removed ;;; -+ lines

[cl-graph.git] / dev / graph-metrics.lisp

diff --git a/dev/graph-metrics.lisp b/dev/graph-metrics.lisp
index df4c395..65c27cc 100644 (file)
--- a/dev/graph-metrics.lisp
+++ b/dev/graph-metrics.lisp
@@ -11,6 +11,13 @@ DISCUSSION
 |#
 (in-package #:metabang.graph)
 
+(eval-always 
+  (import '(cl-mathstats:matrix-trace
+           cl-mathstats:sum-of-array-elements
+           cl-mathstats:matrix-multiply
+           cl-mathstats:normalize-matrix
+           cl-mathstats:combination-count
+           )))
 
 (defun vertex-degree-counts (g)
   "Returns an associative-container mapping edge-counts to the number of vertexes with that edge-count."
@@ -21,7 +28,6 @@ DISCUSSION
        (incf (item-at c (edge-count v)))))
     c))
 
-;;; ---------------------------------------------------------------------------
 
 (defun average-vertex-degree (graph &key 
                                 (vertex-filter (constantly t))
@@ -40,7 +46,6 @@ DISCUSSION
       (values (float (/ total size)))
       nil)))
 
-;;; ---------------------------------------------------------------------------
 
 (defun vertex-degree (vertex &key 
                              (edge-filter (constantly t))
@@ -49,7 +54,6 @@ DISCUSSION
   (declare (inline %vertex-degree)) 
   (%vertex-degree vertex edge-filter edge-size))
 
-;;; ---------------------------------------------------------------------------
 
 (defun %vertex-degree (vertex edge-filter edge-size)
   "Called internally by `vertex-degree` and `average-vertex-degree`."
@@ -61,13 +65,12 @@ DISCUSSION
          (incf degree (funcall edge-size e)))))
     degree))
 
-;;; ---------------------------------------------------------------------------
 
 (defun vertex-degree-summary (graph vertex-classifier
                                     &key (edge-size (constantly 1)))
   "Prints a summary of vertex degrees in `graph` to standard-out. Both the average degree of all vertexes and the average degree between all pairs of vertex classes \(as determined by the vertex-classifier\) will be printed. The `edge-size` parameter is passed on to `vertex-degree` to allow for weighted edges."
   
-  (bind ((counts (node-counts graph :key vertex-classifier))
+  (let ((counts (node-counts graph :key vertex-classifier))
          (kinds (collect-elements counts :transform #'first)))
     (format t "~%Vertex counts: ")
     (loop for (kind count) in counts do
@@ -95,7 +98,6 @@ DISCUSSION
            "Average vertex degree between ~A and ~A:"
            k-1 k-2))))))
 
-;;; ---------------------------------------------------------------------------
 
 #|
 Transitivity or Clustering.
@@ -150,7 +152,6 @@ the sociological literature, where it is referred to as the network density
     (float (/ (vertex-triangle-count vertex)
               (combination-count (edge-count vertex) 2)))))
 
-;;; ---------------------------------------------------------------------------
 
 (defun vertex-triangle-count (vertex)
   (let ((neighbors (neighbor-vertexes vertex)))
@@ -159,7 +160,6 @@ the sociological literature, where it is referred to as the network density
                          (member v neighbors))
                        (neighbor-vertexes neighbor)) 2))))
 
-;;; ---------------------------------------------------------------------------
 
 (defun row-sums (matrix)
   (let* ((row-count (array-dimension matrix 1))
@@ -169,7 +169,6 @@ the sociological literature, where it is referred to as the network density
         (incf (aref result row) (aref matrix column row))))
     result))
 
-;;; ---------------------------------------------------------------------------
 
 (defun column-sums (matrix)
   (let* ((column-count (array-dimension matrix 0))
@@ -179,7 +178,6 @@ the sociological literature, where it is referred to as the network density
         (incf (aref result column) (aref matrix column row))))
     result))
 
-;;; ---------------------------------------------------------------------------
 
 (defmethod assortativity-coefficient ((matrix array))
   
@@ -190,7 +188,6 @@ the sociological literature, where it is referred to as the network density
       (values 1)
       (values (/ (- trace sum-squared) (- 1 sum-squared))))))
 
-;;; ---------------------------------------------------------------------------
 
 (defmethod graph-edge-mixture-matrix ((graph basic-graph) vertex-classifier &key
                                 (edge-weight (constantly 1)))
@@ -219,7 +216,6 @@ the sociological literature, where it is referred to as the network density
      (0.013 0.023 0.306 0.035)
      (0.005 0.007 0.024 0.016)))
 
-;;; ---------------------------------------------------------------------------
 
 ;;OPT we call the classifier a lot, probably better to make a new ht for that