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This is the clusters Reference Manual, version 1.0.0, generated automatically by Declt version 3.0 "Montgomery Scott" on Sun May 15 04:27:16 2022 GMT+0.
• Introduction | What clusters is all about | |
• Systems | The systems documentation | |
• Modules | The modules documentation | |
• Files | The files documentation | |
• Packages | The packages documentation | |
• Definitions | The symbols documentation | |
• Indexes | Concepts, functions, variables and data types |
Variety of clustering tools for the Common Lisp
Package clusters.distance presentes distance functions, intended for use in clustering algorithms. This includes:
Package clusters.metric also presents functions intended for use in clustering algorithms, However, these functions also happen to be true metrics.
Each clustering algorithm has its own package exporting PARAMETERS symbol. This symbol names the class used to hold the algorithm parameters. To use the algorithm, first construct instance of this class, then call CLUSTER function passing the PARAMETERS instance into it along with the DATA. The returned object contains the clusters, and they can be extracted using the CLUSTER-CONTENTS function. The following example has been taken from the tests.
(defun metric (a b)
(coerce (abs (- a b))
'single-float))
(let* ((data (~> (concatenate 'vector
(iota 100 :start 0)
(iota 300 :start 500)
(iota 100 :start 200))
shuffle))
(parameters (make-instance 'clusters.clarans:parameters
:parallelp nil
:medoids-count 10
:max-neighbor 200
:distance-function #'metric))
(clusters (clusters:cluster parameters data))
(cluster-contents (clusters:cluster-contents clusters)))
...)
All PARAMETERS classes contain slots intended bootsrapping silhouette values for the clusters. To obtain the silhouette value from the clustering results simply call the CLUSTERS:SILHOUETTE function. This is particulary useful if you are attempting to find the optimal number of clusters.
Majority of the algorithms in this system have rudementary parallelization, made with the ever so useful LPARALLEL library. Please notice, that this means that (unless you are certain that NIL has been passed as :PARALLELP value) you must avoid calling CLUSTER on the LPARALLEL worker thread. Otherwise: deadlocks.
You can use clusters:silhouette to obtain silhouette values for each of the constructed clusters.
Next: Modules, Previous: Introduction, Up: Top [Contents][Index]
The main system appears first, followed by any subsystem dependency.
• The clusters system |
Marek Kochanowicz
Marek Kochanowicz
BSD simplified
Cluster algorithms in CL, for CL.
1.0.0
clusters.asd (file)
Modules are listed depth-first from the system components tree.
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aux-package.lisp (file)
clusters (system)
utils/
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utils (module)
clusters (system)
metric/
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metric (module)
clusters (system)
distance/
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distance (module)
clusters (system)
common/
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common (module)
clusters (system)
pam/
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pam (module)
clusters (system)
clarans/
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clarans (module)
clusters (system)
k-means/
Files are sorted by type and then listed depth-first from the systems components trees.
• Lisp files |
Next: The clusters/aux-package․lisp file, Previous: Lisp files, Up: Lisp files [Contents][Index]
/home/quickref/quicklisp/dists/quicklisp/software/clusters-20220331-git/clusters.asd
clusters (system)
Next: The clusters/utils/package․lisp file, Previous: The clusters․asd file, Up: Lisp files [Contents][Index]
clusters (system)
aux-package.lisp
defpackage (macro)
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utils (module)
utils/package.lisp
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utils (module)
utils/maps.lisp
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utils (module)
utils/matrix.lisp
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utils (module)
utils/random.lisp
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utils (module)
utils/utils.lisp
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Next: The clusters/metric/docstrings․lisp file, Previous: The clusters/utils/partition․lisp file, Up: Lisp files [Contents][Index]
metric (module)
metric/package.lisp
Next: The clusters/metric/euclid․lisp file, Previous: The clusters/metric/package․lisp file, Up: Lisp files [Contents][Index]
metric (module)
metric/docstrings.lisp
Next: The clusters/metric/svr․lisp file, Previous: The clusters/metric/docstrings․lisp file, Up: Lisp files [Contents][Index]
Next: The clusters/metric/levenshtein․lisp file, Previous: The clusters/metric/euclid․lisp file, Up: Lisp files [Contents][Index]
metric (module)
metric/svr.lisp
svr (function)
Next: The clusters/metric/lcs․lisp file, Previous: The clusters/metric/svr․lisp file, Up: Lisp files [Contents][Index]
metric (module)
metric/levenshtein.lisp
levenshtein (function)
Next: The clusters/metric/hellinger․lisp file, Previous: The clusters/metric/levenshtein․lisp file, Up: Lisp files [Contents][Index]
Next: The clusters/metric/earth-mover․lisp file, Previous: The clusters/metric/lcs․lisp file, Up: Lisp files [Contents][Index]
metric (module)
metric/hellinger.lisp
hellinger (function)
+sqrt2+ (constant)
Next: The clusters/metric/average․lisp file, Previous: The clusters/metric/hellinger․lisp file, Up: Lisp files [Contents][Index]
metric (module)
metric/earth-mover.lisp
earth-mover-metric (function)
Next: The clusters/metric/group-average․lisp file, Previous: The clusters/metric/earth-mover․lisp file, Up: Lisp files [Contents][Index]
Next: The clusters/metric/hausdorff․lisp file, Previous: The clusters/metric/average․lisp file, Up: Lisp files [Contents][Index]
metric (module)
metric/group-average.lisp
group-average (function)
Next: The clusters/distance/package․lisp file, Previous: The clusters/metric/group-average․lisp file, Up: Lisp files [Contents][Index]
Next: The clusters/distance/docstrings․lisp file, Previous: The clusters/metric/hausdorff․lisp file, Up: Lisp files [Contents][Index]
distance (module)
distance/package.lisp
Next: The clusters/distance/bhattacharyya․lisp file, Previous: The clusters/distance/package․lisp file, Up: Lisp files [Contents][Index]
distance (module)
distance/docstrings.lisp
Next: The clusters/distance/sinkhorn․lisp file, Previous: The clusters/distance/docstrings․lisp file, Up: Lisp files [Contents][Index]
distance (module)
distance/bhattacharyya.lisp
bhattacharyya (function)
Next: The clusters/common/package․lisp file, Previous: The clusters/distance/bhattacharyya․lisp file, Up: Lisp files [Contents][Index]
distance (module)
distance/sinkhorn.lisp
sinkhorn (function)
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Next: The clusters/common/types․lisp file, Previous: The clusters/common/package․lisp file, Up: Lisp files [Contents][Index]
common (module)
common/generics.lisp
parallel-p (generic function)
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common (module)
common/types.lisp
parameters-holder (class)
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common (module)
common/utils.lisp
cluster-values (function)
Next: The clusters/common/silhouette․lisp file, Previous: The clusters/common/utils․lisp file, Up: Lisp files [Contents][Index]
common (module)
common/functions.lisp
Next: The clusters/common/methods․lisp file, Previous: The clusters/common/functions․lisp file, Up: Lisp files [Contents][Index]
common (module)
common/silhouette.lisp
silhouette (method)
Next: The clusters/pam/package․lisp file, Previous: The clusters/common/silhouette․lisp file, Up: Lisp files [Contents][Index]
common (module)
common/methods.lisp
Next: The clusters/pam/generics․lisp file, Previous: The clusters/common/methods․lisp file, Up: Lisp files [Contents][Index]
pam (module)
pam/package.lisp
Next: The clusters/pam/types․lisp file, Previous: The clusters/pam/package․lisp file, Up: Lisp files [Contents][Index]
pam (module)
pam/generics.lisp
Next: The clusters/pam/utils․lisp file, Previous: The clusters/pam/generics․lisp file, Up: Lisp files [Contents][Index]
pam (module)
pam/types.lisp
parameters (class)
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pam (module)
pam/utils.lisp
Next: The clusters/clarans/package․lisp file, Previous: The clusters/pam/utils․lisp file, Up: Lisp files [Contents][Index]
pam (module)
pam/methods.lisp
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clarans (module)
clarans/package.lisp
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clarans (module)
clarans/generics.lisp
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clarans (module)
clarans/types.lisp
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clarans (module)
clarans/utils.lisp
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clarans (module)
clarans/methods.lisp
Next: The clusters/k-means/types․lisp file, Previous: The clusters/clarans/methods․lisp file, Up: Lisp files [Contents][Index]
k-means (module)
k-means/package.lisp
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k-means (module)
k-means/types.lisp
parameters (class)
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k-means (module)
k-means/utils.lisp
Previous: The clusters/k-means/utils․lisp file, Up: Lisp files [Contents][Index]
k-means (module)
k-means/methods.lisp
Next: Definitions, Previous: Files, Up: Top [Contents][Index]
Packages are listed by definition order.
Next: The clusters․fancy package, Previous: Packages, Up: Packages [Contents][Index]
aux-package.lisp (file)
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aux-package.lisp (file)
defpackage (macro)
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package.lisp (file)
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package.lisp (file)
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package.lisp (file)
Next: The clusters․pam package, Previous: The clusters․distance package, Up: Packages [Contents][Index]
package.lisp (file)
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package.lisp (file)
parameters (class)
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package.lisp (file)
parameters (class)
Previous: The clusters․clarans package, Up: Packages [Contents][Index]
package.lisp (file)
parameters (class)
Definitions are sorted by export status, category, package, and then by lexicographic order.
• Exported definitions | ||
• Internal definitions |
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• Exported macros | ||
• Exported functions | ||
• Exported generic functions | ||
• Exported classes |
Next: Exported functions, Previous: Exported definitions, Up: Exported definitions [Contents][Index]
aux-package.lisp (file)
Next: Exported generic functions, Previous: Exported macros, Up: Exported definitions [Contents][Index]
Description:
Calculates average distance between two sets, based around the FN metric function
Returns:
Average distance between two sets.
Notes:
–Algorithm described in https://doi.org/10.1007/s13160-012-0089-6
–KEY function is used in conjuction with the TEST function to construct unions and differences between sets. Not for extracting values for the FN itself. This allows FN to operate on the weight, count or other secondary attribute of the set element.
–Quadratic time complexity, suitable only for small sets.
average.lisp (file)
Arguments:
–H1, Frequency vector representing distribution.
–H2, Frequency vector representing distribution.
Description:
Calculates Bhattacharyya distance between two distributions represented as frequency vector.
Returns:
Bhattacharyya distance as single-float.
bhattacharyya.lisp (file)
functions.lisp (file)
functions.lisp (file)
utils.lisp (file)
matrix.lisp (file)
random.lisp (file)
Description:
Calculates the Euclid distance between two simple-arrays of single-float
Returns:
Non-negative-single-float distance.
euclid.lisp (file)
group-average.lisp (file)
matrix.lisp (file)
matrix.lisp (file)
Description:
Hausdorff distance. Accepts vectors as arguments.
hausdorff.lisp (file)
Arguments:
–Q, Frequency vector.
–P, Frequency vector.
Description:
Calculates hellinger distance between two distributions, both represented as histograms.
Returns:
Hellinger distance.
hellinger.lisp (file)
random.lisp (file)
Description:
Largest common subsequence metric for vectors.
lcs.lisp (file)
Description:
Traditional edit distance for strings.
levenshtein.lisp (file)
functions.lisp (file)
matrix.lisp (file)
matrix.lisp (file)
matrix.lisp (file)
functions.lisp (file)
maps.lisp (file)
maps.lisp (file)
partition.lisp (file)
sinkhorn.lisp (file)
matrix.lisp (file)
Arguments:
–A, Vector.
–B, Vector.
Description:
Calculates the subvector representation based metric.
Returns:
Single-float (between 0.0 and 1.0) representing the distance.
Notes:
–Content of a and b vectors must be comparable using EQUAL.
–Algorithm described in https://doi.org/10.1177%2F0049124114540707
–Will return 1.0 if one of the vectors is empty and the second is not empty.
svr.lisp (file)
utils.lisp (file)
maps.lisp (file)
Next: Exported classes, Previous: Exported functions, Up: Exported definitions [Contents][Index]
generics.lisp (file)
methods.lisp (file)
methods.lisp (file)
methods.lisp (file)
generics.lisp (file)
append (short method combination)
Options: :most-specific-first
methods.lisp (file)
methods.lisp (file)
methods.lisp (file)
generics.lisp (file)
methods.lisp (file)
methods.lisp (file)
generics.lisp (file)
methods.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
generics.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
generics.lisp (file)
methods.lisp (file)
methods.lisp (file)
methods.lisp (file)
generics.lisp (file)
append (short method combination)
Options: :most-specific-first
methods.lisp (file)
methods.lisp (file)
methods.lisp (file)
methods.lisp (file)
generics.lisp (file)
methods.lisp (file)
methods.lisp (file)
methods.lisp (file)
generics.lisp (file)
silhouette.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
Previous: Exported generic functions, Up: Exported definitions [Contents][Index]
types.lisp (file)
parameters-holder (class)
:data
data (generic function)
(setf data) (generic function)
:indexes
indexes (generic function)
(setf indexes) (generic function)
Initarg | Value |
---|---|
:data | (serapeum:vect) |
:indexes | nil |
types.lisp (file)
standard-object (class)
:parallelp
parallelp (generic function)
:key-function
key-function (generic function)
:silhouette-sample-count
silhouette-sample-count (generic function)
:silhouette-sample-size
silhouette-sample-size (generic function)
Initarg | Value |
---|---|
:key-function | (function identity) |
:parallelp | nil |
:silhouette-sample-count | 15 |
:silhouette-sample-size | 500 |
types.lisp (file)
parameters (class)
:split-threshold
(setf split-threshold) (generic function)
:merge-threshold
(setf merge-threshold) (generic function)
:select-medoids-attempts-count
(setf select-medoids-attempts-count) (generic function)
:split-merge-attempts-count
(setf split-merge-attempts-count) (generic function)
:medoids-count
(setf medoids-count) (generic function)
Initarg | Value |
---|---|
:split-threshold | nil |
:merge-threshold | nil |
:select-medoids-attempts-count | 20 |
:split-merge-attempts-count | 0 |
types.lisp (file)
parameters (class)
:distance-function
(setf distance-function) (generic function)
:max-neighbor
max-neighbor (generic function)
(setf max-neighbor) (generic function)
:medoids-count
medoids-count (generic function)
(setf medoids-count) (generic function)
types.lisp (file)
parameters (class)
alexandria:non-negative-fixnum
:medoids-count
(setf medoids-count) (generic function)
:iterations
(setf iterations) (generic function)
single-float
:distortion-epsilon
(setf distortion-epsilon) (generic function)
Initarg | Value |
---|---|
:iterations | nil |
types.lisp (file)
parameters-holder (class)
pam-result (class)
vector
:cluster-indexes
cluster-indexes (generic function)
:indexes
indexes (generic function)
vector
:data
data (generic function)
(vector single-float)
:silhouette
silhouette (generic function)
Previous: Exported definitions, Up: Definitions [Contents][Index]
• Internal constants | ||
• Internal macros | ||
• Internal functions | ||
• Internal generic functions | ||
• Internal classes | ||
• Internal types |
Next: Internal macros, Previous: Internal definitions, Up: Internal definitions [Contents][Index]
hellinger.lisp (file)
Next: Internal functions, Previous: Internal constants, Up: Internal definitions [Contents][Index]
svr.lisp (file)
Next: Internal generic functions, Previous: Internal macros, Up: Internal definitions [Contents][Index]
svr.lisp (file)
utils.lisp (file)
silhouette.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
matrix.lisp (file)
utils.lisp (file)
matrix.lisp (file)
svr.lisp (file)
silhouette.lisp (file)
utils.lisp (file)
earth-mover.lisp (file)
matrix.lisp (file)
utils.lisp (file)
svr.lisp (file)
silhouette.lisp (file)
silhouette.lisp (file)
sinkhorn.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
matrix.lisp (file)
svr.lisp (file)
utils.lisp (file)
utils.lisp (file)
utils.lisp (file)
silhouette.lisp (file)
sinkhorn.lisp (file)
sinkhorn.lisp (file)
utils.lisp (file)
utils.lisp (file)
svr.lisp (file)
Next: Internal classes, Previous: Internal functions, Up: Internal definitions [Contents][Index]
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
utils.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
methods.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
generics.lisp (file)
automatically generated reader method
types.lisp (file)
automatically generated writer method
types.lisp (file)
Next: Internal types, Previous: Internal generic functions, Up: Internal definitions [Contents][Index]
types.lisp (file)
algorithm-state (class)
:cluster-contents
access-cluster-contents (generic function)
(setf access-cluster-contents) (generic function)
:medoids-count
(setf access-medoids-count) (generic function)
:unfinished-clusters
access-unfinished-clusters (generic function)
(setf access-unfinished-clusters) (generic function)
:distance-matrix
access-distance-matrix (generic function)
(setf access-distance-matrix) (generic function)
:cluster-size
access-cluster-size (generic function)
(setf access-cluster-size) (generic function)
Initarg | Value |
---|---|
:cluster-contents | nil |
:medoids-count | nil |
:cluster-size | nil |
:distance-matrix | nil |
:unfinished-clusters | nil |
types.lisp (file)
algorithm-state (class)
:medoids
medoids (generic function)
(setf medoids) (generic function)
:distortion
distortion (generic function)
(setf distortion) (generic function)
Initarg | Value |
---|---|
:y | nil |
:medoids | nil |
:distortion | nil |
:d | nil |
types.lisp (file)
algorithm-state (class)
vector
:clusters
read-clusters (generic function)
vector
:medoids
access-medoids (generic function)
(setf access-medoids) (generic function)
Initarg | Value |
---|---|
:clusters | (serapeum:vect) |
:medoids | (serapeum:vect) |
types.lisp (file)
result (class)
read-distance-matrix (method)
:distance-matrix
read-distance-matrix (generic function)
types.lisp (file)
standard-object (class)
:parameters
parameters (generic function)
Previous: Internal classes, Up: Internal definitions [Contents][Index]
types.lisp (file)
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