@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/regression.integration.spec-XJQJAIC3.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/test/regression.integration.spec.js"],
+  "sourcesContent": ["import tape from 'tape'\nimport * as helpers from '../../test/front.helpers.js'\nimport { detectGte, detectOne } from '../../test/test.helpers.js'\n\n/* \nTests:\n    Linear: continuous outcome = \"agedx\", cat. independents = \"sex\" + \"genetic_race\"\n    Linear: continuous outcome = \"agedx\", continuous independent = \"aaclassic_5\"\n\tLinear: continuous outcome = \"agedx\", discrete independent = \"aaclassic_5\"\n\tLinear: continuous outcome = \"agedx\", cubic spline independent = \"aaclassic_5\"\n\tLinear: continuous outcome = \"agedx\", independents = \"sex\" * \"aaclassic_5\"\n\tLinear: continuous outcome = \"agedx\", geneVariant independent = \"TP53\"\n\tLogistic: continuous outcome = \"hrtavg\", continuous independent = \"agedx\"\n\tLogistic: categorical outcome = \"diaggrp\", continuous independent = \"agedx\"\n    Cox: graded outcome = \"Arrhythmias\", continuous independent = \"agedx\"\n\tCox: survival outcome, continuous independent = \"agedx\"\n\nTODO:\n\tTest (maybe in unit?) beta and PR functions\n*/\n\ntape('\\n', test => {\n\ttest.comment('-***- plots/regression -***-')\n\ttest.end()\n})\n\ntape('Linear: continuous outcome = \"agedx\", cat. independents = \"sex\" + \"genetic_race\"', test => {\n\ttest.timeoutAfter(5000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'linear',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [{ id: 'sex' }, { id: 'genetic_race' }]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\t//**** Inputs ****\n\t\ttest.equal(\n\t\t\tregDom.inputs\n\t\t\t\t.selectAll('table')\n\t\t\t\t.nodes()\n\t\t\t\t.filter(t => t.childNodes.length > 1).length,\n\t\t\t2,\n\t\t\t`Should render two tables for independent variables`\n\t\t)\n\n\t\t//**** Results ****\n\t\tlet table, tableLabel, results, testTerm\n\n\t\t//Sample size\n\t\tconst sampleSizeDiv = regDom.results\n\t\t\t.selectAll('div[name^=\"Sample size\"] span')\n\t\t\t.nodes()\n\t\t\t.filter(d => d.innerText == data.sampleSize)\n\t\ttest.ok(\n\t\t\tregDom.results.node().querySelector('div[name^=\"Sample size\"]') && sampleSizeDiv,\n\t\t\t`Should render \"Sample size: ${data.sampleSize}\"`\n\t\t)\n\n\t\t//Residual table\n\t\ttableLabel = 'residuals table'\n\t\ttable = regDom.results.selectAll('table[name^=\"sjpp-residuals-table\"] tr').nodes()\n\t\tresults = checkTableRow(table, 1, data.residuals.rows)\n\t\ttest.equal(results, true, `Should render all residuals data in ${tableLabel}`)\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\t\tconst coefHeader = structuredClone(data.coefficients.header)\n\t\tcoefHeader.splice(3, 2, '95% CI')\n\t\tcoefHeader[2] = coefHeader[2] + String.fromCharCode(160) + '\u24D8'\n\t\tresults = checkTableRow(table, 0, coefHeader)\n\t\ttest.equal(results, true, `Should render all coefficient headers in ${tableLabel}`)\n\t\tconst linearHeaders = coefHeader.filter(d => d === 'Beta' + String.fromCharCode(160) + '\u24D8')\n\t\ttest.equal(linearHeaders.length, 1, `Should render headers specific to linear regression`)\n\t\tconst coefIntercept = [data.coefficients.intercept[0], data.coefficients.intercept[1]]\n\t\tcoefIntercept.push(...getCoefData(data.coefficients.intercept.slice(2)))\n\t\tresults = checkTableRow(table, 1, coefIntercept)\n\t\ttest.equal(results, true, `Should render all intercept data in ${tableLabel}`)\n\n\t\ttestTerm = 'Sex'\n\t\tconst checkValues1 = ['Sex\\nREF\\nFemale', 'Male']\n\t\tcheckValues1.push(...getCoefData(data.coefficients.terms[tid2$id('sex', regression)].categories[1]))\n\t\tresults = checkTableRow(table, 2, checkValues1)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\ttestTerm = 'African Ancestry'\n\t\tconst checkValues2 = ['Genetically defined race\\nREF\\nEuropean Ancestry', testTerm]\n\t\tcheckValues2.push(...getCoefData(data.coefficients.terms[tid2$id('genetic_race', regression)].categories[testTerm]))\n\t\tresults = checkTableRow(table, 3, checkValues2)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\ttestTerm = 'Asian Ancestry'\n\t\tconst checkValues3 = [testTerm]\n\t\tcheckValues3.push(...getCoefData(data.coefficients.terms[tid2$id('genetic_race', regression)].categories[testTerm]))\n\t\tresults = checkTableRow(table, 4, checkValues3)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Type III Stats\n\t\ttableLabel = 'type3 table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Type III statistics\"] table tr').nodes()\n\t\tresults = checkTableRow(table, 0, data.type3.header)\n\t\ttest.equal(results, true, `Should render all header data in ${tableLabel}`)\n\n\t\tresults = checkTableRow(table, 1, data.type3.intercept)\n\t\ttest.equal(results, true, `Should render all intercept data in ${tableLabel}`)\n\n\t\ttestTerm = 'Sex'\n\t\tconst checkValues4 = [testTerm]\n\t\tdata.type3.terms[tid2$id('sex', regression)].forEach(d => checkValues4.push(d))\n\t\tresults = checkTableRow(table, 2, checkValues4)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\ttestTerm = 'Genetically defined race'\n\t\tconst checkValues5 = [testTerm]\n\t\tdata.type3.terms[tid2$id('genetic_race', regression)].forEach(d => checkValues5.push(d))\n\t\tresults = checkTableRow(table, 3, checkValues5)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Other stats\n\t\ttableLabel = 'other summary statistics table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Other summary statistics\"] table tr').nodes()\n\t\tfor (const [i, header] of data.other.header.entries()) {\n\t\t\tresults = checkTableRow(table, i, [header, data.other.rows[i]])\n\t\t\ttest.equal(results, true, `Should render all ${header} data in ${tableLabel}`)\n\t\t}\n\n\t\tconst elem = regDom.inputs.node()\n\t\tconst violinDiv = await detectOne({ selector: '.sjpp-vp-violinDiv', elem })\n\t\ttest.ok(violinDiv, `Should render violin plot for outcome variable`)\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Linear: continuous outcome = \"agedx\", continuous independent = \"aaclassic_5\"', test => {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'linear',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [{ id: 'aaclassic_5', q: { mode: 'continuous' } }]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\t//**** Inputs ****\n\t\tconst violinDivs = await detectGte({ selector: '.sjpp-vp-violinDiv', elem: regDom.inputs.node(), count: 2 })\n\t\ttest.equal(violinDivs.length, 2, `Should render violin plots for outcome and independent variables`)\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\t\ttest.equal(\n\t\t\ttable[2].childNodes[1].innerText,\n\t\t\t'(continuous)',\n\t\t\t`Should correctly identify independent term as 'continuous' in ${tableLabel}`\n\t\t)\n\n\t\tconst values2check = Array.from(table[2].childNodes).slice(3)\n\t\tresults = checkOnlyRowValues(\n\t\t\tvalues2check,\n\t\t\tgetCoefData(data.coefficients.terms[tid2$id('aaclassic_5', regression)].fields)\n\t\t)\n\t\ttest.equal(results, true, `Should render all continous 'aaclassic_5' data in ${tableLabel}`)\n\n\t\t//Type III Stats\n\t\ttableLabel = 'type3 table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Type III statistics\"] table tr').nodes()\n\t\tconst values2check2 = Array.from(table[2].childNodes).slice(1)\n\t\tresults = checkOnlyRowValues(values2check2, data.type3.terms[tid2$id('aaclassic_5', regression)])\n\t\ttest.equal(results, true, `Should render all continous 'aaclassic_5' data in ${tableLabel}`)\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Linear: continuous outcome = \"agedx\", discrete independent = \"aaclassic_5\"', test => {\n\ttest.timeoutAfter(5000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'linear',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [{ id: 'aaclassic_5', q: { mode: 'discrete' } }]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\n\t\tconst $id = tid2$id('aaclassic_5', regression)\n\n\t\tfor (const [i, tr] of table.entries()) {\n\t\t\t//Test all bin values for independent term\n\t\t\tif (i < 2 || i == table.length - 1) continue //Skip header, intercept, and bottom scale rows\n\t\t\tif (i == 2) {\n\t\t\t\t//Skip the beginning cell spanning the remaining rows\n\t\t\t\tconst checkValues = getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[1].innerText])\n\t\t\t\tresults = checkOnlyRowValues(Array.from(tr.childNodes).slice(1), checkValues)\n\t\t\t\ttest.equal(results, true, `Should render all ${tr.childNodes[1].innerText} bin data in ${tableLabel}`)\n\t\t\t} else {\n\t\t\t\tconst checkValues = getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[0].innerText])\n\t\t\t\tresults = checkOnlyRowValues(Array.from(tr.childNodes), checkValues)\n\t\t\t\ttest.equal(results, true, `Should render all ${tr.childNodes[0].innerText} bin data in ${tableLabel}`)\n\t\t\t}\n\t\t}\n\n\t\t//TODO: necessary to check all other values?\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Linear: continuous outcome = \"agedx\", cubic spline independent = \"aaclassic_5\"', test => {\n\ttest.timeoutAfter(9000) // increased to 9 seconds to avoid timeout\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'linear',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'agedx',\n\t\t\t\t\t\tisAtomic: true\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [\n\t\t\t\t\t\t{ id: 'aaclassic_5', q: { mode: 'spline', knots: [{ value: 2000 }, { value: 12000 }, { value: 24000 }] } }\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\t\tconst numOfKnots = regression.Inner.state.config.independent[0].q.knots.length\n\n\t\tconst $id = tid2$id('aaclassic_5', regression)\n\n\t\t//**** Inputs ****\n\t\t// await detectGte({elem: regDom.inputs.node(), selector: '.sjpp-vp-violinDiv', count: 3})\n\t\tconst knotLines = regDom.inputs.selectAll('.sjpp-vp-violinDiv .sjpp-vp-line').nodes()\n\t\ttest.equal(knotLines.length, numOfKnots, `Should render 3 lines over the independent variable violin plot`)\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results\n\n\t\tconst splinePlot = regDom.results.select('div[name^=\"Cubic spline plots\"] img').node()\n\t\ttest.ok(splinePlot, `Should render a cubic spline plot`)\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\n\t\ttest.equal(\n\t\t\tObject.keys(data.coefficients.terms[$id].categories).length,\n\t\t\tnumOfKnots - 1,\n\t\t\t`Should pass data for ${numOfKnots - 1} spline functions`\n\t\t)\n\n\t\tfor (const [i, tr] of table.entries()) {\n\t\t\t//Test all splice values for cubic spline term\n\t\t\tif (i < 2 || i == table.length - 1) continue\n\t\t\tif (i == 2) {\n\t\t\t\t//Skip the beginning cell spanning the remain rows\n\t\t\t\tresults = checkOnlyRowValues(\n\t\t\t\t\tArray.from(tr.childNodes).slice(1),\n\t\t\t\t\tgetCoefData(data.coefficients.terms[$id].categories[tr.childNodes[1].innerText])\n\t\t\t\t)\n\t\t\t\ttest.equal(results, true, `Should render all ${tr.childNodes[1].innerText} data in ${tableLabel}`)\n\t\t\t} else {\n\t\t\t\tresults = checkOnlyRowValues(\n\t\t\t\t\tArray.from(tr.childNodes),\n\t\t\t\t\tgetCoefData(data.coefficients.terms[$id].categories[tr.childNodes[0].innerText])\n\t\t\t\t)\n\t\t\t\ttest.equal(results, true, `Should render all ${tr.childNodes[0].innerText} data in ${tableLabel}`)\n\t\t\t}\n\t\t}\n\n\t\t//TODO: necessary to check all other values?\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Linear: continuous outcome = \"agedx\", independents = \"sex\" * \"aaclassic_5\"', test => {\n\ttest.timeoutAfter(5000)\n\ttest.plan(2)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'linear',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [\n\t\t\t\t\t\t{ id: 'sex', interactions: ['aaclassic_5'] },\n\t\t\t\t\t\t{ id: 'aaclassic_5', q: { mode: 'continuous' }, interactions: ['sex'] }\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\n\t\tconst interactionRow = table[4]\n\t\ttest.equal(\n\t\t\tinteractionRow.childNodes[0].innerText,\n\t\t\t'Sex :\\nCumulative Alkylating Agents (Cyclo ...',\n\t\t\t'Should render interaction term name'\n\t\t)\n\n\t\tconst values2check = Array.from(interactionRow.childNodes).slice(3)\n\t\tconst sex$id = tid2$id('sex', regression)\n\t\tconst aaclassic_5$id = tid2$id('aaclassic_5', regression)\n\t\tconst interaction = data.coefficients.interactions.find(\n\t\t\tinteraction => interaction.term1 == sex$id && interaction.term2 == aaclassic_5$id\n\t\t)\n\t\tif (!interaction) throw 'interaction not found'\n\t\tinteraction.categories[0].lst\n\t\tresults = checkOnlyRowValues(values2check, getCoefData(interaction.categories[0].lst))\n\t\ttest.equal(results, true, `Should render all interaction data in ${tableLabel}`)\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Linear: continuous outcome = \"agedx\", geneVariant independent = \"TP53\"', test => {\n\ttest.timeoutAfter(5000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'linear',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [{ term: { type: 'geneVariant', gene: 'TP53' }, q: { type: 'predefined-groupset' } }]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\n\t\tconst $id = tid2$id('TP53', regression)\n\n\t\tfor (const [i, tr] of table.entries()) {\n\t\t\t//Test all bin values for independent term\n\t\t\tif (i < 2 || i == table.length - 1) continue //Skip header, intercept, and bottom scale rows\n\t\t\tif (i == 2) {\n\t\t\t\t//Skip the beginning cell spanning the remaining rows\n\t\t\t\tconst checkValues = getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[1].innerText])\n\t\t\t\tresults = checkOnlyRowValues(Array.from(tr.childNodes).slice(1), checkValues)\n\t\t\t\ttest.equal(results, true, `Should render all ${tr.childNodes[1].innerText} data in ${tableLabel}`)\n\t\t\t} else {\n\t\t\t\tconst checkValues = getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[0].innerText])\n\t\t\t\tresults = checkOnlyRowValues(Array.from(tr.childNodes), checkValues)\n\t\t\t\ttest.equal(results, true, `Should render all ${tr.childNodes[0].innerText} data in ${tableLabel}`)\n\t\t\t}\n\t\t}\n\n\t\t//TODO: necessary to check all other values?\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Logistic: continuous outcome = \"hrtavg\", continuous independent = \"agedx\"', test => {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'logistic',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'hrtavg',\n\t\t\t\t\t\tisAtomic: true\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [{ id: 'agedx' }]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results, testTerm\n\n\t\t//Sample size\n\t\tconst sampleSizeDiv = regDom.results\n\t\t\t.selectAll('div[name^=\"Sample size\"] span')\n\t\t\t.nodes()\n\t\t\t.filter(d => d.innerText == data.sampleSize)\n\t\ttest.ok(\n\t\t\tregDom.results.node().querySelector('div[name^=\"Sample size\"]') && sampleSizeDiv,\n\t\t\t`Should render \"Sample size: ${data.sampleSize}\"`\n\t\t)\n\n\t\t//Residual table\n\t\ttableLabel = 'Deviance residuals table'\n\t\ttable = regDom.results.selectAll('table[name^=\"sjpp-residuals-table\"] tr').nodes()\n\t\tresults = checkTableRow(table, 1, data.residuals.rows)\n\t\ttest.equal(results, true, `Should render all residuals data in ${tableLabel}`)\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\t\tconst coefHeader = structuredClone(data.coefficients.header)\n\t\tcoefHeader.splice(3, 2, '95% CI')\n\t\tcoefHeader[2] = coefHeader[2] + String.fromCharCode(160) + '\u24D8'\n\t\tresults = checkTableRow(table, 0, coefHeader)\n\t\ttest.equal(results, true, `Should render all coefficient headers in ${tableLabel}`)\n\t\tconst logHeaders = coefHeader.filter(d => d === 'Odds ratio' + String.fromCharCode(160) + '\u24D8')\n\t\ttest.equal(logHeaders.length, 1, `Should render headers specific to logistic regression`)\n\n\t\tconst coefIntercept = [data.coefficients.intercept[0], data.coefficients.intercept[1]]\n\t\tcoefIntercept.push(...getCoefData(data.coefficients.intercept.slice(2)))\n\t\tresults = checkTableRow(table, 1, coefIntercept)\n\t\ttest.equal(results, true, `Should render all intercept data in ${tableLabel}`)\n\n\t\ttestTerm = 'Age (years) at Cancer Diagnosis'\n\t\tconst checkValues1 = [testTerm, '(continuous)']\n\t\tcheckValues1.push(...getCoefData(data.coefficients.terms[tid2$id('agedx', regression)].fields))\n\t\tresults = checkTableRow(table, 2, checkValues1)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Type III Stats\n\t\ttableLabel = 'type3 table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Type III statistics\"] table tr').nodes()\n\t\tresults = checkTableRow(table, 0, data.type3.header)\n\t\ttest.equal(results, true, `Should render all header data in ${tableLabel}`)\n\n\t\tresults = checkTableRow(table, 1, data.type3.intercept)\n\t\ttest.equal(results, true, `Should render all intercept data in ${tableLabel}`)\n\n\t\tconst checkValues2 = [testTerm]\n\t\tdata.type3.terms[tid2$id('agedx', regression)].forEach(d => checkValues2.push(d))\n\t\tresults = checkTableRow(table, 2, checkValues2)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Other stats\n\t\ttableLabel = 'other summary statistics table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Other summary statistics\"] table tr').nodes()\n\t\tfor (const [i, header] of data.other.header.entries()) {\n\t\t\tresults = checkTableRow(table, i, [header, data.other.rows[i]])\n\t\t\ttest.equal(results, true, `Should render all ${header} data in ${tableLabel}`)\n\t\t}\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Logistic: categorical outcome = \"diaggrp\", continuous independent = \"agedx\"', test => {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'logistic',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'diaggrp',\n\t\t\t\t\t\tisAtomic: true\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [{ id: 'agedx' }]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results, testTerm\n\n\t\t//Sample size\n\t\tconst sampleSizeDiv = regDom.results\n\t\t\t.selectAll('div[name^=\"Sample size\"] span')\n\t\t\t.nodes()\n\t\t\t.filter(d => d.innerText == data.sampleSize)\n\t\ttest.ok(\n\t\t\tregDom.results.node().querySelector('div[name^=\"Sample size\"]') && sampleSizeDiv,\n\t\t\t`Should render \"Sample size: ${data.sampleSize}\"`\n\t\t)\n\n\t\t//Residual table\n\t\ttableLabel = 'Deviance residuals table'\n\t\ttable = regDom.results.selectAll('table[name^=\"sjpp-residuals-table\"] tr').nodes()\n\t\tresults = checkTableRow(table, 1, data.residuals.rows)\n\t\ttest.equal(results, true, `Should render all residuals data in ${tableLabel}`)\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\t\tconst coefHeader = structuredClone(data.coefficients.header)\n\t\tcoefHeader.splice(3, 2, '95% CI')\n\t\tcoefHeader[2] = coefHeader[2] + String.fromCharCode(160) + '\u24D8'\n\t\tresults = checkTableRow(table, 0, coefHeader)\n\t\ttest.equal(results, true, `Should render all coefficient headers in ${tableLabel}`)\n\t\tconst logHeaders = coefHeader.filter(d => d === 'Odds ratio' + String.fromCharCode(160) + '\u24D8')\n\t\ttest.equal(logHeaders.length, 1, `Should render headers specific to logistic regression`)\n\n\t\tconst coefIntercept = [data.coefficients.intercept[0], data.coefficients.intercept[1]]\n\t\tcoefIntercept.push(...getCoefData(data.coefficients.intercept.slice(2)))\n\t\tresults = checkTableRow(table, 1, coefIntercept)\n\t\ttest.equal(results, true, `Should render all intercept data in ${tableLabel}`)\n\n\t\ttestTerm = 'Age (years) at Cancer Diagnosis'\n\t\tconst checkValues1 = [testTerm, '(continuous)']\n\t\tcheckValues1.push(...getCoefData(data.coefficients.terms[tid2$id('agedx', regression)].fields))\n\t\tresults = checkTableRow(table, 2, checkValues1)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Type III Stats\n\t\ttableLabel = 'type3 table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Type III statistics\"] table tr').nodes()\n\t\tresults = checkTableRow(table, 0, data.type3.header)\n\t\ttest.equal(results, true, `Should render all header data in ${tableLabel}`)\n\n\t\tresults = checkTableRow(table, 1, data.type3.intercept)\n\t\ttest.equal(results, true, `Should render all intercept data in ${tableLabel}`)\n\n\t\tconst checkValues2 = [testTerm]\n\t\tdata.type3.terms[tid2$id('agedx', regression)].forEach(d => checkValues2.push(d))\n\t\tresults = checkTableRow(table, 2, checkValues2)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Other stats\n\t\ttableLabel = 'other summary statistics table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Other summary statistics\"] table tr').nodes()\n\t\tfor (const [i, header] of data.other.header.entries()) {\n\t\t\tresults = checkTableRow(table, i, [header, data.other.rows[i]])\n\t\t\ttest.equal(results, true, `Should render all ${header} data in ${tableLabel}`)\n\t\t}\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Cox: graded outcome = \"Arrhythmias\", continuous independent = \"agedx\"', test => {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'cox',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'Arrhythmias'\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [{ id: 'agedx' }]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\t//#of events instead of residuals table, no intercept in coefficent, stats test table\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results, testTerm\n\n\t\t//Sample size\n\t\tconst sampleSizeDiv = regDom.results\n\t\t\t.selectAll('div[name^=\"Sample size\"] span')\n\t\t\t.nodes()\n\t\t\t.filter(d => d.innerText == data.sampleSize)\n\t\ttest.ok(\n\t\t\tregDom.results.node().querySelector('div[name^=\"Sample size\"]') && sampleSizeDiv,\n\t\t\t`Should render \"Sample size: ${data.sampleSize}\"`\n\t\t)\n\n\t\t//Number of events\n\t\tconst numOfEventsDiv = regDom.results\n\t\t\t.selectAll('div[name^=\"Number of events\"] span')\n\t\t\t.nodes()\n\t\t\t.filter(d => d.innerText == data.eventCnt)\n\t\ttest.ok(\n\t\t\tregDom.results.node().querySelector('div[name^=\"Number of events\"]') && numOfEventsDiv,\n\t\t\t`Should render \"Number of events: ${data.eventCnt}\"`\n\t\t)\n\n\t\ttest.ok(\n\t\t\t!regDom.results.select('table[name^=\"sjpp-residuals-table\"]').node(),\n\t\t\t`Should not render residuals table in cox regression`\n\t\t)\n\n\t\tconst $id = tid2$id('agedx', regression)\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\t\tconst coefHeader = structuredClone(data.coefficients.header)\n\t\tcoefHeader.splice(2, 2)\n\t\tcoefHeader.splice(3, 2, '95% CI')\n\t\tcoefHeader[2] = coefHeader[2] + String.fromCharCode(160) + '\u24D8'\n\t\tresults = checkTableRow(table, 0, coefHeader)\n\t\ttest.equal(results, true, `Should render all coefficient headers in ${tableLabel}`)\n\t\tconst coxHeaders = coefHeader.filter(d => d === 'HR' + String.fromCharCode(160) + '\u24D8')\n\t\ttest.equal(coxHeaders.length, 1, `Should render headers specific to cox regression in ${tableLabel}`)\n\n\t\ttestTerm = 'Age (years) at Cancer Diagnosis'\n\t\tconst checkValues1 = [testTerm, '(continuous)']\n\t\tdata.coefficients.terms[$id].fields.splice(0, 2)\n\t\tcheckValues1.push(...getCoefData(data.coefficients.terms[$id].fields))\n\t\tresults = checkTableRow(table, 1, checkValues1)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Type III Stats\n\t\ttableLabel = 'type3 table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Type III statistics\"] table tr').nodes()\n\t\tresults = checkTableRow(table, 0, data.type3.header)\n\t\ttest.equal(results, true, `Should render all header data in ${tableLabel}`)\n\n\t\tconst checkValues2 = [testTerm]\n\t\tdata.type3.terms[$id].forEach(d => checkValues2.push(d))\n\t\tresults = checkTableRow(table, 1, checkValues2)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Statistical tests\n\t\ttableLabel = 'Statistical tests table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Statistical tests\"] table tr').nodes()\n\t\tresults = checkTableRow(table, 0, data.tests.header)\n\t\ttest.equal(results, true, `Should render all header data in ${tableLabel}`)\n\t\tfor (const [i, row] of data.tests.rows.entries()) {\n\t\t\tresults = checkTableRow(table, i + 1, row)\n\t\t\ttest.equal(results, true, `Should render all ${row} data in ${tableLabel}`)\n\t\t}\n\n\t\t//Other stats\n\t\ttableLabel = 'other summary statistics table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Other summary statistics\"] table tr').nodes()\n\t\tfor (const [i, header] of data.other.header.entries()) {\n\t\t\tresults = checkTableRow(table, i, [header, data.other.rows[i]])\n\t\t\ttest.equal(results, true, `Should render all ${header} data in ${tableLabel}`)\n\t\t}\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Cox: survival outcome, continuous independent = \"agedx\"', test => {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'regression',\n\t\t\t\t\tregressionType: 'cox',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'os'\n\t\t\t\t\t},\n\t\t\t\t\tindependent: [{ id: 'agedx' }]\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(regression) {\n\t\tconst data = await getData(regression)\n\t\tconst regDom = regression.Inner.dom\n\n\t\tconst $id = tid2$id('agedx', regression)\n\n\t\t//#of events instead of residuals table, no intercept in coefficent, stats test table\n\n\t\t//**** Results ****\n\t\tlet tableLabel, table, results, testTerm\n\n\t\t//Sample size\n\t\tconst sampleSizeDiv = regDom.results\n\t\t\t.selectAll('div[name^=\"Sample size\"] span')\n\t\t\t.nodes()\n\t\t\t.filter(d => d.innerText == data.sampleSize)\n\t\ttest.ok(\n\t\t\tregDom.results.node().querySelector('div[name^=\"Sample size\"]') && sampleSizeDiv,\n\t\t\t`Should render \"Sample size: ${data.sampleSize}\"`\n\t\t)\n\n\t\t//Number of events\n\t\tconst numOfEventsDiv = regDom.results\n\t\t\t.selectAll('div[name^=\"Number of events\"] span')\n\t\t\t.nodes()\n\t\t\t.filter(d => d.innerText == data.eventCnt)\n\t\ttest.ok(\n\t\t\tregDom.results.node().querySelector('div[name^=\"Number of events\"]') && numOfEventsDiv,\n\t\t\t`Should render \"Number of events: ${data.eventCnt}\"`\n\t\t)\n\n\t\ttest.ok(\n\t\t\t!regDom.results.select('table[name^=\"sjpp-residuals-table\"]').node(),\n\t\t\t`Should not render residuals table in cox regression`\n\t\t)\n\n\t\t//Coefficients table\n\t\ttableLabel = 'coefficients table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Coefficients\"] table tr').nodes()\n\t\tconst coefHeader = structuredClone(data.coefficients.header)\n\t\tcoefHeader.splice(2, 2)\n\t\tcoefHeader.splice(3, 2, '95% CI')\n\t\tcoefHeader[2] = coefHeader[2] + String.fromCharCode(160) + '\u24D8'\n\t\tresults = checkTableRow(table, 0, coefHeader)\n\t\ttest.equal(results, true, `Should render all coefficient headers in ${tableLabel}`)\n\t\tconst coxHeaders = coefHeader.filter(d => d === 'HR' + String.fromCharCode(160) + '\u24D8')\n\t\ttest.equal(coxHeaders.length, 1, `Should render headers specific to cox regression in ${tableLabel}`)\n\n\t\ttestTerm = 'Age (years) at Cancer Diagnosis'\n\t\tconst checkValues1 = [testTerm, '(continuous)']\n\t\tdata.coefficients.terms[$id].fields.splice(0, 2)\n\t\tcheckValues1.push(...getCoefData(data.coefficients.terms[$id].fields))\n\t\tresults = checkTableRow(table, 1, checkValues1)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Type III Stats\n\t\ttableLabel = 'type3 table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Type III statistics\"] table tr').nodes()\n\t\tresults = checkTableRow(table, 0, data.type3.header)\n\t\ttest.equal(results, true, `Should render all header data in ${tableLabel}`)\n\n\t\tconst checkValues2 = [testTerm]\n\t\tdata.type3.terms[$id].forEach(d => checkValues2.push(d))\n\t\tresults = checkTableRow(table, 1, checkValues2)\n\t\ttest.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`)\n\n\t\t//Statistical tests\n\t\ttableLabel = 'Statistical tests table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Statistical tests\"] table tr').nodes()\n\t\tresults = checkTableRow(table, 0, data.tests.header)\n\t\ttest.equal(results, true, `Should render all header data in ${tableLabel}`)\n\t\tfor (const [i, row] of data.tests.rows.entries()) {\n\t\t\tresults = checkTableRow(table, i + 1, row)\n\t\t\ttest.equal(results, true, `Should render all ${row} data in ${tableLabel}`)\n\t\t}\n\n\t\t//Other stats\n\t\ttableLabel = 'other summary statistics table'\n\t\ttable = regDom.results.selectAll('div[name^=\"Other summary statistics\"] table tr').nodes()\n\t\tfor (const [i, header] of data.other.header.entries()) {\n\t\t\tresults = checkTableRow(table, i, [header, data.other.rows[i]])\n\t\t\ttest.equal(results, true, `Should render all ${header} data in ${tableLabel}`)\n\t\t}\n\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\n/*************************\n reusable helper functions\n**************************/\n\nconst runpp = helpers.getRunPp('mass', {\n\tstate: {\n\t\tnav: {\n\t\t\theader_mode: 'hide_search',\n\t\t\tactiveTab: 1\n\t\t},\n\t\tvocab: {\n\t\t\tdslabel: 'TermdbTest',\n\t\t\tgenome: 'hg38-test'\n\t\t}\n\t},\n\tdebug: 1\n})\n\nasync function getData(regression) {\n\tconst data = await regression.Inner.app.Inner.api.vocabApi.getRegressionData(getDataRequestOpts(regression))\n\n\tfunction getDataRequestOpts(regression) {\n\t\tconst c = regression.Inner.config\n\t\tconst opts = {\n\t\t\tregressionType: c.regressionType,\n\t\t\toutcome: c.outcome,\n\t\t\tindependent: c.independent\n\t\t}\n\t\topts.filter = regression.Inner.inputs.parent.filter\n\n\t\treturn opts\n\t}\n\n\treturn data.resultLst[0].data\n}\n\nfunction checkTableRow(table, idx, dataArray) {\n\tconst checkArray = []\n\tlet issuesFound = 0\n\ttable[idx].childNodes.forEach(t => {\n\t\tcheckArray.push(t.innerText)\n\t})\n\tdataArray.forEach(d => {\n\t\tif (!checkArray.some(t => t == d)) {\n\t\t\t++issuesFound\n\t\t}\n\t})\n\tif (issuesFound === 0) return true\n\telse return false\n}\n\nfunction checkOnlyRowValues(valueNodes, dataArray) {\n\tconst checkArray = []\n\tlet issuesFound = 0\n\tvalueNodes.forEach(t => {\n\t\tcheckArray.push(t.innerText)\n\t})\n\tdataArray.forEach(d => {\n\t\tif (!checkArray.some(t => t == d)) {\n\t\t\t++issuesFound\n\t\t}\n\t})\n\tif (issuesFound === 0) return true\n\telse return false\n}\n\nfunction getCoefData(in_data) {\n\tconst out_data = structuredClone(in_data)\n\t// combine 95% CI columns\n\tout_data.splice(1, 2, `${out_data[1]} \u2013 ${out_data[2]}`)\n\treturn out_data\n}\n\nfunction tid2$id(tid, regression) {\n\tconst t = regression.Inner.inputs.independent.inputLst.find(i => {\n\t\tconst id = i.term.id || i.term.term.id || i.term.term.name\n\t\treturn id == tid\n\t})\n\tif (t) return t.term.$id\n\tthrow 'unknown ' + tid\n}\n"],
+  "mappings": 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+  "names": ["tape", "interaction", "regression"]
+}

package/dist/regression.results-3YNM6LLQ.js

@@ -0,0 +1,38 @@
+import {
+  RegressionResults,
+  showLDlegend
+} from "./chunk-X6URQAFD.js";
+import "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  RegressionResults,
+  showLDlegend
+};
+//# sourceMappingURL=regression.results-3YNM6LLQ.js.map