@milaboratories/miplots4 1.0.176 → 1.0.178

package/dist/discrete/layers/stats/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":["../../../../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    };\n}\n"],"names":["getAllKeyPairs","keys","res","key1","index","key2","getStatsData","layer","facetKeys","primaryKeys","y","data","facetKey","values","groups","primaryKey","group","pValue","calculatePValue","referenceKey","NO_GROUPED","referenceGroup","keysAndGroupsNonEmpty","key","pValues","adjustPValues","gr1","gr2","keysPair","getFacetStringKey"],"mappings":";;;;AASA,SAASA,EAAgBC,GAAiB;AACtC,SAAOA,EACF,MAAM,GAAE,EAAE,EACV;AAAA,IACG,CAACC,GAA6BC,GAAMC,MAChCF,EAAI,OAAOD,EAAK,MAAMG,IAAQ,CAAC,EAAE,IAAI,CAAAC,MAAQ,CAACF,GAAME,CAAI,CAAC,CAAC;AAAA,IAC9D,CAAA;AAAA,EAAC;AAEb;AAEO,SAASC,EACZC,GACAC,GACAC,GACAC,GACAC,GACS;AACT,SAAO;AAAA,IACH,MAAM;AAAA,IACN,QAAQH,EAAU,OAAO,CAACN,GAA0BU,MAAa;AAC7D,UAAIC,IAA+B,CAAA;AACnC,cAAQN,EAAM,UAAA;AAAA,QACV,KAAK,WAAW;AACZ,gBAAMO,IAASL,EACV,IAAI,CAAAM,MAAcJ,EAAK,oBAAoB,CAAC,GAAGC,GAAUG,CAAU,GAAGL,EAAE,KAAK,CAAC,EAC9E,OAAO,CAACM,MAAUA,EAAM,SAAS,CAAC;AACvC,cAAIF,EAAO,SAAS;AAChB;AAEJ,gBAAMG,IAASC,EAAgBJ,GAAQP,EAAM,YAAYA,EAAM,MAAM;AACrE,UAAAM,IAAS,CAAC,CAAC,CAAC,SAAS,GAAGI,CAAM,CAAC;AAC/B;AAAA,QACJ;AAAA,QACA,KAAK,kBAAkB;AACnB,gBAAME,IAAeZ,EAAM,mBAAmB,OAAOa,IAAa,OAAOb,EAAM,cAAc;AAC7F,cAAIY,MAAiBC,KAAc,CAACX,EAAY,SAASU,CAAY;AACjE,kBAAM,IAAI,MAAM,mBAAmB,OAAOA,CAAY,CAAC,QAAQZ,EAAM,UAAU,kCAAkC;AAErH,gBAAMc,IAAiBV,EAAK,oBAAoB,CAAC,GAAGC,GAAUO,CAAY,GAAGT,EAAE,KAAK;AACpF,cAAIW,EAAe,WAAW,GAAG;AAC7B,YAAAR,IAAS,CAAA;AACT;AAAA,UACJ;AAGA,gBAAMS,IADOb,EAAY,OAAO,CAAAc,MAAOA,MAAQJ,CAAY,EAEtD,IAAI,CAAAJ,MAAc,CAACA,GAAYJ,EAAK,oBAAoB,CAAC,GAAGC,GAAUG,CAAU,GAAGL,EAAE,KAAK,CAAC,CAAuB,EAClH,OAAO,CAAC,CAAA,EAAGM,CAAK,MAAMA,EAAM,SAAS,CAAC;AAC3C,cAAIM,EAAsB,SAAS,KAAKf,EAAM,qBAAqB;AAC/D;AAEJ,gBAAMiB,IAAUC;AAAA,YACZH,EAAsB;AAAA,cAAI,CAAC,CAAA,EAAEN,CAAK,MAC9BE;AAAA,gBACI,CAACG,GAAgBL,CAAK;AAAA,gBACtBT,EAAM;AAAA,gBACNA,EAAM;AAAA,cAAA;AAAA,YACV;AAAA,YAEJA,EAAM;AAAA,UAAA;AAEV,UAAAM,IAASS,EAAsB,IAAI,CAAC,CAACP,CAAU,GAAGX,MAAU,CAAC,CAACW,CAAU,GAAGS,EAAQpB,CAAK,CAAC,CAAC;AAC1F;AAAA,QACJ;AAAA,QACA,KAAK,YAAY;AAEb,gBAAMkB,IADYtB,EAAeS,CAAW,EAEvC,IAAI,CAAC,CAACN,GAAME,CAAI,MAAM;AAAA,YACnB,CAACF,GAAME,CAAI;AAAA,YACX;AAAA,cACIM,EAAK,oBAAoB,CAAC,GAAGC,GAAUT,CAAI,GAAGO,EAAE,KAAK;AAAA,cACrDC,EAAK,oBAAoB,CAAC,GAAGC,GAAUP,CAAI,GAAGK,EAAE,KAAK;AAAA,YAAA;AAAA,UACzD,CACuB,EAC1B,OAAO,CAAC,CAAA,EAAE,CAACgB,GAAKC,CAAG,CAAC,MAAMD,EAAI,UAAUC,EAAI,MAAM;AAEvD,cAAIL,EAAsB,SAAS;AAC/B;AAEJ,gBAAME,IAAUC;AAAA,YACZH,EAAsB,IAAI,CAAC,CAAA,EAAER,CAAM,MAAMI,EAAgBJ,GAAQP,EAAM,YAAYA,EAAM,MAAM,CAAC;AAAA,YAChGA,EAAM;AAAA,UAAA;AAEV,UAAAM,IAASS,EAAsB,IAAI,CAAC,CAACM,CAAQ,GAAGxB,MAAU,CAACwB,GAAUJ,EAAQpB,CAAK,CAAC,CAAC;AACpF;AAAA,QACJ;AAAA,QACA;AACI,gBAAM,IAAI,MAAM,kBAAkB;AAAA,MACtC;AAEJ,aAAAF,EAAI2B,EAAkBjB,CAAQ,CAAC,IAAIC,GAC5BX;AAAA,IACX,GAAG,CAAA,CAAE;AAAA,IACL,MAAM;AAAA,MACF,UAAUK,EAAM;AAAA,MAChB,YAAYA,EAAM;AAAA,MAClB,QAAQA,EAAM;AAAA,MACd,IAAIA,EAAM;AAAA,MACV,oBAAoBA,EAAM;AAAA,IAAA;AAAA,EAC9B;AAER;"}
+{"version":3,"file":"index.js","names":[],"sources":["../../../../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     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package/dist/discrete/layers/stats/pValueCalculation.js

@@ -1,50 +1,41 @@
-import l from "../../../_virtual/index6.js";
-import s from "../../../_virtual/index7.js";
-import f from "../../../_virtual/index8.js";
-import m from "../../../_virtual/index9.js";
-import h from "../../../_virtual/index10.js";
-import { MannWhitneyU as c } from "./MannWhitneyU.js";
-import n from "../../../_virtual/lodash.js";
-function u(t, a, r) {
-  switch (a) {
-    case "ttest": {
-      if (t.length > 2)
-        throw new Error("more than 2 datasets passed");
-      if (r) {
-        if (t[0].length !== t[1].length)
-          throw Error("Different size groups in paired test");
-        return s(t[0], t[1]).pValue;
-      }
-      const e = f(t[0], t[1]).pValue;
-      return isNaN(e) ? 1 : e;
-    }
-    case "anova": {
-      const e = l(
-        n.flatten(t),
-        n.flatten(t.map((i, o) => i.map(() => String(o))))
-      ).pValue;
-      return isNaN(e) ? 1 : e;
-    }
-    case "wilcoxon": {
-      if (t.length > 2)
-        throw new Error("more than 2 datasets passed");
-      if (r) {
-        if (t[0].length !== t[1].length)
-          throw Error("Different size groups in paired test");
-        return h(t[0], t[1]).pValue;
-      }
-      const e = new c().mannWhitneyUTest(t[0], t[1]);
-      return isNaN(e) ? 1 : e;
-    }
-    case "kruskalWallis": {
-      const e = m(...t).pValue;
-      return isNaN(e) ? 1 : e;
-    }
-    default:
-      throw new Error("Unknown test method");
-  }
+import { MannWhitneyU as e } from "./MannWhitneyU.js";
+import t from "lodash";
+import n from "@stdlib/stats-anova1";
+import r from "@stdlib/stats-ttest";
+import i from "@stdlib/stats-ttest2";
+import a from "@stdlib/stats-kruskal-test";
+import o from "@stdlib/stats-wilcoxon";
+function s(s, c, l) {
+	switch (c) {
+		case "ttest": {
+			if (s.length > 2) throw Error("more than 2 datasets passed");
+			if (l) {
+				if (s[0].length !== s[1].length) throw Error("Different size groups in paired test");
+				return r(s[0], s[1]).pValue;
+			}
+			let e = i(s[0], s[1]).pValue;
+			return isNaN(e) ? 1 : e;
+		}
+		case "anova": {
+			let e = n(t.flatten(s), t.flatten(s.map((e, t) => e.map(() => String(t))))).pValue;
+			return isNaN(e) ? 1 : e;
+		}
+		case "wilcoxon": {
+			if (s.length > 2) throw Error("more than 2 datasets passed");
+			if (l) {
+				if (s[0].length !== s[1].length) throw Error("Different size groups in paired test");
+				return o(s[0], s[1]).pValue;
+			}
+			let t = new e().mannWhitneyUTest(s[0], s[1]);
+			return isNaN(t) ? 1 : t;
+		}
+		case "kruskalWallis": {
+			let e = a(...s).pValue;
+			return isNaN(e) ? 1 : e;
+		}
+		default: throw Error("Unknown test method");
+	}
 }
-export {
-  u as calculatePValue
-};
-//# sourceMappingURL=pValueCalculation.js.map
+export { s as calculatePValue };
+
+//# sourceMappingURL=pValueCalculation.js.map

package/dist/discrete/layers/stats/pValueCalculation.js.map

@@ -1 +1 @@
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+{"version":3,"file":"pValueCalculation.js","names":[],"sources":["../../../../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            // @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"],"mappings":";;;;;;;AASA,SAAgB,EAAgB,GAAoB,GAA4B,GAAiB;AAC7F,SAAQ,GAAR;EACI,KAAK,SAAS;AACV,OAAI,EAAO,SAAS,EAChB,OAAU,MAAM,8BAA8B;AAElD,OAAI,GAAQ;AACR,QAAI,EAAO,GAAG,WAAW,EAAO,GAAG,OAC/B,OAAM,MAAM,uCAAuC;AAEvD,WAAO,EAAM,EAAO,IAAI,EAAO,GAAG,CAAC;;GAGvC,IAAM,IAAM,EAAO,EAAO,IAAI,EAAO,GAAG,CAAC;AACzC,UAAO,MAAM,EAAI,GAAG,IAAI;;EAE5B,KAAK,SAAS;GACV,IAAM,IAAM,EACR,EAAO,QAAQ,EAAO,EACtB,EAAO,QAAQ,EAAO,KAAK,GAAG,MAAU,EAAE,UAAU,OAAO,EAAM,CAAC,CAAC,CAAC,CACvE,CAAC;AACF,UAAO,MAAM,EAAI,GAAG,IAAI;;EAE5B,KAAK,YAAY;AACb,OAAI,EAAO,SAAS,EAChB,OAAU,MAAM,8BAA8B;AAElD,OAAI,GAAQ;AACR,QAAI,EAAO,GAAG,WAAW,EAAO,GAAG,OAC/B,OAAM,MAAM,uCAAuC;AAEvD,WAAO,EAAS,EAAO,IAAI,EAAO,GAAG,CAAC;;GAE1C,IAAM,IAAO,IAAI,GAAc,CAAC,iBAAiB,EAAO,IAAI,EAAO,GAAG;AACtE,UAAO,MAAM,EAAI,GAAG,IAAI;;EAE5B,KAAK,iBAAiB;GAGlB,IAAM,IAAM,EAAQ,GAAG,EAAO,CAAC;AAC/B,UAAO,MAAM,EAAI,GAAG,IAAI;;EAE5B,QACI,OAAU,MAAM,sBAAsB"}

package/dist/discrete/layers/stats/pValueCorrection.js

@@ -1,191 +1,140 @@
-import b from "../../../_virtual/lodash.js";
-function E(t, e) {
-  let r;
-  if (t == e) {
-    r = new Array(e + 1);
-    for (let n = 0; n < r.length; ++n)
-      r[n] = n + 1;
-  } else if (t < e) {
-    r = new Array(e - t + 1);
-    for (let n = 0; n < r.length; ++n)
-      r[n] = t + n;
-  } else {
-    r = new Array(t - e + 1);
-    for (let n = 0; n < r.length; ++n)
-      r[n] = t - n;
-  }
-  return r;
+import e from "lodash";
+function t(e, t) {
+	let n;
+	if (e == t) {
+		n = Array(t + 1);
+		for (let e = 0; e < n.length; ++e) n[e] = e + 1;
+	} else if (e < t) {
+		n = Array(t - e + 1);
+		for (let t = 0; t < n.length; ++t) n[t] = e + t;
+	} else {
+		n = Array(e - t + 1);
+		for (let t = 0; t < n.length; ++t) n[t] = e - t;
+	}
+	return n;
 }
-function m(t, e) {
-  return b.orderBy(
-    t.map((r, n) => [r, n]),
-    ([r]) => r,
-    [e ? "desc" : "asc"]
-  ).map(([, r]) => r);
+function n(t, n) {
+	return e.orderBy(t.map((e, t) => [e, t]), ([e]) => e, [n ? "desc" : "asc"]).map(([, e]) => e);
 }
-function H(t) {
-  if (t.length < 1)
-    throw new Error("cummin requires at least one element");
-  const e = new Array(t.length);
-  let r = t[0];
-  for (let n = 0; n < t.length; ++n)
-    t[n] < r && (r = t[n]), e[n] = r;
-  return e;
+function r(e) {
+	if (e.length < 1) throw Error("cummin requires at least one element");
+	let t = Array(e.length), n = e[0];
+	for (let r = 0; r < e.length; ++r) e[r] < n && (n = e[r]), t[r] = n;
+	return t;
 }
-function x(t) {
-  if (t.length < 1)
-    throw new Error("cummax requires at least one element");
-  const e = new Array(t.length);
-  let r = t[0];
-  for (let n = 0; n < t.length; ++n)
-    t[n] > r && (r = t[n]), e[n] = r;
-  return e;
+function i(e) {
+	if (e.length < 1) throw Error("cummax requires at least one element");
+	let t = Array(e.length), n = e[0];
+	for (let r = 0; r < e.length; ++r) e[r] > n && (n = e[r]), t[r] = n;
+	return t;
 }
-function y(t, e) {
-  if (t.length < 1)
-    throw new Error("pmin requires at least one element");
-  return t.map((r) => Math.min(r, e));
+function a(e, t) {
+	if (e.length < 1) throw Error("pmin requires at least one element");
+	return e.map((e) => Math.min(e, t));
 }
-function z(t) {
-  if (t.length < 1)
-    throw new Error("pAdjust requires at least one element");
-  return Math.min(...t);
+function o(e) {
+	if (e.length < 1) throw Error("pAdjust requires at least one element");
+	return Math.min(...e);
 }
-function B(t) {
-  const e = t.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const r = new Array(e);
-  for (let n = 0; n < e; ++n) {
-    const o = t[n] * e;
-    if (o >= 1)
-      r[n] = 1;
-    else if (0 <= o)
-      r[n] = o;
-    else
-      throw new Error(`${o} is outside [0, 1)`);
-  }
-  return r;
+function s(e) {
+	let t = e.length;
+	if (t < 1) throw Error("pAdjust requires at least one element");
+	let n = Array(t);
+	for (let r = 0; r < t; ++r) {
+		let i = e[r] * t;
+		if (i >= 1) n[r] = 1;
+		else if (0 <= i) n[r] = i;
+		else throw Error(`${i} is outside [0, 1)`);
+	}
+	return n;
 }
-function p(t) {
-  const e = t.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const r = m(t, !1), n = r.slice(), o = new Array(e).fill(0);
-  for (let c = 0; c < e; ++c)
-    o[c] = (e - c) * t[r[c]];
-  const s = m(n, !1), a = x(o), u = y(a, 1), f = new Array(e);
-  for (let c = 0; c < e; ++c)
-    f[c] = u[s[c]];
-  return f;
+function c(e) {
+	let t = e.length;
+	if (t < 1) throw Error("pAdjust requires at least one element");
+	let r = n(e, !1), o = r.slice(), s = Array(t).fill(0);
+	for (let n = 0; n < t; ++n) s[n] = (t - n) * e[r[n]];
+	let c = n(o, !1), l = a(i(s), 1), u = Array(t);
+	for (let e = 0; e < t; ++e) u[e] = l[c[e]];
+	return u;
 }
-function M(t) {
-  const e = t.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const r = E(e, e), n = m(t, !1), o = new Array(e);
-  for (let l = 0; l < e; ++l)
-    o[l] = t[n[l]];
-  const s = n.slice(), a = m(s, !1), u = new Array(e), f = new Array(e), c = new Array(e);
-  for (let l = 0; l < e; ++l)
-    c[l] = o[l] * e / r[l];
-  const q = z(c);
-  u.fill(q), f.fill(q);
-  for (let l = e; l >= 2; --l) {
-    const A = E(1, e - l + 1);
-    for (let i = 0; i < e - l + 1; ++i)
-      A[i]--;
-    const h = l - 1, w = new Array(h);
-    for (let i = 0; i < h; ++i)
-      w[i] = e - l + 2 + i - 1;
-    let g = l * o[w[0]] / 2;
-    for (let i = 1; i < h; ++i) {
-      const j = o[w[i]] * l / (2 + i);
-      j < g && (g = j);
-    }
-    for (let i = 0; i < e - l + 1; ++i)
-      u[A[i]] = Math.min(o[A[i]] * l, g);
-    for (let i = 0; i < h; ++i)
-      u[w[i]] = u[e - l];
-    for (let i = 0; i < e; ++i)
-      f[i] < u[i] && (f[i] = u[i]);
-  }
-  for (let l = 0; l < e; ++l)
-    u[l] = f[a[l]];
-  return u;
+function l(e) {
+	let r = e.length;
+	if (r < 1) throw Error("pAdjust requires at least one element");
+	let i = t(r, r), a = n(e, !1), s = Array(r);
+	for (let t = 0; t < r; ++t) s[t] = e[a[t]];
+	let c = n(a.slice(), !1), l = Array(r), u = Array(r), d = Array(r);
+	for (let e = 0; e < r; ++e) d[e] = s[e] * r / i[e];
+	let f = o(d);
+	l.fill(f), u.fill(f);
+	for (let e = r; e >= 2; --e) {
+		let n = t(1, r - e + 1);
+		for (let t = 0; t < r - e + 1; ++t) n[t]--;
+		let i = e - 1, a = Array(i);
+		for (let t = 0; t < i; ++t) a[t] = r - e + 2 + t - 1;
+		let o = e * s[a[0]] / 2;
+		for (let t = 1; t < i; ++t) {
+			let n = s[a[t]] * e / (2 + t);
+			n < o && (o = n);
+		}
+		for (let t = 0; t < r - e + 1; ++t) l[n[t]] = Math.min(s[n[t]] * e, o);
+		for (let t = 0; t < i; ++t) l[a[t]] = l[r - e];
+		for (let e = 0; e < r; ++e) u[e] < l[e] && (u[e] = l[e]);
+	}
+	for (let e = 0; e < r; ++e) l[e] = u[c[e]];
+	return l;
 }
-class D {
-  constructor(e, r, n) {
-    this.ni = e, this.o = r, this.ro = n;
-  }
-  result(e) {
-    const r = H(e), n = y(r, 1), o = new Array(e.length);
-    for (let s = 0; s < e.length; ++s)
-      o[s] = n[this.ro[s]];
-    return o;
-  }
-}
-function d(t) {
-  const e = t.length, r = new Array(e), n = m(t, !0);
-  for (let s = 0; s < e; ++s) {
-    if (t[s] < 0 || t[s] > 1)
-      throw new Error("array[" + s + "] = " + t[s] + " is outside [0, 1]");
-    r[s] = e / (e - s);
-  }
-  const o = m(n, !1);
-  return new D(r, n, o);
+var u = class {
+	constructor(e, t, n) {
+		this.ni = e, this.o = t, this.ro = n;
+	}
+	result(e) {
+		let t = a(r(e), 1), n = Array(e.length);
+		for (let r = 0; r < e.length; ++r) n[r] = t[this.ro[r]];
+		return n;
+	}
+};
+function d(e) {
+	let t = e.length, r = Array(t), i = n(e, !0);
+	for (let n = 0; n < t; ++n) {
+		if (e[n] < 0 || e[n] > 1) throw Error("array[" + n + "] = " + e[n] + " is outside [0, 1]");
+		r[n] = t / (t - n);
+	}
+	return new u(r, i, n(i, !1));
 }
-function I(t) {
-  const e = t.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const r = d(t), n = new Array(e);
-  for (let o = 0; o < e; ++o)
-    n[o] = r.ni[o] * t[r.o[o]];
-  return r.result(n);
+function f(e) {
+	let t = e.length;
+	if (t < 1) throw Error("pAdjust requires at least one element");
+	let n = d(e), r = Array(t);
+	for (let i = 0; i < t; ++i) r[i] = n.ni[i] * e[n.o[i]];
+	return n.result(r);
 }
-function k(t) {
-  const e = t.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const r = d(t), 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 * r.ni[s] * t[r.o[s]];
-  return r.result(n);
+function p(e) {
+	let t = e.length;
+	if (t < 1) throw Error("pAdjust requires at least one element");
+	let n = d(e), r = Array(t), i = 0;
+	for (let e = 1; e < t + 1; ++e) i += 1 / e;
+	for (let a = 0; a < t; ++a) r[a] = i * n.ni[a] * e[n.o[a]];
+	return n.result(r);
 }
-function L(t) {
-  const e = t.length;
-  if (e < 1)
-    throw new Error("pAdjust requires at least one element");
-  const r = d(t), n = new Array(e);
-  for (let o = 0; o < e; ++o)
-    n[o] = (o + 1) * t[r.o[o]];
-  return r.result(n);
+function m(e) {
+	let t = e.length;
+	if (t < 1) throw Error("pAdjust requires at least one element");
+	let n = d(e), r = Array(t);
+	for (let i = 0; i < t; ++i) r[i] = (i + 1) * e[n.o[i]];
+	return n.result(r);
 }
-function $(t, e) {
-  switch (e) {
-    case "BenjaminiHochberg":
-      return I(t);
-    case "BenjaminiYekutieli":
-      return k(t);
-    case "Bonferroni":
-      return B(t);
-    case "Hochberg":
-      return L(t);
-    case "Holm":
-      return p(t);
-    case "Hommel":
-      return M(t);
-    case null:
-      return t;
-    default:
-      throw new Error(`Unknown p-value correction method: ${e}`);
-  }
+function h(e, t) {
+	switch (t) {
+		case "BenjaminiHochberg": return f(e);
+		case "BenjaminiYekutieli": return p(e);
+		case "Bonferroni": return s(e);
+		case "Hochberg": return m(e);
+		case "Holm": return c(e);
+		case "Hommel": return l(e);
+		case null: return e;
+		default: throw Error(`Unknown p-value correction method: ${t}`);
+	}
 }
-export {
-  $ as adjustPValues
-};
-//# sourceMappingURL=pValueCorrection.js.map
+export { h as adjustPValues };
+
+//# sourceMappingURL=pValueCorrection.js.map

package/dist/discrete/layers/stats/pValueCorrection.js.map

@@ -1 +1 @@
-{"version":3,"file":"pValueCorrection.js","sources":["../../../../src/discrete/layers/stats/pValueCorrection.ts"],"sourcesContent":["import type {PValueCorrectionMethod} from '../../../types';\nimport lodash from 'lodash';\n\n// calculations from https://github.com/milaboratory/miplots/blob/559b13065f17dfc7c4dd332247dd1ce0183affcc/src/main/java/com/milaboratory/miplots/stat/util/PValueCorrection.java#L43\nfunction seqLen(start:number, end:number) {\n    let result:number[];\n    if (start == end) {\n        result = new Array(end + 1);\n        for (let i = 0; i < result.length; ++i) {\n            result[i] = i + 1;\n        }\n    } else if (start < end) {\n        result = new Array(end - start + 1);\n        for (let i = 0; i < result.length; ++i) {\n            result[i] = start + i;\n        }\n    } else {\n        result = new Array(start - end + 1);\n        for (let i = 0; i < result.length; ++i) {\n            result[i] = start - i;\n        }\n    }\n    return result;\n}\n\nfunction order(array:number[], decreasing:boolean):number[] {\n    return lodash.orderBy(\n        array.map((value, index) => [value, index]),\n        ([value]) => value,\n        [decreasing ? 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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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+{"version":3,"file":"pValueCorrection.js","names":[],"sources":["../../../../src/discrete/layers/stats/pValueCorrection.ts"],"sourcesContent":["import type {PValueCorrectionMethod} from '../../../types';\nimport lodash from 'lodash';\n\n// calculations from https://github.com/milaboratory/miplots/blob/559b13065f17dfc7c4dd332247dd1ce0183affcc/src/main/java/com/milaboratory/miplots/stat/util/PValueCorrection.java#L43\nfunction seqLen(start:number, end:number) {\n    let result:number[];\n    if (start == end) {\n        result = new Array(end + 1);\n        for (let i = 0; i < result.length; ++i) {\n            result[i] = i + 1;\n        }\n    } else if (start < end) {\n        result = new Array(end - start + 1);\n        for (let i = 0; i < result.length; ++i) {\n            result[i] = start + i;\n        }\n    } else {\n        result = new Array(start - end + 1);\n        for (let i = 0; i < result.length; ++i) {\n            result[i] = start - i;\n        }\n    }\n    return result;\n}\n\nfunction order(array:number[], decreasing:boolean):number[] {\n    return lodash.orderBy(\n        array.map((value, index) => [value, index]),\n        ([value]) => value,\n        [decreasing ? '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 < size; ++i) {\n        npi[i] = p[i] * size / indices[i];\n    }\n    const min = doubleArrayMin(npi);\n    q.fill(min);\n    pa.fill(min);\n    for (let j = size; j >= 2; --j) {\n        const ij = seqLen(1, size - j + 1);\n        for (let i = 0; i < size - j + 1; ++i) {\n            ij[i]--;\n        }\n        const i2Length = j - 1;\n        const i2 = new Array(i2Length);\n        for (let i = 0; i < i2Length; ++i) {\n            i2[i] = size - j + 2 + i - 1;\n        }\n        let q1 = j * p[i2[0]] / 2.0;\n        for (let i = 1; i < i2Length; ++i) {\n            const temp_q1 = p[i2[i]] * j / (2.0 + i);\n            if (temp_q1 < q1) {\n                q1 = temp_q1;\n            }\n        }\n        for (let i = 0; i < size - j + 1; ++i) {\n            q[ij[i]] = Math.min(p[ij[i]] * j, q1);\n        }\n        for (let i = 0; i < i2Length; ++i) {\n            q[i2[i]] = q[size - j];\n        }\n        for (let i = 0; i < size; ++i) {\n            if (pa[i] < q[i]) {\n                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 / (size - i);\n    }\n    const ro = order(o, false);\n    return new IntermediateData(ni, o, ro);\n}\n\nfunction BenjaminiHochberg(pvalues:number[]) {\n    const size = pvalues.length;\n    if (size < 1)\n        throw new Error('pAdjust requires at least one element');\n\n    const data = computeIntermediateData(pvalues);\n    const cumminInput:number[] = new Array(size);\n    for (let i = 0; i < size; ++i) {\n        cumminInput[i] = data.ni[i] * pvalues[data.o[i]];\n    }\n    return data.result(cumminInput);\n}\n\nfunction BenjaminiYekutieli(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 data:IntermediateData = computeIntermediateData(pvalues);\n    const cumminInput = new Array(size);\n    let q = 0;\n    for (let i = 1; i < size + 1; ++i) {\n        q += 1 / i;\n    }\n    for (let i = 0; i < size; ++i) {\n        cumminInput[i] = q * data.ni[i] * pvalues[data.o[i]];\n    }\n    return data.result(cumminInput);\n}\n\nfunction Hochberg(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 data:IntermediateData = computeIntermediateData(pvalues);\n    const cumminInput = new Array(size);\n    for (let i = 0; i < size; ++i) {\n        cumminInput[i] = (i + 1) * pvalues[data.o[i]];\n    }\n    return data.result(cumminInput);\n}\n\nexport function adjustPValues(pValues:number[], method:PValueCorrectionMethod | null) {\n    switch (method) {\n        case 'BenjaminiHochberg': {\n            return BenjaminiHochberg(pValues);\n        }\n        case 'BenjaminiYekutieli': {\n            return BenjaminiYekutieli(pValues);\n        }\n        case 'Bonferroni': {\n            return Bonferoni(pValues);\n        }\n        case 'Hochberg': {\n            return Hochberg(pValues);\n        }\n        case 'Holm': {\n            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