count
Initform

0

Readers

trie-count (function)

Writers

(setf trie-count) (function)

Slot: test
Initform

(quote eql)

Readers

trie-test (function)

Writers

(setf trie-test) (function)

Slot: branch
Readers

trie-branch (function)

Writers

(setf trie-branch) (function)


Previous: , Up: Internal definitions   [Contents][Index]

6.2.7 Classes

Class: cluster ()
Package

cl-bayesnet

Source

message.lisp (file)

Direct superclasses

potential-container (class)

Direct methods
Direct slots
Slot: mark
Readers

mark (generic function)

Writers

(setf mark) (generic function)

Slot: clean-potential
Initargs

:clean-potential

Readers

clean-potential (generic function)

Class: jt-node ()
Package

cl-bayesnet

Source

message.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: index
Initargs

:index

Readers

index (generic function)

Slot: assignment
Initargs

:assignment

Readers

assignment (generic function)

Slot: evidence
Initargs

:evidence

Readers

evi (generic function)

Writers

(setf evi) (generic function)

Slot: obs
Initargs

:obs

Readers

obs (generic function)

Writers

(setf obs) (generic function)

Slot: name
Initargs

:name

Readers

name (generic function)

Slot: states
Initargs

:states

Readers

states (generic function)

Slot: join-tree
Initargs

:join-tree

Readers

join-tree-of (generic function)

Writers

(setf join-tree-of) (generic function)

Class: potential-container ()
Package

cl-bayesnet

Source

message.lisp (file)

Direct superclasses

standard-object (class)

Direct subclasses
Direct methods
Direct slots
Slot: mask
Initargs

:mask

Readers

mask (generic function)

Slot: potential
Initargs

:potential

Readers

potential (generic function)

Writers

(setf potential) (generic function)

Class: sep-set ()
Package

cl-bayesnet

Source

message.lisp (file)

Direct superclasses

potential-container (class)


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

Appendix A Indexes


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

A.1 Concepts

Jump to:   C   F   L   M  
Index Entry  Section

C
cl-bayesnet.asd: The cl-bayesnet<dot>asd file
cl-bayesnet/src: The cl-bayesnet/src module
cl-bayesnet/src/bn-utils.lisp: The cl-bayesnet/src/bn-utils<dot>lisp file
cl-bayesnet/src/bn.lisp: The cl-bayesnet/src/bn<dot>lisp file
cl-bayesnet/src/clique-tree.lisp: The cl-bayesnet/src/clique-tree<dot>lisp file
cl-bayesnet/src/compiler.lisp: The cl-bayesnet/src/compiler<dot>lisp file
cl-bayesnet/src/emit-c.lisp: The cl-bayesnet/src/emit-c<dot>lisp file
cl-bayesnet/src/evidence.lisp: The cl-bayesnet/src/evidence<dot>lisp file
cl-bayesnet/src/message.lisp: The cl-bayesnet/src/message<dot>lisp file
cl-bayesnet/src/packages.lisp: The cl-bayesnet/src/packages<dot>lisp file
cl-bayesnet/src/parse-network.lisp: The cl-bayesnet/src/parse-network<dot>lisp file
cl-bayesnet/src/test.lisp: The cl-bayesnet/src/test<dot>lisp file
cl-bayesnet/src/tries.lisp: The cl-bayesnet/src/tries<dot>lisp file
cl-bayesnet/src/utils.lisp: The cl-bayesnet/src/utils<dot>lisp file

F
File, Lisp, cl-bayesnet.asd: The cl-bayesnet<dot>asd file
File, Lisp, cl-bayesnet/src/bn-utils.lisp: The cl-bayesnet/src/bn-utils<dot>lisp file
File, Lisp, cl-bayesnet/src/bn.lisp: The cl-bayesnet/src/bn<dot>lisp file
File, Lisp, cl-bayesnet/src/clique-tree.lisp: The cl-bayesnet/src/clique-tree<dot>lisp file
File, Lisp, cl-bayesnet/src/compiler.lisp: The cl-bayesnet/src/compiler<dot>lisp file
File, Lisp, cl-bayesnet/src/emit-c.lisp: The cl-bayesnet/src/emit-c<dot>lisp file
File, Lisp, cl-bayesnet/src/evidence.lisp: The cl-bayesnet/src/evidence<dot>lisp file
File, Lisp, cl-bayesnet/src/message.lisp: The cl-bayesnet/src/message<dot>lisp file
File, Lisp, cl-bayesnet/src/packages.lisp: The cl-bayesnet/src/packages<dot>lisp file
File, Lisp, cl-bayesnet/src/parse-network.lisp: The cl-bayesnet/src/parse-network<dot>lisp file
File, Lisp, cl-bayesnet/src/test.lisp: The cl-bayesnet/src/test<dot>lisp file
File, Lisp, cl-bayesnet/src/tries.lisp: The cl-bayesnet/src/tries<dot>lisp file
File, Lisp, cl-bayesnet/src/utils.lisp: The cl-bayesnet/src/utils<dot>lisp file

L
Lisp File, cl-bayesnet.asd: The cl-bayesnet<dot>asd file
Lisp File, cl-bayesnet/src/bn-utils.lisp: The cl-bayesnet/src/bn-utils<dot>lisp file
Lisp File, cl-bayesnet/src/bn.lisp: The cl-bayesnet/src/bn<dot>lisp file
Lisp File, cl-bayesnet/src/clique-tree.lisp: The cl-bayesnet/src/clique-tree<dot>lisp file
Lisp File, cl-bayesnet/src/compiler.lisp: The cl-bayesnet/src/compiler<dot>lisp file
Lisp File, cl-bayesnet/src/emit-c.lisp: The cl-bayesnet/src/emit-c<dot>lisp file
Lisp File, cl-bayesnet/src/evidence.lisp: The cl-bayesnet/src/evidence<dot>lisp file
Lisp File, cl-bayesnet/src/message.lisp: The cl-bayesnet/src/message<dot>lisp file
Lisp File, cl-bayesnet/src/packages.lisp: The cl-bayesnet/src/packages<dot>lisp file
Lisp File, cl-bayesnet/src/parse-network.lisp: The cl-bayesnet/src/parse-network<dot>lisp file
Lisp File, cl-bayesnet/src/test.lisp: The cl-bayesnet/src/test<dot>lisp file
Lisp File, cl-bayesnet/src/tries.lisp: The cl-bayesnet/src/tries<dot>lisp file
Lisp File, cl-bayesnet/src/utils.lisp: The cl-bayesnet/src/utils<dot>lisp file

M
Module, cl-bayesnet/src: The cl-bayesnet/src module

Jump to:   C   F   L   M  

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

A.2 Functions

Jump to:   %   (   *   +  
A   B   C   D   E   F   G   H   I   J   K   L   M   N   O   P   Q   R   S   T   U   V   W   X  
Index Entry  Section

%
%evidence: Internal generic functions
%evidence: Internal generic functions
%evidence-1: Internal functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%query: Internal generic functions
%trie-map-key-value: Internal functions
%trie-map-trie: Internal functions

(
(setf %evidence): Internal generic functions
(setf %evidence): Internal generic functions
(setf assignment): Internal generic functions
(setf assignment): Internal generic functions
(setf cliques): Internal generic functions
(setf cliques): Internal generic functions
(setf compiled): Internal generic functions
(setf compiled): Internal generic functions
(setf consistent): Internal generic functions
(setf consistent): Internal generic functions
(setf evi): Internal generic functions
(setf evi): Internal generic functions
(setf evidence): Exported generic functions
(setf form-count): Internal generic functions
(setf form-count): Internal generic functions
(setf forms): Internal generic functions
(setf forms): Internal generic functions
(setf index): Internal generic functions
(setf index): Internal generic functions
(setf join-tree-of): Internal generic functions
(setf join-tree-of): Internal generic functions
(setf mark): Internal generic functions
(setf mark): Internal generic functions
(setf node-vec): Internal generic functions
(setf node-vec): Internal generic functions
(setf obs): Internal generic functions
(setf obs): Internal generic functions
(setf obs): Internal generic functions
(setf parent-indices): Internal generic functions
(setf parent-indices): Internal generic functions
(setf parent-vec): Internal generic functions
(setf parent-vec): Internal generic functions
(setf potential): Internal generic functions
(setf potential): Internal generic functions
(setf symmetric): Internal functions
(setf table): Internal generic functions
(setf table): Internal generic functions
(setf tree): Internal generic functions
(setf tree): Internal generic functions
(setf trie-branch): Internal functions
(setf trie-count): Internal functions
(setf trie-test): Internal functions
(setf trie-value): Internal functions

*
*-lookup: Internal generic functions
*-lookup: Internal generic functions

+
+-lookup: Internal generic functions
+-lookup: Internal generic functions

A
add-evidence: Exported generic functions
add-evidence: Exported generic functions
add-evidence: Exported generic functions
add-evidence: Exported generic functions
add-form: Internal functions
aif: Internal macros
all-sep-sets: Internal generic functions
all-sep-sets: Internal generic functions
assign-nodes: Internal functions
assignment: Internal generic functions
assignment: Internal generic functions
assignment: Internal generic functions
assignment: Internal generic functions
awhen: Internal macros

B
best: Internal functions
best-in-array: Internal functions
best-in-hash: Internal functions
best-in-list: Internal functions
best-root: Internal functions
best-traversal: Internal functions

C
clean-potential: Internal generic functions
clean-potential: Internal generic functions
clear-evidence: Exported generic functions
clear-evidence: Exported generic functions
clear-evidence: Exported generic functions
clear-evidence: Exported generic functions
clique-tree: Internal functions
cliques: Internal generic functions
cliques: Internal generic functions
cluster-node: Internal functions
clusters: Internal generic functions
clusters: Internal generic functions
collect-evidence: Internal functions
compiled: Internal generic functions
compiled: Internal generic functions
compose: Internal functions
connect: Internal functions
consistent: Internal generic functions
consistent: Internal generic functions
copy-array: Internal functions
copy-trie: Internal functions
cpt-incf: Internal functions
cpt-index: Internal functions
cycle: Internal functions

D
degen-prob: Internal functions
delete-node: Internal functions
dimension-list: Internal functions
dimension-list-but-one: Internal functions
distribute-evidence: Internal functions
do-trie-branches: Internal macros
do-trie-values: Internal macros
do-upper: Internal macros

E
edge<: Internal functions
edge=: Internal functions
emit-c-double: Internal functions
emit-c-forms: Internal functions
emit-c-net: Internal functions
emit-c-preamble: Internal functions
evi: Internal generic functions
evi: Internal generic functions
evi: Internal generic functions
evidence: Exported generic functions
evidence: Exported generic functions
evidence: Exported generic functions
evidence: Exported generic functions
evidence: Exported generic functions
evidence-1: Internal generic functions
evidence-1: Internal generic functions
evidence-1: Internal generic functions
evidence-index: Exported generic functions
evidence-index: Exported generic functions
evidence-index: Exported generic functions
evidence-index: Exported generic functions
evidence-index: Exported generic functions

F
find-temporary-file: Internal functions
float-to-fixnums: Internal functions
floyd-warshall: Internal functions
form-count: Internal generic functions
form-count: Internal generic functions
forms: Internal generic functions
forms: Internal generic functions
Function, %evidence-1: Internal functions
Function, %trie-map-key-value: Internal functions
Function, %trie-map-trie: Internal functions
Function, (setf symmetric): Internal functions
Function, (setf trie-branch): Internal functions
Function, (setf trie-count): Internal functions
Function, (setf trie-test): Internal functions
Function, (setf trie-value): Internal functions
Function, add-form: Internal functions
Function, assign-nodes: Internal functions
Function, best: Internal functions
Function, best-in-array: Internal functions
Function, best-in-hash: Internal functions
Function, best-in-list: Internal functions
Function, best-root: Internal functions
Function, best-traversal: Internal functions
Function, clique-tree: Internal functions
Function, cluster-node: Internal functions
Function, collect-evidence: Internal functions
Function, compose: Internal functions
Function, connect: Internal functions
Function, copy-array: Internal functions
Function, copy-trie: Internal functions
Function, cpt-incf: Internal functions
Function, cpt-index: Internal functions
Function, cycle: Internal functions
Function, degen-prob: Internal functions
Function, delete-node: Internal functions
Function, dimension-list: Internal functions
Function, dimension-list-but-one: Internal functions
Function, distribute-evidence: Internal functions
Function, edge<: Internal functions
Function, edge=: Internal functions
Function, emit-c-double: Internal functions
Function, emit-c-forms: Internal functions
Function, emit-c-net: Internal functions
Function, emit-c-preamble: Internal functions
Function, find-temporary-file: Internal functions
Function, float-to-fixnums: Internal functions
Function, floyd-warshall: Internal functions
Function, gen-clique: Internal functions
Function, gen-cliques: Internal functions
Function, gen-evidence: Internal functions
Function, gen-instructions: Internal functions
Function, gen-parameter: Internal functions
Function, gen-separator: Internal functions
Function, get-*: Internal functions
Function, get-+: Internal functions
Function, get-match: Internal functions
Function, hash-to-trie: Internal functions
Function, interpret: Internal functions
Function, jt-obs: Internal functions
Function, jt-prob: Internal functions
Function, jt-propagate: Internal functions
Function, jt-retract: Internal functions
Function, junction-p: Internal functions
Function, keyify: Internal functions
Function, load-ace: Exported functions
Function, load-dne: Exported functions
Function, load-xmlbif: Exported functions
Function, make-join-tree: Internal functions
Function, make-potential: Internal functions
Function, make-trie: Internal functions
Function, make-trie-hash: Internal functions
Function, make-vector: Internal functions
Function, map-int: Internal functions
Function, map-pairs: Internal functions
Function, maparray: Internal functions
Function, marginalise: Internal functions
Function, match: Internal functions
Function, moral: Internal functions
Function, neighbour: Internal functions
Function, neighbours: Internal functions
Function, net-graph: Internal functions
Function, net-masks: Internal functions
Function, node-combinations: Internal functions
Function, normalize: Internal functions
Function, num-arcs: Internal functions
Function, num-nodes-1: Internal functions
Function, num-states-1: Internal functions
Function, order-vector: Internal functions
Function, parse-ace-node: Internal functions
Function, parse-ace-potential: Internal functions
Function, parse-ace-stream: Internal functions
Function, parse-netica-net: Internal functions
Function, parse-netica-node: Internal functions
Function, parse-netica-stream: Internal functions
Function, path: Internal functions
Function, post-process-plus: Internal functions
Function, post-process-times: Internal functions
Function, preprocess-network: Internal functions
Function, preprocess-node: Internal functions
Function, push-form: Internal functions
Function, query: Exported functions
Function, random-choose: Internal functions
Function, random-evidence: Internal functions
Function, random-graph: Internal functions
Function, random-network: Internal functions
Function, random-prob: Internal functions
Function, random-table: Internal functions
Function, roots: Internal functions
Function, sep-cost: Internal functions
Function, sep-mass: Internal functions
Function, sep-sets: Internal functions
Function, set-*: Internal functions
Function, set-+: Internal functions
Function, set-match: Internal functions
Function, split: Internal functions
Function, split-probs: Internal functions
Function, statep: Internal functions
Function, symmetric: Internal functions
Function, table-lookup: Internal functions
Function, test-net-random: Internal functions
Function, traverse: Internal functions
Function, tree-depth: Internal functions
Function, trie-bottom-p: Internal functions
Function, trie-branch: Internal functions
Function, trie-branch-count: Internal functions
Function, trie-branch-values: Internal functions
Function, trie-clear: Internal functions
Function, trie-count: Internal functions
Function, trie-insert: Internal functions
Function, trie-list-bottom: Internal functions
Function, trie-list-depth: Internal functions
Function, trie-list-values: Internal functions
Function, trie-map-b: Internal functions
Function, trie-map-branches: Internal functions
Function, trie-map-key-value: Internal functions
Function, trie-map-trie: Internal functions
Function, trie-map-values: Internal functions
Function, trie-p: Internal functions
Function, trie-prune: Internal functions
Function, trie-search: Internal functions
Function, trie-test: Internal functions
Function, trie-value: Internal functions
Function, use-compiled-c: Exported functions
Function, use-interpreted: Exported functions
Function, use-join-tree: Exported functions
Function, vecfn: Internal functions
Function, weight-cluster: Internal functions
Function, xmlbif-add-definition: Internal functions
Function, xmlbif-add-variable: Internal functions

G
gen-clique: Internal functions
gen-cliques: Internal functions
gen-evidence: Internal functions
gen-instructions: Internal functions
gen-parameter: Internal functions
gen-separator: Internal functions
Generic Function, %evidence: Internal generic functions
Generic Function, %query: Internal generic functions
Generic Function, (setf %evidence): Internal generic functions
Generic Function, (setf assignment): Internal generic functions
Generic Function, (setf cliques): Internal generic functions
Generic Function, (setf compiled): Internal generic functions
Generic Function, (setf consistent): Internal generic functions
Generic Function, (setf evi): Internal generic functions
Generic Function, (setf evidence): Exported generic functions
Generic Function, (setf form-count): Internal generic functions
Generic Function, (setf forms): Internal generic functions
Generic Function, (setf index): Internal generic functions
Generic Function, (setf join-tree-of): Internal generic functions
Generic Function, (setf mark): Internal generic functions
Generic Function, (setf node-vec): Internal generic functions
Generic Function, (setf obs): Internal generic functions
Generic Function, (setf parent-indices): Internal generic functions
Generic Function, (setf parent-vec): Internal generic functions
Generic Function, (setf potential): Internal generic functions
Generic Function, (setf table): Internal generic functions
Generic Function, (setf tree): Internal generic functions
Generic Function, *-lookup: Internal generic functions
Generic Function, +-lookup: Internal generic functions
Generic Function, add-evidence: Exported generic functions
Generic Function, all-sep-sets: Internal generic functions
Generic Function, assignment: Internal generic functions
Generic Function, clean-potential: Internal generic functions
Generic Function, clear-evidence: Exported generic functions
Generic Function, cliques: Internal generic functions
Generic Function, clusters: Internal generic functions
Generic Function, compiled: Internal generic functions
Generic Function, consistent: Internal generic functions
Generic Function, evi: Internal generic functions
Generic Function, evidence: Exported generic functions
Generic Function, evidence-1: Internal generic functions
Generic Function, evidence-index: Exported generic functions
Generic Function, form-count: Internal generic functions
Generic Function, forms: Internal generic functions
Generic Function, index: Internal generic functions
Generic Function, join-tree-of: Internal generic functions
Generic Function, links: Internal generic functions
Generic Function, mark: Internal generic functions
Generic Function, mask: Internal generic functions
Generic Function, match-lookup: Internal generic functions
Generic Function, message-pass: Internal generic functions
Generic Function, name: Exported generic functions
Generic Function, net: Exported generic functions
Generic Function, node: Exported generic functions
Generic Function, node-order: Exported generic functions
Generic Function, node-vec: Internal generic functions
Generic Function, nodes: Internal generic functions
Generic Function, num-nodes: Exported generic functions
Generic Function, num-states: Exported generic functions
Generic Function, obs: Internal generic functions
Generic Function, parent-indices: Internal generic functions
Generic Function, parent-vec: Internal generic functions
Generic Function, parents: Exported generic functions
Generic Function, potential: Internal generic functions
Generic Function, properties: Internal generic functions
Generic Function, set-name: Internal generic functions
Generic Function, set-net: Internal generic functions
Generic Function, set-node-order: Internal generic functions
Generic Function, set-parents: Internal generic functions
Generic Function, set-states: Internal generic functions
Generic Function, shuffle: Internal generic functions
Generic Function, states: Exported generic functions
Generic Function, table: Internal generic functions
Generic Function, tree: Internal generic functions
get-*: Internal functions
get-+: Internal functions
get-match: Internal functions

H
hash-to-trie: Internal functions

I
index: Internal generic functions
index: Internal generic functions
index: Internal generic functions
interpret: Internal functions

J
join-tree-of: Internal generic functions
join-tree-of: Internal generic functions
jt-obs: Internal functions
jt-prob: Internal functions
jt-propagate: Internal functions
jt-retract: Internal functions
junction-p: Internal functions

K
keyify: Internal functions

L
links: Internal generic functions
links: Internal generic functions
load-ace: Exported functions
load-dne: Exported functions
load-xmlbif: Exported functions

M
Macro, aif: Internal macros
Macro, awhen: Internal macros
Macro, do-trie-branches: Internal macros
Macro, do-trie-values: Internal macros
Macro, do-upper: Internal macros
Macro, multf: Internal macros
Macro, multiply-floats: Internal macros
Macro, reset-potential: Internal macros
Macro, returnit: Internal macros
Macro, save-evidence: Internal macros
Macro, sum-floats: Internal macros
Macro, vlength: Internal macros
Macro, while: Internal macros
Macro, with-calculation: Internal macros
Macro, with-calculation-context: Internal macros
Macro, with-evidence: Exported macros
Macro, with-gensyms: Internal macros
make-join-tree: Internal functions
make-potential: Internal functions
make-trie: Internal functions
make-trie-hash: Internal functions
make-vector: Internal functions
map-int: Internal functions
map-pairs: Internal functions
maparray: Internal functions
marginalise: Internal functions
mark: Internal generic functions
mark: Internal generic functions
mask: Internal generic functions
mask: Internal generic functions
match: Internal functions
match-lookup: Internal generic functions
match-lookup: Internal generic functions
message-pass: Internal generic functions
message-pass: Internal generic functions
Method, %evidence: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, %query: Internal generic functions
Method, (setf %evidence): Internal generic functions
Method, (setf assignment): Internal generic functions
Method, (setf cliques): Internal generic functions
Method, (setf compiled): Internal generic functions
Method, (setf consistent): Internal generic functions
Method, (setf evi): Internal generic functions
Method, (setf form-count): Internal generic functions
Method, (setf forms): Internal generic functions
Method, (setf index): Internal generic functions
Method, (setf join-tree-of): Internal generic functions
Method, (setf mark): Internal generic functions
Method, (setf node-vec): Internal generic functions
Method, (setf obs): Internal generic functions
Method, (setf obs): Internal generic functions
Method, (setf parent-indices): Internal generic functions
Method, (setf parent-vec): Internal generic functions
Method, (setf potential): Internal generic functions
Method, (setf table): Internal generic functions
Method, (setf tree): Internal generic functions
Method, *-lookup: Internal generic functions
Method, +-lookup: Internal generic functions
Method, add-evidence: Exported generic functions
Method, add-evidence: Exported generic functions
Method, add-evidence: Exported generic functions
Method, all-sep-sets: Internal generic functions
Method, assignment: Internal generic functions
Method, assignment: Internal generic functions
Method, assignment: Internal generic functions
Method, clean-potential: Internal generic functions
Method, clear-evidence: Exported generic functions
Method, clear-evidence: Exported generic functions
Method, clear-evidence: Exported generic functions
Method, cliques: Internal generic functions
Method, clusters: Internal generic functions
Method, compiled: Internal generic functions
Method, consistent: Internal generic functions
Method, evi: Internal generic functions
Method, evi: Internal generic functions
Method, evidence: Exported generic functions
Method, evidence: Exported generic functions
Method, evidence: Exported generic functions
Method, evidence: Exported generic functions
Method, evidence-1: Internal generic functions
Method, evidence-1: Internal generic functions
Method, evidence-index: Exported generic functions
Method, evidence-index: Exported generic functions
Method, evidence-index: Exported generic functions
Method, evidence-index: Exported generic functions
Method, form-count: Internal generic functions
Method, forms: Internal generic functions
Method, index: Internal generic functions
Method, index: Internal generic functions
Method, join-tree-of: Internal generic functions
Method, links: Internal generic functions
Method, mark: Internal generic functions
Method, mask: Internal generic functions
Method, match-lookup: Internal generic functions
Method, message-pass: Internal generic functions
Method, name: Exported generic functions
Method, name: Exported generic functions
Method, name: Exported generic functions
Method, net: Exported generic functions
Method, net: Exported generic functions
Method, node: Exported generic functions
Method, node: Exported generic functions
Method, node: Exported generic functions
Method, node: Exported generic functions
Method, node-order: Exported generic functions
Method, node-vec: Internal generic functions
Method, nodes: Internal generic functions
Method, nodes: Internal generic functions
Method, num-nodes: Exported generic functions
Method, num-states: Exported generic functions
Method, obs: Internal generic functions
Method, obs: Internal generic functions
Method, parent-indices: Internal generic functions
Method, parent-vec: Internal generic functions
Method, parents: Exported generic functions
Method, potential: Internal generic functions
Method, properties: Internal generic functions
Method, properties: Internal generic functions
Method, set-name: Internal generic functions
Method, set-name: Internal generic functions
Method, set-net: Internal generic functions
Method, set-node-order: Internal generic functions
Method, set-parents: Internal generic functions
Method, set-states: Internal generic functions
Method, shuffle: Internal generic functions
Method, shuffle: Internal generic functions
Method, shuffle: Internal generic functions
Method, states: Exported generic functions
Method, states: Exported generic functions
Method, table: Internal generic functions
Method, tree: Internal generic functions
moral: Internal functions
multf: Internal macros
multiply-floats: Internal macros

N
name: Exported generic functions
name: Exported generic functions
name: Exported generic functions
name: Exported generic functions
neighbour: Internal functions
neighbours: Internal functions
net: Exported generic functions
net: Exported generic functions
net: Exported generic functions
net-graph: Internal functions
net-masks: Internal functions
node: Exported generic functions
node: Exported generic functions
node: Exported generic functions
node: Exported generic functions
node: Exported generic functions
node-combinations: Internal functions
node-order: Exported generic functions
node-order: Exported generic functions
node-vec: Internal generic functions
node-vec: Internal generic functions
nodes: Internal generic functions
nodes: Internal generic functions
nodes: Internal generic functions
normalize: Internal functions
num-arcs: Internal functions
num-nodes: Exported generic functions
num-nodes: Exported generic functions
num-nodes-1: Internal functions
num-states: Exported generic functions
num-states: Exported generic functions
num-states-1: Internal functions

O
obs: Internal generic functions
obs: Internal generic functions
obs: Internal generic functions
order-vector: Internal functions

P
parent-indices: Internal generic functions
parent-indices: Internal generic functions
parent-vec: Internal generic functions
parent-vec: Internal generic functions
parents: Exported generic functions
parents: Exported generic functions
parse-ace-node: Internal functions
parse-ace-potential: Internal functions
parse-ace-stream: Internal functions
parse-netica-net: Internal functions
parse-netica-node: Internal functions
parse-netica-stream: Internal functions
path: Internal functions
post-process-plus: Internal functions
post-process-times: Internal functions
potential: Internal generic functions
potential: Internal generic functions
preprocess-network: Internal functions
preprocess-node: Internal functions
properties: Internal generic functions
properties: Internal generic functions
properties: Internal generic functions
push-form: Internal functions

Q
query: Exported functions

R
random-choose: Internal functions
random-evidence: Internal functions
random-graph: Internal functions
random-network: Internal functions
random-prob: Internal functions
random-table: Internal functions
reset-potential: Internal macros
returnit: Internal macros
roots: Internal functions

S
save-evidence: Internal macros
sep-cost: Internal functions
sep-mass: Internal functions
sep-sets: Internal functions
set-*: Internal functions
set-+: Internal functions
set-match: Internal functions
set-name: Internal generic functions
set-name: Internal generic functions
set-name: Internal generic functions
set-net: Internal generic functions
set-net: Internal generic functions
set-node-order: Internal generic functions
set-node-order: Internal generic functions
set-parents: Internal generic functions
set-parents: Internal generic functions
set-states: Internal generic functions
set-states: Internal generic functions
shuffle: Internal generic functions
shuffle: Internal generic functions
shuffle: Internal generic functions
shuffle: Internal generic functions
split: Internal functions
split-probs: Internal functions
statep: Internal functions
states: Exported generic functions
states: Exported generic functions
states: Exported generic functions
sum-floats: Internal macros
symmetric: Internal functions

T
table: Internal generic functions
table: Internal generic functions
table-lookup: Internal functions
test-net-random: Internal functions
traverse: Internal functions
tree: Internal generic functions
tree: Internal generic functions
tree-depth: Internal functions
trie-bottom-p: Internal functions
trie-branch: Internal functions
trie-branch-count: Internal functions
trie-branch-values: Internal functions
trie-clear: Internal functions
trie-count: Internal functions
trie-insert: Internal functions
trie-list-bottom: Internal functions
trie-list-depth: Internal functions
trie-list-values: Internal functions
trie-map-b: Internal functions
trie-map-branches: Internal functions
trie-map-key-value: Internal functions
trie-map-trie: Internal functions
trie-map-values: Internal functions
trie-p: Internal functions
trie-prune: Internal functions
trie-search: Internal functions
trie-test: Internal functions
trie-value: Internal functions

U
use-compiled-c: Exported functions
use-interpreted: Exported functions
use-join-tree: Exported functions

V
vecfn: Internal functions
vlength: Internal macros

W
weight-cluster: Internal functions
while: Internal macros
with-calculation: Internal macros
with-calculation-context: Internal macros
with-evidence: Exported macros
with-gensyms: Internal macros

X
xmlbif-add-definition: Internal functions
xmlbif-add-variable: Internal functions

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A.3 Variables

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Index Entry  Section

*
*-lookup: Exported classes
*calculation-context*: Internal special variables
*gcc-format-string*: Internal special variables
*temporary-directory*: Internal special variables

+
+-lookup: Exported classes
+trie-hash-threshold+: Internal constants

A
all-sep-sets: Exported classes
assignment: Exported classes
assignment: Exported classes
assignment: Internal classes

B
branch: Internal structures

C
clean-potential: Internal classes
cliques: Exported classes
clusters: Exported classes
compiled: Exported classes
consistent: Exported classes
Constant, +trie-hash-threshold+: Internal constants
count: Internal structures

E
evidence: Exported classes
evidence: Exported classes
evidence: Internal classes

F
form-count: Exported classes
forms: Exported classes

I
index: Exported classes
index: Internal classes

J
join-tree: Internal classes

L
links: Exported classes

M
mark: Internal classes
mask: Internal classes
match-lookup: Exported classes

N
name: Exported classes
name: Exported classes
name: Internal classes
net: Exported classes
net: Exported classes
node-order: Exported classes
node-vec: Exported classes
nodes: Exported classes
nodes: Exported classes
num-nodes: Exported classes
num-states: Exported classes

O
obs: Exported classes
obs: Internal classes

P
parent-indices: Exported classes
parent-vec: Exported classes
parents: Exported classes
potential: Internal classes
properties: Exported classes
properties: Exported classes

S
Slot, *-lookup: Exported classes
Slot, +-lookup: Exported classes
Slot, all-sep-sets: Exported classes
Slot, assignment: Exported classes
Slot, assignment: Exported classes
Slot, assignment: Internal classes
Slot, branch: Internal structures
Slot, clean-potential: Internal classes
Slot, cliques: Exported classes
Slot, clusters: Exported classes
Slot, compiled: Exported classes
Slot, consistent: Exported classes
Slot, count: Internal structures
Slot, evidence: Exported classes
Slot, evidence: Exported classes
Slot, evidence: Internal classes
Slot, form-count: Exported classes
Slot, forms: Exported classes
Slot, index: Exported classes
Slot, index: Internal classes
Slot, join-tree: Internal classes
Slot, links: Exported classes
Slot, mark: Internal classes
Slot, mask: Internal classes
Slot, match-lookup: Exported classes
Slot, name: Exported classes
Slot, name: Exported classes
Slot, name: Internal classes
Slot, net: Exported classes
Slot, net: Exported classes
Slot, node-order: Exported classes
Slot, node-vec: Exported classes
Slot, nodes: Exported classes
Slot, nodes: Exported classes
Slot, num-nodes: Exported classes
Slot, num-states: Exported classes
Slot, obs: Exported classes
Slot, obs: Internal classes
Slot, parent-indices: Exported classes
Slot, parent-vec: Exported classes
Slot, parents: Exported classes
Slot, potential: Internal classes
Slot, properties: Exported classes
Slot, properties: Exported classes
Slot, states: Exported classes
Slot, states: Internal classes
Slot, table: Exported classes
Slot, test: Internal structures
Slot, tree: Exported classes
Slot, value: Internal structures
Special Variable, *calculation-context*: Internal special variables
Special Variable, *gcc-format-string*: Internal special variables
Special Variable, *temporary-directory*: Internal special variables
states: Exported classes
states: Internal classes

T
table: Exported classes
test: Internal structures
tree: Exported classes

V
value: Internal structures

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

A.4 Data types

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Index Entry  Section

C
cl-bayesnet: The cl-bayesnet system
cl-bayesnet: The cl-bayesnet package
Class, cluster: Internal classes
Class, instructions: Exported classes
Class, join-tree: Exported classes
Class, jt-node: Internal classes
Class, net: Exported classes
Class, node: Exported classes
Class, potential-container: Internal classes
Class, sep-set: Internal classes
cluster: Internal classes

I
instructions: Exported classes

J
join-tree: Exported classes
jt-node: Internal classes

N
net: Exported classes
node: Exported classes

P
Package, cl-bayesnet: The cl-bayesnet package
potential-container: Internal classes

S
sep-set: Internal classes
Structure, trie: Internal structures
System, cl-bayesnet: The cl-bayesnet system

T
trie: Internal structures

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