@milaboratories/graph-maker 1.1.175 → 1.1.177

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/MannWhitneyU.js

@@ -1,147 +0,0 @@
-import f from "../../../node_modules/lodash/lodash.js";
-var m = Object.defineProperty, y = (h, t, n) => t in h ? m(h, t, { enumerable: !0, configurable: !0, writable: !0, value: n }) : h[t] = n, P = (h, t, n) => y(h, t + "", n);
-function b(h) {
-  const t = Math.abs(h), n = 1 / (1 + t / 2), e = n * Math.exp(-t * t - 1.26551223 + n * (1.00002368 + n * (0.37409196 + n * (0.09678418 + n * (-0.18628806 + n * (0.27886807 + n * (-1.13520398 + n * (1.48851587 + n * (-0.82215223 + n * 0.17087277)))))))));
-  return h >= 0 ? e : 2 - e;
-}
-function w(h) {
-  return 0.5 * b(-h / Math.sqrt(2));
-}
-class v {
-  constructor(t, n) {
-    this.value = t, this.position = n;
-  }
-  getValue() {
-    return this.value;
-  }
-  getPosition() {
-    return this.position;
-  }
-}
-function A(h) {
-  const t = new Array(h.length);
-  for (let s = 0; s < h.length; s++)
-    t[s] = new v(h[s], s);
-  const n = U(t);
-  t.sort((s, l) => s.getValue() - l.getValue());
-  const e = new Array(t.length);
-  let r = 1;
-  e[t[0].getPosition()] = r;
-  let o = [];
-  o.push(t[0].getPosition());
-  for (let s = 1; s < t.length; s++)
-    t[s].getValue() > t[s - 1].getValue() && (r = s + 1, o.length > 1 && p(e, o), o = []), o.push(t[s].getPosition()), e[t[s].getPosition()] = r;
-  return o.length > 1 && p(e, o), E(e, n), e;
-}
-function p(h, t) {
-  const n = (2 * h[t[0]] + t.length - 1) / 2;
-  t.forEach((e) => {
-    h[e] = n;
-  });
-}
-function E(h, t) {
-  t.forEach((n) => {
-    h[n] = NaN;
-  });
-}
-function U(h) {
-  const t = [];
-  for (let n = 0; n < h.length; n++)
-    isNaN(h[n].getValue()) && t.push(n);
-  return t;
-}
-class L {
-  constructor() {
-    P(this, "SMALL_SAMPLE_SIZE", 50);
-  }
-  mannWhitneyU(t, n) {
-    const e = [...t, ...n], r = A(e);
-    let o = 0;
-    for (let i = 0; i < t.length; i++)
-      o += r[i];
-    const s = o - t.length * (t.length + 1) / 2, l = t.length * n.length - s;
-    return Math.min(s, l);
-  }
-  mannWhitneyUTest(t, n, e) {
-    if (typeof e > "u")
-      return t.length + n.length <= this.SMALL_SAMPLE_SIZE && Object.keys(this.tiesMap(t, n)).length === 0 ? this.mannWhitneyUTest(t, n, !0) : this.mannWhitneyUTest(t, n, !1);
-    const r = this.tiesMap(t, n), o = this.mannWhitneyU(t, n);
-    if (e) {
-      if (Object.keys(r).length !== 0)
-        throw new Error();
-      return this.exactP(t.length, n.length, o);
-    }
-    return this.approximateP(
-      o,
-      t.length,
-      n.length,
-      this.varU(t.length, n.length, r)
-    );
-  }
-  approximateP(t, n, e, r) {
-    const o = n * e / 2;
-    if (o == t)
-      return 1;
-    const s = -Math.abs(t - o + 0.5) / Math.sqrt(r);
-    return 2 * w(s);
-  }
-  exactP(t, n, e) {
-    const r = n * t;
-    if (e > r)
-      return 1;
-    const o = e < r / 2 ? e : r / 2 - e;
-    let s = 0, l = 0;
-    for (; l <= o; )
-      s += this.uDensity(t, n, l), l++;
-    return 2 * s;
-  }
-  uDensity(t, n, e) {
-    if (e < 0 || e > n * t)
-      return 0;
-    const r = this.uFrequencies(t, n);
-    return r[Math.round(e + 1)] / f.sum(r);
-  }
-  uFrequencies(t, n) {
-    const e = Math.max(n, t);
-    if (e > 100)
-      throw Error("n or m > 100");
-    const r = Math.min(n, t), o = new Array(t * n + 2), s = new Array(t * n + 2);
-    for (let i = 1; i < o.length; i++)
-      o[i] = i <= e + 1 ? 1 : 0;
-    s[1] = 0;
-    let l = e;
-    for (let i = 2; i <= r; i++) {
-      s[i] = 0, l = l + e;
-      let u = l + 2;
-      const M = 1 + l / 2;
-      let g = i;
-      for (let a = 1; a <= M; a++) {
-        g++, u = u - 1;
-        const c = o[a] + s[a];
-        o[a] = c, s[g] = c - o[u], o[u] = c;
-      }
-    }
-    return o;
-  }
-  varU(t, n, e) {
-    const r = t * n;
-    if (Object.keys(e).length === 0)
-      return r * (t + n + 1) / 12;
-    const o = f.sum(Object.values(e).map((l) => l * l * l - l)), s = t + n;
-    return r / 12 * (s + 1 - o / (s * (s - 1)));
-  }
-  tiesMap(t, n) {
-    const e = {};
-    for (let r = 0; r < t.length; r++)
-      e[t[r]] = e[t[r]] ? e[t[r]] + 1 : 1;
-    for (let r = 0; r < n.length; r++)
-      e[n[r]] = e[n[r]] ? e[n[r]] + 1 : 1;
-    for (const r in e)
-      e[r] === 1 && delete e[r];
-    return e;
-  }
-}
-export {
-  L as MannWhitneyU
-};
-//# sourceMappingURL=MannWhitneyU.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/MannWhitneyU.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"MannWhitneyU.js","sources":["../../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/stats/MannWhitneyU.ts"],"sourcesContent":["import lodash from 'lodash';\n\n// Normal distribution - complementary error function\n// https://en.wikipedia.org/wiki/Error_function#Complementary_error_function\n// https://github.com/errcw/gaussian/blob/master/lib/gaussian.js#L5\nfunction erfc(x:number):number {\n    const z = Math.abs(x);\n    const t = 1 / (1 + z / 2);\n    const r = t * Math.exp(-z * z - 1.26551223 + t * (1.00002368 +\n        t * (0.37409196 + t * (0.09678418 + t * (-0.18628806 +\n            t * (0.27886807 + t * (-1.13520398 + t * (1.48851587 +\n                t * (-0.82215223 + t * 0.17087277)))))))));\n    return x >= 0 ? r : 2 - r;\n}\n// Normal distribution - cumulative probability, for mean = 0, standardDeviation = 1\n// https://github.com/errcw/gaussian/blob/master/lib/gaussian.js#L54\nfunction standardNormalCumulativeProbability (x:number):number {\n    return 0.5 * erfc(-x / (Math.sqrt(2)));\n}\n\n// Natural ranking\n// https://github.com/apache/commons-math/blob/ece74cff78ae7858827f1913bb63854601d88c06/commons-math-legacy/src/main/java/org/apache/commons/math4/legacy/stat/ranking/NaturalRanking.java#L195\nclass IntDoublePair {\n    constructor(private value:number, private position:number) {}\n    public getValue() {\n        return this.value;\n    }\n    public getPosition() {\n        return this.position;\n    }\n}\n// with NaNStrategy.FIXED, TiesStrategy.AVERAGE https://github.com/milaboratory/miplots/blob/559b13065f17dfc7c4dd332247dd1ce0183affcc/src/main/kotlin/com/milaboratory/miplots/stat/util/MannWhitneyU.kt#L36\nfunction rank(data:number[]) {\n    // Array recording initial positions of data to be ranked\n    const ranks:IntDoublePair[] = new Array(data.length);\n    for (let i = 0; i < data.length; i++) {\n        ranks[i] = new IntDoublePair(data[i], i);\n    }\n\n    // Recode, remove or record positions of NaNs\n    const nanPositions = getNanPositions(ranks);\n    // Sort the IntDoublePairs\n    ranks.sort((a, b) => a.getValue() - b.getValue());\n\n    // Walk the sorted array, filling output array using sorted positions,\n    // resolving ties as we go\n    const out:number[] = new Array(ranks.length);\n    let pos = 1;  // position in sorted array\n    out[ranks[0].getPosition()] = pos;\n    let tiesTrace = [];\n    tiesTrace.push(ranks[0].getPosition());\n\n    for (let i = 1; i < ranks.length; i++) {\n        if (ranks[i].getValue() > ranks[i - 1].getValue()) {\n            // tie sequence has ended (or had length 1)\n            pos = i + 1;\n            if (tiesTrace.length > 1) {  // if seq is nontrivial, resolve\n                resolveTie(out, tiesTrace);\n            }\n            tiesTrace = [];\n            tiesTrace.push(ranks[i].getPosition());\n        } else {\n            // tie sequence continues\n            tiesTrace.push(ranks[i].getPosition());\n        }\n        out[ranks[i].getPosition()] = pos;\n    }\n\n    if (tiesTrace.length > 1) {  // handle tie sequence at end\n        resolveTie(out, tiesTrace);\n    }\n    restoreNaNs(out, nanPositions);\n    return out;\n}\n\nfunction resolveTie(ranks:number[], tiesTrace:number[]) {\n    // constant value of ranks over tiesTrace\n    const c = ranks[tiesTrace[0]];\n    const value = (2 * c + tiesTrace.length - 1) / 2;\n\n    tiesTrace.forEach((trace) => {\n        ranks[trace] = value;\n    });\n}\n\nfunction restoreNaNs(ranks:number[], nanPositions:number[]) {\n    nanPositions.forEach((position) => {\n        ranks[position] = NaN;\n    });\n}\n\nfunction getNanPositions(ranks:IntDoublePair[] ) {\n    const out = [];\n    for (let i = 0; i < ranks.length; i++) {\n        if (isNaN(ranks[i].getValue())){\n            out.push(i);\n        }\n    }\n    return out;\n}\n\n// https://github.com/milaboratory/miplots/blob/559b13065f17dfc7c4dd332247dd1ce0183affcc/src/main/kotlin/com/milaboratory/miplots/stat/util/MannWhitneyU.kt#L36\nexport class MannWhitneyU {\n    SMALL_SAMPLE_SIZE = 50;\n\n    mannWhitneyU (x: number[], y: number[]): number {\n        const z = [...x, ...y];\n        const ranks = rank(z);\n        let sumRankX = 0;\n\n        /*\n         * The ranks for x is in the first x.length entries in ranks because x\n         * is in the first x.length entries in z\n         */for (let i = 0; i < x.length; i++) {\n            sumRankX += ranks[i];\n        }\n\n        /*\n         * U1 = R1 - (n1 * (n1 + 1)) / 2 where R1 is sum of ranks for sample 1,\n         * e.g. x, n1 is the number of observations in sample 1.\n         */\n        const U1 = sumRankX - x.length * (x.length + 1) / 2;\n\n        /*\n         * U1 + U2 = n1 * n2\n         */\n        const U2 = x.length * y.length - U1;\n        return Math.min(U1, U2);\n    }\n\n    mannWhitneyUTest(x: number[], y: number[], exact?:boolean): number {\n        if (typeof exact === 'undefined') {\n            // If samples are both small and there are no ties, perform exact test\n            if (x.length + y.length <= this.SMALL_SAMPLE_SIZE && Object.keys(this.tiesMap(x, y)).length === 0) {\n                return this.mannWhitneyUTest(x, y, true);\n            }\n            // Normal approximation\n            return this.mannWhitneyUTest(x, y, false);\n        }\n\n        const tiesMap = this.tiesMap(x, y);\n        const u = this.mannWhitneyU(x, y);\n        if (exact) {\n            if (Object.keys(tiesMap).length !== 0) {\n                throw new Error();\n            }\n            return this.exactP(x.length, y.length, u);\n        }\n        return this.approximateP(\n            u, x.length, y.length,\n            this.varU(x.length, y.length, tiesMap)\n        );\n    }\n\n    approximateP(u: number, n1: number, n2: number, varU: number): number {\n        const mu = n1 * n2 / 2;\n\n        // If u == mu, return 1\n        if (mu == u) {\n            return 1.0;\n        }\n\n        // Force z <= 0 so we get tail probability. Also apply continuity\n        // correction\n        const z = -Math.abs(u - mu + 0.5) / Math.sqrt(varU);\n        return 2 * standardNormalCumulativeProbability(z);\n    }\n\n    exactP(n: number, m: number, u: number): number {\n        const nm = m * n;\n        if (u > nm) { // Quick exit if u is out of range\n            return 1.0;\n        }\n        // Need to convert u to a mean deviation, so cumulative probability is\n        // tail probability\n        const crit = (u < nm / 2) ? u : nm / 2 - u;\n        let cum = 0;\n        let ct = 0;\n        while (ct <= crit) {\n            cum += this.uDensity(n, m, ct);\n            ct++;\n        }\n        return 2 * cum;\n    }\n\n    uDensity(n: number, m: number, u: number): number {\n        if (u < 0 || u > m * n) {\n            return 0;\n        }\n        const freq = this.uFrequencies(n, m);\n        return freq[Math.round(u + 1)] / lodash.sum(freq);\n    }\n\n    uFrequencies(n: number, m: number): number[] {\n        const max = Math.max(m, n);\n        if (max > 100) {\n            throw Error('n or m > 100');\n        }\n        const min = Math.min(m, n);\n        const out = new Array(n * m + 2);\n        const work = new Array(n * m + 2);\n        for (let i = 1; i < out.length; i++) {\n            out[i] = (i <= max + 1) ? 1 : 0;\n        }\n        work[1] = 0;\n        let in_ = max;\n        for (let i = 2; i <= min; i++) {\n            work[i] = 0;\n            in_ = in_ + max;\n            let n1 = in_ + 2;\n            const l = (1 + in_ / 2);\n            let k = i;\n            for (let j = 1; j <= l; j++) {\n                k++;\n                n1 = n1 - 1;\n                const sum_ = out[j] + work[j];\n                out[j] = sum_;\n                work[k] = sum_ - out[n1];\n                out[n1] = sum_;\n            }\n        }\n        return out;\n    }\n\n    varU(n: number, m: number, tiesMap: Record<number, number>): number {\n        const nm = n * m;\n        if (Object.keys(tiesMap).length === 0) {\n            return nm * (n + m + 1) / 12.0;\n        }\n        const tSum = lodash.sum(Object.values(tiesMap).map(( value) => value * value * value - value));\n        const totalN = n + m;\n        return nm / 12 * (totalN + 1 - tSum / (totalN * (totalN - 1)));\n    }\n\n    tiesMap(x: number[], y: number[]): Record<number, number> {\n        const tiesMap: Record<number, number> = {};\n        for (let i = 0; i < x.length; i++) {\n            tiesMap[x[i]] = tiesMap[x[i]] ? tiesMap[x[i]] + 1 : 1;\n        }\n        for (let i = 0; i < y.length; i++) {\n            tiesMap[y[i]] = tiesMap[y[i]] ? tiesMap[y[i]] + 1 : 1;\n        }\n        for (const key in tiesMap) {\n            if (tiesMap[key] === 1) {\n                delete tiesMap[key];\n            }\n        }\n        return tiesMap;\n    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package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/index.js

@@ -1,84 +0,0 @@
-import { NO_GROUPED as m } from "../../../DataFrame.js";
-import { calculatePValue as p } from "./pValueCalculation.js";
-import { adjustPValues as h } from "./pValueCorrection.js";
-import { getFacetStringKey as v } from "../../utils/getFacetStringKey.js";
-function y(t) {
-  return t.slice(0, -1).reduce(
-    (g, l, a) => g.concat(t.slice(a + 1).map((s) => [l, s])),
-    []
-  );
-}
-function w(t, g, l, a, s) {
-  return {
-    type: "stats",
-    values: g.reduce((f, i) => {
-      let u = [];
-      switch (t.statType) {
-        case "overall": {
-          const r = l.map((e) => s.getColumnByGrouping([...i, e], a.value)).filter((e) => e.length > 0);
-          if (r.length < 2)
-            break;
-          const c = p(r, t.testMethod, t.paired);
-          u = [[["overall"], c]];
-          break;
-        }
-        case "referenceGroup": {
-          const r = t.referenceGroup === null ? m : String(t.referenceGroup);
-          if (r !== m && !l.includes(r))
-            throw new Error(`Reference group ${String(r)} for ${t.testMethod} test is not in available groups`);
-          const c = s.getColumnByGrouping([...i, r], a.value);
-          if (c.length === 0) {
-            u = [];
-            break;
-          }
-          const e = l.filter((n) => n !== r).map((n) => [n, s.getColumnByGrouping([...i, n], a.value)]).filter(([, n]) => n.length > 0);
-          if (e.length < 2 && t.correctionMethod !== null)
-            break;
-          const o = h(
-            e.map(
-              ([, n]) => p(
-                [c, n],
-                t.testMethod,
-                t.paired
-              )
-            ),
-            t.correctionMethod
-          );
-          u = e.map(([n], d) => [[n], o[d]]);
-          break;
-        }
-        case "pairwise": {
-          const r = y(l).map(([e, o]) => [
-            [e, o],
-            [
-              s.getColumnByGrouping([...i, e], a.value),
-              s.getColumnByGrouping([...i, o], a.value)
-            ]
-          ]).filter(([, [e, o]]) => e.length && o.length);
-          if (r.length < 1)
-            break;
-          const c = h(
-            r.map(([, e]) => p(e, t.testMethod, t.paired)),
-            t.correctionMethod
-          );
-          u = r.map(([e], o) => [e, c[o]]);
-          break;
-        }
-        default:
-          throw new Error("Unknown statType");
-      }
-      return f[v(i)] = u, f;
-    }, {}),
-    meta: {
-      statType: t.statType,
-      testMethod: t.testMethod,
-      format: t.format,
-      ns: t.ns,
-      significanceLevels: t.significanceLevels
-    }
-  };
-}
-export {
-  w as getStatsData
-};
-//# sourceMappingURL=index.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sources":["../../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/stats/index.ts"],"sourcesContent":["import type {DataFrame, GroupKey} from '../../../DataFrame';\nimport {NO_GROUPED} from '../../../DataFrame';\nimport type {DiscreteSettingsImpl, StatLayer} from '../../DiscreteSettingsImpl';\nimport {calculatePValue} from './pValueCalculation';\nimport {adjustPValues} from './pValueCorrection';\nimport type {StatsData} from '../types';\nimport {getFacetStringKey} from '../../utils/getFacetStringKey';\n\n// all available pairs of unequal keys from array of keys\nfunction getAllKeyPairs (keys:GroupKey[]) {\n    return keys\n        .slice(0,-1)\n        .reduce(\n            (res: [GroupKey, GroupKey][], key1, index) =>\n                res.concat(keys.slice(index + 1).map(key2 => [key1, key2])),\n            []\n        );\n}\n\nexport function getStatsData(\n    layer: StatLayer,\n    facetKeys: GroupKey[][],\n    primaryKeys: GroupKey[],\n    y: DiscreteSettingsImpl['y'],\n    data: DataFrame\n): StatsData {\n    return {\n        type: 'stats',\n        values: facetKeys.reduce((res: StatsData['values'], facetKey) => {\n            let values: [string[], number][] = [];\n            switch (layer.statType) {\n                case 'overall': {\n                    const groups = primaryKeys\n                        .map(primaryKey => data.getColumnByGrouping([...facetKey, primaryKey], y.value))\n                        .filter((group) => group.length > 0);\n                    if (groups.length < 2) {\n                        break;\n                    }\n                    const pValue = calculatePValue(groups, layer.testMethod, layer.paired);\n                    values = [[['overall'], pValue]];\n                    break;\n                }\n                case 'referenceGroup': {\n                    const referenceKey = layer.referenceGroup === null ? NO_GROUPED : String(layer.referenceGroup);\n                    if (referenceKey !== NO_GROUPED && !primaryKeys.includes(referenceKey)) {\n                        throw new Error(`Reference group ${String(referenceKey)} for ${layer.testMethod} test is not in available groups`);\n                    }\n                    const referenceGroup = data.getColumnByGrouping([...facetKey, referenceKey], y.value);\n                    if (referenceGroup.length === 0) {\n                        values = [];\n                        break;\n                    }\n\n                    const keys = primaryKeys.filter(key => key !== referenceKey);\n                    const keysAndGroupsNonEmpty:[string, number[]][] = keys\n                        .map(primaryKey => [primaryKey, data.getColumnByGrouping([...facetKey, primaryKey], y.value)] as [string, number[]])\n                        .filter(([, group]) => group.length > 0);\n                    if (keysAndGroupsNonEmpty.length < 2 && layer.correctionMethod !== null) {\n                        break;\n                    }\n                    const pValues = adjustPValues(\n                        keysAndGroupsNonEmpty.map(([,group]) =>\n                            calculatePValue(\n                                [referenceGroup, group],\n                                layer.testMethod,\n                                layer.paired\n                            )\n                        ),\n                        layer.correctionMethod\n                    );\n                    values = keysAndGroupsNonEmpty.map(([primaryKey], index) => [[primaryKey], pValues[index]]);\n                    break;\n                }\n                case 'pairwise': {\n                    const keysPairs = getAllKeyPairs(primaryKeys);\n                    const keysAndGroupsNonEmpty:[string[], number[][]][] = keysPairs\n                        .map(([key1, key2]) => [\n                            [key1, key2],\n                            [\n                                data.getColumnByGrouping([...facetKey, key1], y.value),\n                                data.getColumnByGrouping([...facetKey, key2], y.value)\n                            ]\n                        ] as [string[], number[][]])\n                        .filter(([,[gr1, gr2]]) => gr1.length && gr2.length);\n\n                    if (keysAndGroupsNonEmpty.length < 1) {\n                        break;\n                    }\n                    const pValues = adjustPValues(\n                        keysAndGroupsNonEmpty.map(([,groups]) => calculatePValue(groups, layer.testMethod, layer.paired)),\n                        layer.correctionMethod\n                    );\n                    values = keysAndGroupsNonEmpty.map(([keysPair], index) => [keysPair, pValues[index]]);\n                    break;\n                }\n                default: {\n                    throw new Error('Unknown statType');\n                }\n            }\n            res[getFacetStringKey(facetKey)] = values;\n            return res;\n        }, {}),\n        meta: {\n            statType: layer.statType,\n            testMethod: layer.testMethod,\n            format: layer.format,\n            ns: layer.ns,\n            significanceLevels: layer.significanceLevels\n        },\n    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package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/pValueCalculation.js

@@ -1,50 +0,0 @@
-import i from "../../../node_modules/@stdlib/stats-anova1/lib/index.js";
-import f from "../../../node_modules/@stdlib/stats-ttest/lib/index.js";
-import l from "../../../node_modules/@stdlib/stats-ttest2/lib/index.js";
-import p from "../../../node_modules/@stdlib/stats-kruskal-test/lib/index.js";
-import m from "../../../node_modules/@stdlib/stats-wilcoxon/lib/index.js";
-import { MannWhitneyU as u } from "./MannWhitneyU.js";
-import n from "../../../node_modules/lodash/lodash.js";
-function E(e, a, t) {
-  switch (a) {
-    case "ttest": {
-      if (e.length > 2)
-        throw new Error("more than 2 datasets passed");
-      if (t) {
-        if (e[0].length !== e[1].length)
-          throw Error("Different size groups in paired test");
-        return f(e[0], e[1]).pValue;
-      }
-      const r = l(e[0], e[1]).pValue;
-      return isNaN(r) ? 1 : r;
-    }
-    case "anova": {
-      const r = i(
-        n.flatten(e),
-        n.flatten(e.map((o, s) => o.map(() => String(s))))
-      ).pValue;
-      return isNaN(r) ? 1 : r;
-    }
-    case "wilcoxon": {
-      if (e.length > 2)
-        throw new Error("more than 2 datasets passed");
-      if (t) {
-        if (e[0].length !== e[1].length)
-          throw Error("Different size groups in paired test");
-        return m(e[0], e[1]).pValue;
-      }
-      const r = new u().mannWhitneyUTest(e[0], e[1]);
-      return isNaN(r) ? 1 : r;
-    }
-    case "kruskalWallis": {
-      const r = p(...e).pValue;
-      return isNaN(r) ? 1 : r;
-    }
-    default:
-      throw new Error("Unknown test method");
-  }
-}
-export {
-  E as calculatePValue
-};
-//# sourceMappingURL=pValueCalculation.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/pValueCalculation.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"pValueCalculation.js","sources":["../../../../../../../../node_modules/@milaboratories/miplots4/src/discrete/layers/stats/pValueCalculation.ts"],"sourcesContent":["import anova1 from '@stdlib/stats-anova1';\nimport ttest from '@stdlib/stats-ttest';\nimport ttest2 from '@stdlib/stats-ttest2';\nimport kruskal from '@stdlib/stats-kruskal-test';\nimport wilcoxon from '@stdlib/stats-wilcoxon';\nimport {MannWhitneyU} from './MannWhitneyU';\nimport type {StatTestMethod} from '../../../types';\nimport lodash from 'lodash';\n\nexport function calculatePValue(groups: number[][], testMethod: StatTestMethod, paired: boolean) {\n    switch (testMethod) {\n        case 'ttest': {\n            if (groups.length > 2) {\n                throw new Error('more than 2 datasets passed');\n            }\n            if (paired) {\n                if (groups[0].length !== groups[1].length) {\n                    throw Error('Different size groups in paired test');\n                }\n                return ttest(groups[0], groups[1]).pValue;\n            }\n\n            const res = ttest2(groups[0], groups[1]).pValue;\n            return isNaN(res) ? 1 : res;\n        }\n        case 'anova': {\n            const res = anova1(\n                lodash.flatten(groups),\n                lodash.flatten(groups.map((g, index) => g.map(() => String(index))))\n            ).pValue;\n            return isNaN(res) ? 1 : res;\n        }\n        case 'wilcoxon': {\n            if (groups.length > 2) {\n                throw new Error('more than 2 datasets passed');\n            }\n            if (paired) {\n                if (groups[0].length !== groups[1].length) {\n                    throw Error('Different size groups in paired test');\n                }\n                return wilcoxon(groups[0], groups[1]).pValue;\n            }\n            const res =  new MannWhitneyU().mannWhitneyUTest(groups[0], groups[1]);\n            return isNaN(res) ? 1 : res;\n        }\n        case 'kruskalWallis': {\n            // eslint-disable-next-line @typescript-eslint/ban-ts-comment\n            // @ts-ignore\n            // NB: kruskal test works correct with more than 3 groups, but only 1,2 or 3 groups in its signature\n            const res = kruskal(...groups).pValue;\n            return isNaN(res) ? 1 : res;\n        }\n        default: {\n            throw new Error('Unknown test method');\n        }\n    }\n}\n"],"names":["calculatePValue","groups","testMethod","paired","ttest","res","ttest2","anova1","lodash","g","index","wilcoxon","MannWhitneyU","kruskal"],"mappings":";;;;;;;AASO,SAASA,EAAgBC,GAAoBC,GAA4BC,GAAiB;AAC7F,UAAQD,GAAAA;AAAAA,IACJ,KAAK,SAAS;AACV,UAAID,EAAO,SAAS;AAChB,cAAM,IAAI,MAAM,6BAA6B;AAEjD,UAAIE,GAAQ;AACR,YAAIF,EAAO,CAAC,EAAE,WAAWA,EAAO,CAAC,EAAE;AAC/B,gBAAM,MAAM,sCAAsC;AAEtD,eAAOG,EAAMH,EAAO,CAAC,GAAGA,EAAO,CAAC,CAAC,EAAE;AAAA,MACvC;AAEA,YAAMI,IAAMC,EAAOL,EAAO,CAAC,GAAGA,EAAO,CAAC,CAAC,EAAE;AACzC,aAAO,MAAMI,CAAG,IAAI,IAAIA;AAAAA,IAC5B;AAAA,IACA,KAAK,SAAS;AACV,YAAMA,IAAME;AAAAA,QACRC,EAAO,QAAQP,CAAM;AAAA,QACrBO,EAAO,QAAQP,EAAO,IAAI,CAACQ,GAAGC,MAAUD,EAAE,IAAI,MAAM,OAAOC,CAAK,CAAC,CAAC,CAAC;AAAA,MAAA,EACrE;AACF,aAAO,MAAML,CAAG,IAAI,IAAIA;AAAAA,IAC5B;AAAA,IACA,KAAK,YAAY;AACb,UAAIJ,EAAO,SAAS;AAChB,cAAM,IAAI,MAAM,6BAA6B;AAEjD,UAAIE,GAAQ;AACR,YAAIF,EAAO,CAAC,EAAE,WAAWA,EAAO,CAAC,EAAE;AAC/B,gBAAM,MAAM,sCAAsC;AAEtD,eAAOU,EAASV,EAAO,CAAC,GAAGA,EAAO,CAAC,CAAC,EAAE;AAAA,MAC1C;AACA,YAAMI,IAAO,IAAIO,EAAAA,EAAe,iBAAiBX,EAAO,CAAC,GAAGA,EAAO,CAAC,CAAC;AACrE,aAAO,MAAMI,CAAG,IAAI,IAAIA;AAAAA,IAC5B;AAAA,IACA,KAAK,iBAAiB;AAIlB,YAAMA,IAAMQ,EAAQ,GAAGZ,CAAM,EAAE;AAC/B,aAAO,MAAMI,CAAG,IAAI,IAAIA;AAAAA,IAC5B;AAAA,IACA;AACI,YAAM,IAAI,MAAM,qBAAqB;AAAA,EAAA;AAGjD;","x_google_ignoreList":[0]}

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/pValueCorrection.js

@@ -1,191 +0,0 @@
-import q from "../../../node_modules/lodash/lodash.js";
-function E(r, e) {
-  let t;
-  if (r == e) {
-    t = new Array(e + 1);
-    for (let n = 0; n < t.length; ++n)
-      t[n] = n + 1;
-  } else if (r < e) {
-    t = new Array(e - r + 1);
-    for (let n = 0; n < t.length; ++n)
-      t[n] = r + n;
-  } else {
-    t = new Array(r - e + 1);
-    for (let n = 0; n < t.length; ++n)
-      t[n] = r - n;
-  }
-  return t;
-}
-function c(r, e) {
-  return q.orderBy(
-    r.map((t, n) => [t, n]),
-    ([t]) => t,
-    [e ? "desc" : "asc"]
-  ).map(([, t]) => t);
-}
-function B(r) {
-  if (r.length < 1)
-    throw new Error("cummin requires at least one element");
-  const e = new Array(r.length);
-  let t = r[0];
-  for (let n = 0; n < r.length; ++n)
-    r[n] < t && (t = r[n]), e[n] = t;
-  return e;
-}
-function H(r) {
-  if (r.length < 1)
-    throw new Error("cummax requires at least one element");
-  const e = new Array(r.length);
-  let t = r[0];
-  for (let n = 0; n < r.length; ++n)
-    r[n] > t && (t = r[n]), e[n] = t;
-  return e;
-}
-function j(r, e) {
-  if (r.length < 1)
-    throw new Error("pmin requires at least one element");
-  return r.map((t) => Math.min(t, e));
-}
-function M(r) {
-  if (r.length < 1)
-    throw new Error("pAdjust requires at least one element");
-  return Math.min(...r);
-}
-function k(r) {
-  const e = r.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const t = new Array(e);
-  for (let n = 0; n < e; ++n) {
-    const o = r[n] * e;
-    if (o >= 1)
-      t[n] = 1;
-    else if (0 <= o)
-      t[n] = o;
-    else
-      throw new Error(`${o} is outside [0, 1)`);
-  }
-  return t;
-}
-function x(r) {
-  const e = r.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const t = c(r, !1), n = t.slice(), o = new Array(e).fill(0);
-  for (let a = 0; a < e; ++a)
-    o[a] = (e - a) * r[t[a]];
-  const s = c(n, !1), m = H(o), u = j(m, 1), f = new Array(e);
-  for (let a = 0; a < e; ++a)
-    f[a] = u[s[a]];
-  return f;
-}
-function $(r) {
-  const e = r.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const t = E(e, e), n = c(r, !1), o = new Array(e);
-  for (let i = 0; i < e; ++i)
-    o[i] = r[n[i]];
-  const s = n.slice(), m = c(s, !1), u = new Array(e), f = new Array(e), a = new Array(e);
-  for (let i = 0; i < e; ++i)
-    a[i] = o[i] * e / t[i];
-  const p = M(a);
-  u.fill(p), f.fill(p);
-  for (let i = e; i >= 2; --i) {
-    const A = E(1, e - i + 1);
-    for (let l = 0; l < e - i + 1; ++l)
-      A[l]--;
-    const w = i - 1, h = new Array(w);
-    for (let l = 0; l < w; ++l)
-      h[l] = e - i + 2 + l - 1;
-    let g = i * o[h[0]] / 2;
-    for (let l = 1; l < w; ++l) {
-      const d = o[h[l]] * i / (2 + l);
-      d < g && (g = d);
-    }
-    for (let l = 0; l < e - i + 1; ++l)
-      u[A[l]] = Math.min(o[A[l]] * i, g);
-    for (let l = 0; l < w; ++l)
-      u[h[l]] = u[e - i];
-    for (let l = 0; l < e; ++l)
-      f[l] < u[l] && (f[l] = u[l]);
-  }
-  for (let i = 0; i < e; ++i)
-    u[i] = f[m[i]];
-  return u;
-}
-class b {
-  constructor(e, t, n) {
-    this.ni = e, this.o = t, this.ro = n;
-  }
-  result(e) {
-    const t = B(e), n = j(t, 1), o = new Array(e.length);
-    for (let s = 0; s < e.length; ++s)
-      o[s] = n[this.ro[s]];
-    return o;
-  }
-}
-function y(r) {
-  const e = r.length, t = new Array(e), n = c(r, !0);
-  for (let s = 0; s < e; ++s) {
-    if (r[s] < 0 || r[s] > 1)
-      throw new Error("array[" + s + "] = " + r[s] + " is outside [0, 1]");
-    t[s] = e / (e - s);
-  }
-  const o = c(n, !1);
-  return new b(t, n, o);
-}
-function v(r) {
-  const e = r.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const t = y(r), n = new Array(e);
-  for (let o = 0; o < e; ++o)
-    n[o] = t.ni[o] * r[t.o[o]];
-  return t.result(n);
-}
-function z(r) {
-  const e = r.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const t = y(r), n = new Array(e);
-  let o = 0;
-  for (let s = 1; s < e + 1; ++s)
-    o += 1 / s;
-  for (let s = 0; s < e; ++s)
-    n[s] = o * t.ni[s] * r[t.o[s]];
-  return t.result(n);
-}
-function D(r) {
-  const e = r.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const t = y(r), n = new Array(e);
-  for (let o = 0; o < e; ++o)
-    n[o] = (o + 1) * r[t.o[o]];
-  return t.result(n);
-}
-function L(r, e) {
-  switch (e) {
-    case "BenjaminiHochberg":
-      return v(r);
-    case "BenjaminiYekutieli":
-      return z(r);
-    case "Bonferroni":
-      return k(r);
-    case "Hochberg":
-      return D(r);
-    case "Holm":
-      return x(r);
-    case "Hommel":
-      return $(r);
-    case null:
-      return r;
-    default:
-      throw new Error(`Unknown p-value correction method: ${e}`);
-  }
-}
-export {
-  L as adjustPValues
-};
-//# sourceMappingURL=pValueCorrection.js.map

package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/stats/pValueCorrection.js.map

@@ -1 +0,0 @@
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'desc' : 'asc']\n    ).map(([, index]) => index);\n}\n\nfunction cummin(array:number[]):number[] {\n    if (array.length < 1)\n        throw new Error('cummin requires at least one element');\n    const output = new Array(array.length);\n    let cumulativeMin = array[0];\n    for (let i = 0; i < array.length; ++i) {\n        if (array[i] < cumulativeMin)\n            cumulativeMin = array[i];\n        output[i] = cumulativeMin;\n    }\n    return output;\n}\n\nfunction cummax(array:number[]):number[] {\n    if (array.length < 1) {\n        throw new Error('cummax requires at least one element');\n    }\n    const output = new Array(array.length);\n    let cumulativeMax = array[0];\n    for (let i = 0; i < array.length; ++i) {\n        if (array[i] > cumulativeMax)\n            cumulativeMax = array[i];\n        output[i] = cumulativeMax;\n    }\n    return output;\n}\n\nfunction pminx(array:number[], x:number):number[] {\n    if (array.length < 1) {\n        throw new Error('pmin requires at least one element');\n    }\n    return array.map((el) => Math.min(el, x));\n}\n\nfunction doubleArrayMin(array:number[]):number {\n    if (array.length < 1)\n        throw new Error('pAdjust requires at least one element');\n    return Math.min(...array);\n}\n\nfunction Bonferoni(pvalues:number[]):number[] {\n    const size = pvalues.length;\n    if (size < 1)\n        throw new Error('pAdjust requires at least one element');\n\n    const result:number[] = new Array(size);\n    for (let i = 0; i < size; ++i) {\n        const b = pvalues[i] * size;\n        if (b >= 1) {\n            result[i] = 1;\n        } else if (0 <= b) {\n            result[i] = b;\n        } else {\n            throw new Error(`${b} is outside [0, 1)`);\n        }\n    }\n    return result;\n}\n\nfunction Holm(pvalues:number[]):number[] {\n    const size = pvalues.length;\n    if (size < 1)\n        throw new Error('pAdjust requires at least one element');\n\n    const o = order(pvalues, false);\n    const o2Double = o.slice();\n    const cummaxInput = new Array(size).fill(0);\n    for (let i = 0; i < size; ++i) {\n        cummaxInput[i] = (size - i) * pvalues[o[i]];\n    }\n    const ro = order(o2Double, false);\n    const cummaxOutput = cummax(cummaxInput);\n    const pmin = pminx(cummaxOutput, 1.0);\n    const result = new Array(size);\n    for (let i = 0; i < size; ++i) {\n        result[i] = pmin[ro[i]];\n    }\n    return result;\n}\n\nfunction Hommel(pvalues:number[]):number[] {\n    const size = pvalues.length;\n    if (size < 1)\n        throw new Error('pAdjust requires at least one element');\n    const indices = seqLen(size, size);\n    const o = order(pvalues, false);\n    const p = new Array(size);\n    for (let i = 0; i < size; ++i) {\n        p[i] = pvalues[o[i]];\n    }\n    const o2Double = o.slice();\n    const ro = order(o2Double, false);\n    const q = new Array(size);\n    const pa = new Array(size);\n    const npi = new Array(size);\n    for (let i = 0; i < 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       pa[i] = q[i];\n            }\n        }\n    }\n    for (let i = 0; i < size; ++i) {\n        q[i] = pa[ro[i]];\n    }\n    return q;\n}\n\nclass IntermediateData {\n    constructor(readonly ni: number[], readonly o: number[], readonly ro: number[]) {}\n    result(cumminInput:number[]):number[] {\n        const cumminArray:number[] = cummin(cumminInput);\n        const pmin:number[] = pminx(cumminArray, 1);\n        const result:number[] = new Array(cumminInput.length);\n        for (let i = 0; i < cumminInput.length; ++i) {\n            result[i] = pmin[this.ro[i]];\n        }\n        return result;\n    }\n}\n\nfunction computeIntermediateData(pvalues:number[]) {\n    const size = pvalues.length;\n    const ni = new Array(size);\n    const o = order(pvalues, true);\n    for (let i = 0; i < size; ++i) {\n        if (pvalues[i] < 0 || pvalues[i] > 1) {\n            throw new Error('array[' + i + '] = ' + pvalues[i] + ' is outside [0, 1]');\n        }\n        ni[i] = size / 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package/dist/node_modules/@milaboratories/miplots4/dist/discrete/layers/violins.js

@@ -1,89 +0,0 @@
-import { getFacetStringKey as _ } from "../utils/getFacetStringKey.js";
-import { quantileSorted as S } from "../../node_modules/d3-array/src/quantile.js";
-import $ from "../../node_modules/d3-scale/src/linear.js";
-import B from "../../node_modules/d3-array/src/max.js";
-import A from "../../node_modules/d3-shape/src/area.js";
-import D from "../../node_modules/d3-shape/src/curve/basis.js";
-import C from "../../node_modules/d3-shape/src/line.js";
-import j from "../../node_modules/d3-array/src/mean.js";
-var I = Object.defineProperty, O = (r, n, i) => n in r ? I(r, n, { enumerable: !0, configurable: !0, writable: !0, value: i }) : r[n] = i, l = (r, n, i) => O(r, typeof n != "symbol" ? n + "" : n, i);
-const L = 40;
-function z(r, n) {
-  return function(i) {
-    return n.map(function(m) {
-      return [m, j(i, (o) => r(m - o))];
-    });
-  };
-}
-function F(r) {
-  return function(n) {
-    return 1 / Math.sqrt(2 * Math.PI) * Math.pow(Math.E, -0.5 * Math.pow(n / r, 2));
-  };
-}
-function K(r) {
-  const n = j(r);
-  return j(r.map((i) => Math.pow(i - n, 2)));
-}
-function N(r) {
-  return Math.sqrt(K(r));
-}
-function R(r, n, i) {
-  const m = (i - n) / 1.34, o = N(r);
-  return 1.06 * Math.min(o, m) * Math.pow(r.length, -1 / 5);
-}
-class X {
-  constructor(n, i, m, o, y, d) {
-    if (l(this, "getArea"), l(this, "getLine"), l(this, "maxDensity"), l(this, "primaryGrouping"), l(this, "secondaryGrouping"), l(this, "key"), l(this, "boundsY"), l(this, "quartiles"), n.length === 0)
-      throw Error("Unable to calculate violin on empty data");
-    if (o !== "auto" && o < 1)
-      throw Error(`Unable to calculate violin with ${o} steps`);
-    this.primaryGrouping = String(y), this.secondaryGrouping = String(d), this.key = `violin_${this.primaryGrouping}_${this.secondaryGrouping}`;
-    const x = (e) => i === "log" ? Math.log10(e) : e, u = (e) => i === "log" ? Math.pow(10, e) : e, a = n.filter((e) => i === "log" && Number(e) === 0 ? (console.warn("Value = 0 on chart with log scale, it was removed from calculation"), !1) : !0).map(x).sort((e, s) => e - s), p = a[0], g = a[a.length - 1], v = g - p, b = S(a, 0.25), c = S(a, 0.5), k = S(a, 0.75);
-    this.quartiles = { q1: u(b), q2: u(c), q3: u(k) };
-    const w = R(a, b, k), P = o !== "auto" ? o : w / 3 > v / L ? L : v / (w / 3), U = m ? p : p - 3 * w, V = m ? g : g + 3 * w, Y = $().domain([U, V]).ticks(P);
-    this.boundsY = {
-      min: u(Y[0]),
-      max: u(Y[Y.length - 1])
-    };
-    const M = z(F(w), Y)(a).map(([e, s]) => [u(e), s]);
-    this.maxDensity = B(M, ([, e]) => e), this.getArea = (e, s, G, E) => {
-      const f = e === "vertical", q = E ?? this.maxDensity, h = $().domain([-q, q]).range([-G / 2, G / 2]);
-      return f ? A().curve(D).x0((t) => h(t[1])).x1((t) => h(-t[1])).y((t) => s(t[0]))(M) : A().curve(D).y0((t) => h(t[1])).y1((t) => h(-t[1])).x((t) => s(t[0]))(M);
-    }, this.getLine = (e, s, G, E) => {
-      const f = e === "vertical", q = E ?? this.maxDensity, h = $().domain([-q, q]).range([-G / 2, G / 2]);
-      return C().curve(D).x(f ? (t) => h(t[1]) : (t) => s(t[0])).y(f ? (t) => s(t[0]) : (t) => h(t[1]))(M) + " " + C().curve(D).x(f ? (t) => h(-t[1]) : (t) => s(t[0])).y(f ? (t) => s(t[0]) : (t) => h(-t[1]))(M);
-    };
-  }
-}
-function nt(r, n, i, m, o) {
-  let y = 0, d = 1 / 0, x = -1 / 0;
-  return {
-    type: "violin",
-    geoms: n.facet.reduce((u, a) => {
-      const p = _(a);
-      return u[p] = [], n.primary.forEach((g) => {
-        n.secondary.forEach((v) => {
-          const b = i.getColumnByGrouping([...a, g, v], m.value);
-          if (!b.length)
-            return;
-          const c = new X(
-            b,
-            o.scale,
-            r.stat.trim,
-            r.stat.stepsCount,
-            g,
-            v
-          );
-          c.maxDensity > y && (y = c.maxDensity), c.boundsY.min < d && (d = c.boundsY.min), c.boundsY.max > x && (x = c.boundsY.max), u[p].push(c);
-        });
-      }), u;
-    }, {}),
-    meta: { maxDensity: y, minY: d, maxY: x },
-    aes: r.aes
-  };
-}
-export {
-  X as Violin,
-  nt as getViolinsData
-};
-//# sourceMappingURL=violins.js.map