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the graph + * @param {list} order - a permutation + * @returns {integer} the bandwidth + */ export function bandwidth(graph, order) { if (!order) { order = range(graph.nodes().length); @@ -18,11 +24,12 @@ export function bandwidth(graph, order) { return max; } -/* - * Bandwith - * Maximum distace between two endpoints over all edges - * - * @matrix: a permuted matrix +/** + * Compute the bandwidth of an adjacency matrix, + * i.e. the maximum distace between two endpoints + * over all edges. + * @param {Matrix} matrix - the matrix + * @returns {integer} the bandwidth */ export function bandwidth_matrix(matrix) { let max = 0; diff --git a/src/distance.js b/src/distance.js index d784650..01d01da 100644 --- a/src/distance.js +++ b/src/distance.js @@ -1,113 +1,122 @@ function isNum(a, b) { return !(isNaN(a) || isNaN(b) || a == Infinity || b == Infinity); } -export const distance = { - euclidean(a, b) { - let s = 0; - for (let i = a.length-1; i >= 0; i--) { - if (isNum(a[i], b[i])) { - const x = a[i] - b[i]; - s += x * x; - } +export const distance = {}; + +distance.euclidean = function(a, b) { + let s = 0; + for (let i = a.length-1; i >= 0; i--) { + if (isNum(a[i], b[i])) { + const x = a[i] - b[i]; + s += x * x; } - return Math.sqrt(s); - }, - manhattan(a, b) { + } + return Math.sqrt(s); +}; + +distance.manhattan = function(a, b) { + let s = 0; + for (let i = a.length-1; i >= 0; i--) { + if (isNum(a[i], b[i])) { + s += Math.abs(a[i] - b[i]); + } + } + return s; +}; + +distance.minkowski = function(p) { + return (a, b) => { let s = 0; for (let i = a.length-1; i >= 0; i--) { if (isNum(a[i], b[i])) { - s += Math.abs(a[i] - b[i]); + s += Math.pow(Math.abs(a[i] - b[i]), p); } } - return s; - }, - minkowski(p) { - return (a, b) => { - let s = 0; - for (let i = a.length-1; i >= 0; i--) { - if (isNum(a[i], b[i])) { - s += Math.pow(Math.abs(a[i] - b[i]), p); - } - } - return Math.pow(s, 1 / p); - }; - }, - chebyshev(a, b) { - let max = 0; - for (let i = a.length-1; i >= 0; i--) { - if (isNum(a[i], b[i])) { - const x = Math.abs(a[i] - b[i]); - if (x > max) { - max = x; - } + return Math.pow(s, 1 / p); + }; +}; + + +distance.chebyshev = function(a, b) { + let max = 0; + for (let i = a.length-1; i >= 0; i--) { + if (isNum(a[i], b[i])) { + const x = Math.abs(a[i] - b[i]); + if (x > max) { + max = x; } } - return max; - }, - hamming(a, b) { - let d = 0; - for (let i = a.length-1; i >= 0; i--) { - if (isNum(a[i], b[i])) { - if (a[i] !== b[i]) { - d++; - } + } + return max; +}; + +distance.hamming = function(a, b) { + let d = 0; + for (let i = a.length-1; i >= 0; i--) { + if (isNum(a[i], b[i])) { + if (a[i] !== b[i]) { + d++; } } - return d; - }, - jaccard(a, b) { - let n = 0; - let s = 0; - for (let i = a.length-1; i >= 0; i--) { - if (isNum(a[i], b[i])) { - if (a[i] === b[i]) { - s++; - } - n++; + } + return d; +}; + +distance.jaccard = function(a, b) { + let n = 0; + let s = 0; + for (let i = a.length-1; i >= 0; i--) { + if (isNum(a[i], b[i])) { + if (a[i] === b[i]) { + s++; } + n++; } - if (n === 0) { - return 0; - } - return s / n; - }, - braycurtis(a, b) { - let s0 = 0; - let s1 = 0; - for (let i = a.length-1; i >= 0; i--) { - const ai = a[i]; - const bi = b[i]; - if (isNum(ai, bi)) { - s0 += Math.abs(ai - bi); - s1 += Math.abs(ai + bi); - } + } + if (n === 0) { + return 0; + } + return s / n; +}; + +distance.braycurtis = function(a, b) { + let s0 = 0; + let s1 = 0; + for (let i = a.length-1; i >= 0; i--) { + const ai = a[i]; + const bi = b[i]; + if (isNum(ai, bi)) { + s0 += Math.abs(ai - bi); + s1 += Math.abs(ai + bi); } - if (s1 === 0) { - return 0; + } + if (s1 === 0) { + return 0; + } + return s0 / s1; +}; + +// A distance measure based on Moran's I +// Note that this distance can be both negative (similar) and positive (not similar, the higher the distance, the less similar a and b) +// +// N. van Beusekom, W. Meulemans, B. Speckmann, Simultaneous Orderings for Graph Collections +// IEEE Transactions on Visualization and Computer Graphics, vol. 28, no. 1, pp. 1-10, Jan. 2022 +distance.morans = function(matrix) { + let m = 0; + const n = matrix.length * matrix[0].length; + for (let i = 0; i < matrix.length; i++) { + for (let j = 0; j < matrix[0].length; j++) { + m += matrix[i][j]; } - return s0 / s1; - }, - // A distance measure based on Moran's I - // Note that this distance can be both negative (similar) and positive (not similar, the higher the distance, the less similar a and b) - // - // N. van Beusekom, W. Meulemans, B. Speckmann, Simultaneous Orderings for Graph Collections - // IEEE Transactions on Visualization and Computer Graphics, vol. 28, no. 1, pp. 1-10, Jan. 2022 - morans(matrix) { - let m = 0; - const n = matrix.length * matrix[0].length; - for (let i = 0; i < matrix.length; i++) { - for (let j = 0; j < matrix[0].length; j++) { - m += matrix[i][j]; + } + return (a, b) => { + let result = 0; + for (let i = 0; i < a.length; i++) { + if (isNum(a[i], b[i])) { + result += (a[i] * n - m) * (b[i] * n - m); } } - return (a, b) => { - let result = 0; - for (let i = 0; i < a.length; i++) { - if (isNum(a[i], b[i])) { - result += (a[i] * n - m) * (b[i] * n - m); - } - } - return -1 * result; - }; - }, + return -1 * result; + }; }; +