@qe-libs/rena-wasm 0.1.6 → 0.1.7

package/README.md

@@ -136,7 +136,13 @@ columns in the data.
 // dims = [nRoleValues, 2]  →  Teacher uses window=4, Student uses window=2.
 const model = ena.fit(rows, {
   codes, units, conversations,
-  ordered: true,   // directed (n² connections); also works without a tensor
+  ordered: true,   // directed (n² connections); also works without a tensor.
+                   // Ordered models follow ona::model(): zero-network units are
+                   // left out of the centring mean but shifted by it, nodes use
+                   // directed positions, and points/nodes are centred on the origin.
+                   // connectionNames / rotation.adjacencyKey list all n² directed
+                   // connections as R names them: column j*n + i is
+                   // "codes[i] & codes[j]", ground codes[i] → response codes[j].
   tensor: {
     dims:         [2, 2],   // [nRoleValues=2, weight/window=2]
     dimsSender:   [0],      // axis 0 is a sender factor

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@qe-libs/rena-wasm",
-  "version": "0.1.6",
+  "version": "0.1.7",
   "description": "JavaScript/WebAssembly ENA pipeline — thin orchestration layer over @qe-libs/libqe-wasm",
   "main": "src/index.js",
   "type": "module",

package/src/index.js

@@ -90,19 +90,45 @@ function computeVariance(points, nUnits, dims) {
 
 /**
  * Build the adjacency key — list of [codeA, codeB] pairs for each connection.
- * Matches R's enadata$adjacency.matrix (column-major upper triangle order).
+ * Matches R's rotation$adjacency.key.
+ *
+ * Unordered: the upper triangle in column-major order (choose_two(n) pairs).
+ * Ordered: all n² directed connections in column-major order — column
+ * j*n + i is [codes[i], codes[j]], ground codes[i] → response codes[j]
+ * (as R names it "codes[i] & codes[j]").
  *
  * @param {string[]} codes
+ * @param {boolean}  [ordered=false]
  * @returns {string[][]}  length nConnections, each entry is [codeI, codeJ]
  */
-function buildAdjacencyKey(codes) {
+function buildAdjacencyKey(codes, ordered = false) {
     const key = [];
+    if (ordered) {
+        for (let j = 0; j < codes.length; j++)
+            for (let i = 0; i < codes.length; i++)
+                key.push([codes[i], codes[j]]);
+        return key;
+    }
     for (let j = 1; j < codes.length; j++)
         for (let i = 0; i < j; i++)
             key.push([codes[i], codes[j]]);
     return key;
 }
 
+/**
+ * Connection names, "codeA & codeB" per connection, in network column order
+ * (= R's colnames(set$connection.counts)).
+ *
+ * @param {object}   qe
+ * @param {string[]} codes
+ * @param {boolean}  [ordered=false]
+ * @returns {string[]}
+ */
+function connectionNamesFor(qe, codes, ordered = false) {
+    if (!ordered) return qe.connection_names(codes);
+    return buildAdjacencyKey(codes, true).map(([a, b]) => `${a} & ${b}`);
+}
+
 // ── ENA result object ─────────────────────────────────────────────────────────
 
 class ENAModel {
@@ -250,16 +276,18 @@ function applyCodeMask(networks, codeMask, nCodes, nUnits, nConnections, ordered
 
 function runPipeline(qe, rawNetworks, nUnits, nConnections, codes, unitLabels,
                      metaData, rotMethod, groupA, groupB, dims, gParams,
-                     rowConnectionCounts = null, directedNodes = false) {
-    const connectionNames = qe.connection_names(codes);
+                     rowConnectionCounts = null, ordered = false) {
+    const connectionNames = connectionNamesFor(qe, codes, ordered);
 
     // Sphere norm → lineWeights (= R's set$line.weights)
     const lineWeights = sphereNorm(qe, rawNetworks, nUnits, nConnections);
 
     // Center → pointsForProjection (= R's model$points.for.projection)
     //          centerVec             (= R's rotation$center.vec)
+    // Ordered (ONA) models follow ona::model(): zero-network units are left
+    // out of the mean but still shifted by it.
     const { centered: pointsForProjection, centerVec } =
-        center(qe, lineWeights, nUnits, nConnections);
+        center(qe, lineWeights, nUnits, nConnections, ordered);
 
     // Rotate
     let rot;
@@ -298,17 +326,30 @@ function runPipeline(qe, rawNetworks, nUnits, nConnections, codes, unitLabels,
     // Matches rENA's lws.positions.sq, which regresses the projected points onto
     // the SPHERE-normed line weights (enaset$line.weights) — not the centered
     // networks.  Verified node-for-node against R rENA on rs.data.new.csv.
-    // `directedNodes` (ordered networks, used by pria()) solves with libqe's
-    // directed_node_positions, as rENA's optimize() does for ordered sets.
+    // Ordered (ONA) models use libqe's directed_node_positions, as
+    // ona::model() does (via rENA's optimize()).
     const { nodes, centroids } = nodePositions(
-        qe, lineWeights, nUnits, nConnections, points, dims, directedNodes
+        qe, lineWeights, nUnits, nConnections, points, dims, ordered
     );
 
+    // ONA: translate points and nodes so the points' mean is at the origin
+    // (ona::model's center_to_origin; centroids are left as computed, as in R).
+    if (ordered) {
+        const nCodes = nodes.length / dims;
+        for (let d = 0; d < dims; d++) {
+            let mean = 0;
+            for (let u = 0; u < nUnits; u++) mean += points[u * dims + d];
+            mean /= nUnits;
+            for (let u = 0; u < nUnits; u++) points[u * dims + d] -= mean;
+            for (let c = 0; c < nCodes; c++) nodes[c * dims + d] -= mean;
+        }
+    }
+
     // Variance explained (= R's model$variance)
     const variance = computeVariance(points, nUnits, dims);
 
     // Adjacency key (= R's rotation$adjacency.key)
-    const adjacencyKey = buildAdjacencyKey(codes);
+    const adjacencyKey = buildAdjacencyKey(codes, ordered);
 
     return new ENAModel({
         // top-level
@@ -416,7 +457,7 @@ export default async function loadENA() {
 
             return runPipeline(qe, rawNetworks, nUnits, nConnections, codes,
                                unitLabels, metaData, rotMethod, groupA, groupB,
-                               dims, gParams, rowConnectionCounts);
+                               dims, gParams, rowConnectionCounts, ordered);
         },
 
         /**
@@ -460,7 +501,7 @@ export default async function loadENA() {
 
             applyCodeMask(networks, codeMask, codes.length, nUnits, nConnections, ordered);
 
-            const connectionNames = qe.connection_names(codes);
+            const connectionNames = connectionNamesFor(qe, codes, ordered);
             return {
                 connectionCounts: networks, rowConnectionCounts, unitLabels, connectionNames,
                 metaData, nUnits, nConnections,
@@ -525,7 +566,8 @@ export default async function loadENA() {
                 );
                 const model = runPipeline(
                     qe, raw, nUnits, nConnections, codes,
-                    unitLabels, metaData, 'svd', undefined, undefined, dims
+                    unitLabels, metaData, 'svd', undefined, undefined, dims,
+                    undefined, null, ordered
                 );
                 allPoints.push(model.points);
             }
@@ -745,8 +787,6 @@ export default async function loadENA() {
                             networks[u * nConn + c] = raw[u * nConnections + cols[c]];
                     keptCodes = codes.filter((_, i) => keep(i));
                 }
-                // Ordered models are scored with directed node positions (R's
-                // ordered pipeline), independent of how fit() places nodes.
                 return runPipeline(qe, networks, nUnits, nConn, keptCodes,
                                    unitLabels, metaData, rotation, groupA, groupB,
                                    nConn, gParams, null, ordered);

package/src/pipeline.js

@@ -133,11 +133,15 @@ export function sphereNorm(qe, networks, nUnits, nConnections) {
  * Subtract column means (center the network space).
  * Excludes all-zero rows from the mean calculation (zero-network exclusion).
  *
+ * @param {boolean} [shiftZeroRows=false]  Also subtract the mean from all-zero
+ *   rows, as rENA's center(exclude_zero_networks = TRUE) does -- the ONA
+ *   convention (ona::model). By default zero-network rows stay at zero, as in
+ *   rENA's ena.make.set().
  * @returns {{ centered: Float64Array, centerVec: Float64Array }}
- *   centered  — mean-subtracted networks (zero-network rows left at zero)
+ *   centered  — mean-subtracted networks
  *   centerVec — the column means used for centering (= R's rotation$center.vec)
  */
-export function center(qe, networks, nUnits, nConnections) {
+export function center(qe, networks, nUnits, nConnections, shiftZeroRows = false) {
     // Identify non-zero rows
     const active = [];
     for (let u = 0; u < nUnits; u++) {
@@ -160,7 +164,7 @@ export function center(qe, networks, nUnits, nConnections) {
     const activeSet = new Set(active);
     const centered  = new Float64Array(networks.length);
     for (let u = 0; u < nUnits; u++) {
-        if (!activeSet.has(u)) continue;          // leave zero-network row as zero
+        if (!shiftZeroRows && !activeSet.has(u)) continue;   // leave zero-network row as zero
         for (let c = 0; c < nConnections; c++) {
             centered[u * nConnections + c] = networks[u * nConnections + c] - means[c];
         }