@sjcrh/proteinpaint-client 2.201.0 → 2.202.0

package/dist/regression.integration.spec-BKM5UI7H.js

@@ -0,0 +1,838 @@
+import {
+  detectGte,
+  detectOne
+} from "./chunk-Z2TA7NML.js";
+import {
+  getRunPp
+} from "./chunk-VJCJCDFI.js";
+import {
+  require_tape
+} from "./chunk-TUMA63WX.js";
+import "./chunk-57GCW5SF.js";
+import "./chunk-WGRJEQT7.js";
+import "./chunk-KSA3ND7Z.js";
+import "./chunk-FESRWKYY.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-Y45RZL4F.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-E2JRANYL.js";
+import "./chunk-E2GHT7RH.js";
+import "./chunk-HOCICSX4.js";
+import "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// plots/test/regression.integration.spec.js
+var import_tape = __toESM(require_tape(), 1);
+(0, import_tape.default)("\n", (test) => {
+  test.comment("-***- plots/regression -***-");
+  test.end();
+});
+(0, import_tape.default)('Linear: continuous outcome = "agedx", cat. independents = "sex" + "genetic_race"', (test) => {
+  test.timeoutAfter(5e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "linear",
+          outcome: {
+            id: "agedx"
+          },
+          independent: [{ id: "sex" }, { id: "genetic_race" }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    test.equal(
+      regDom.inputs.selectAll("table").nodes().filter((t) => t.childNodes.length > 1).length,
+      2,
+      `Should render two tables for independent variables`
+    );
+    let table, tableLabel, results, testTerm;
+    const sampleSizeDiv = regDom.results.selectAll('div[name^="Sample size"] span').nodes().filter((d) => d.innerText == data.sampleSize);
+    test.ok(
+      regDom.results.node().querySelector('div[name^="Sample size"]') && sampleSizeDiv,
+      `Should render "Sample size: ${data.sampleSize}"`
+    );
+    tableLabel = "residuals table";
+    table = regDom.results.selectAll('table[name^="sjpp-residuals-table"] tr').nodes();
+    results = checkTableRow(table, 1, data.residuals.rows);
+    test.equal(results, true, `Should render all residuals data in ${tableLabel}`);
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    const coefHeader = structuredClone(data.coefficients.header);
+    coefHeader.splice(3, 2, "95% CI");
+    coefHeader[2] = coefHeader[2] + String.fromCharCode(160) + "\u24D8";
+    results = checkTableRow(table, 0, coefHeader);
+    test.equal(results, true, `Should render all coefficient headers in ${tableLabel}`);
+    const linearHeaders = coefHeader.filter((d) => d === "Beta" + String.fromCharCode(160) + "\u24D8");
+    test.equal(linearHeaders.length, 1, `Should render headers specific to linear regression`);
+    const coefIntercept = [data.coefficients.intercept[0], data.coefficients.intercept[1]];
+    coefIntercept.push(...getCoefData(data.coefficients.intercept.slice(2)));
+    results = checkTableRow(table, 1, coefIntercept);
+    test.equal(results, true, `Should render all intercept data in ${tableLabel}`);
+    testTerm = "Sex";
+    const checkValues1 = ["Sex\nREF\nFemale", "Male"];
+    checkValues1.push(...getCoefData(data.coefficients.terms[tid2$id("sex", regression)].categories[1]));
+    results = checkTableRow(table, 2, checkValues1);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    testTerm = "African Ancestry";
+    const checkValues2 = ["Genetically defined race\nREF\nEuropean Ancestry", testTerm];
+    checkValues2.push(...getCoefData(data.coefficients.terms[tid2$id("genetic_race", regression)].categories[testTerm]));
+    results = checkTableRow(table, 3, checkValues2);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    testTerm = "Asian Ancestry";
+    const checkValues3 = [testTerm];
+    checkValues3.push(...getCoefData(data.coefficients.terms[tid2$id("genetic_race", regression)].categories[testTerm]));
+    results = checkTableRow(table, 4, checkValues3);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "type3 table";
+    table = regDom.results.selectAll('div[name^="Type III statistics"] table tr').nodes();
+    results = checkTableRow(table, 0, data.type3.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    results = checkTableRow(table, 1, data.type3.intercept);
+    test.equal(results, true, `Should render all intercept data in ${tableLabel}`);
+    testTerm = "Sex";
+    const checkValues4 = [testTerm];
+    data.type3.terms[tid2$id("sex", regression)].forEach((d) => checkValues4.push(d));
+    results = checkTableRow(table, 2, checkValues4);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    testTerm = "Genetically defined race";
+    const checkValues5 = [testTerm];
+    data.type3.terms[tid2$id("genetic_race", regression)].forEach((d) => checkValues5.push(d));
+    results = checkTableRow(table, 3, checkValues5);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "other summary statistics table";
+    table = regDom.results.selectAll('div[name^="Other summary statistics"] table tr').nodes();
+    for (const [i, header] of data.other.header.entries()) {
+      results = checkTableRow(table, i, [header, data.other.rows[i]]);
+      test.equal(results, true, `Should render all ${header} data in ${tableLabel}`);
+    }
+    const elem = regDom.inputs.node();
+    const violinDiv = await detectOne({ selector: ".sjpp-vp-violinDiv", elem });
+    test.ok(violinDiv, `Should render violin plot for outcome variable`);
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Linear: continuous outcome = "agedx", continuous independent = "aaclassic_5"', (test) => {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "linear",
+          outcome: {
+            id: "agedx"
+          },
+          independent: [{ id: "aaclassic_5", q: { mode: "continuous" } }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    const violinDivs = await detectGte({ selector: ".sjpp-vp-violinDiv", elem: regDom.inputs.node(), count: 2 });
+    test.equal(violinDivs.length, 2, `Should render violin plots for outcome and independent variables`);
+    let tableLabel, table, results;
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    test.equal(
+      table[2].childNodes[1].innerText,
+      "(continuous)",
+      `Should correctly identify independent term as 'continuous' in ${tableLabel}`
+    );
+    const values2check = Array.from(table[2].childNodes).slice(3);
+    results = checkOnlyRowValues(
+      values2check,
+      getCoefData(data.coefficients.terms[tid2$id("aaclassic_5", regression)].fields)
+    );
+    test.equal(results, true, `Should render all continous 'aaclassic_5' data in ${tableLabel}`);
+    tableLabel = "type3 table";
+    table = regDom.results.selectAll('div[name^="Type III statistics"] table tr').nodes();
+    const values2check2 = Array.from(table[2].childNodes).slice(1);
+    results = checkOnlyRowValues(values2check2, data.type3.terms[tid2$id("aaclassic_5", regression)]);
+    test.equal(results, true, `Should render all continous 'aaclassic_5' data in ${tableLabel}`);
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Linear: continuous outcome = "agedx", discrete independent = "aaclassic_5"', (test) => {
+  test.timeoutAfter(5e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "linear",
+          outcome: {
+            id: "agedx"
+          },
+          independent: [{ id: "aaclassic_5", q: { mode: "discrete" } }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    let tableLabel, table, results;
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    const $id = tid2$id("aaclassic_5", regression);
+    for (const [i, tr] of table.entries()) {
+      if (i < 2 || i == table.length - 1) continue;
+      if (i == 2) {
+        const checkValues = getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[1].innerText]);
+        results = checkOnlyRowValues(Array.from(tr.childNodes).slice(1), checkValues);
+        test.equal(results, true, `Should render all ${tr.childNodes[1].innerText} bin data in ${tableLabel}`);
+      } else {
+        const checkValues = getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[0].innerText]);
+        results = checkOnlyRowValues(Array.from(tr.childNodes), checkValues);
+        test.equal(results, true, `Should render all ${tr.childNodes[0].innerText} bin data in ${tableLabel}`);
+      }
+    }
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Linear: continuous outcome = "agedx", cubic spline independent = "aaclassic_5"', (test) => {
+  test.timeoutAfter(9e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "linear",
+          outcome: {
+            id: "agedx",
+            isAtomic: true
+          },
+          independent: [
+            { id: "aaclassic_5", q: { mode: "spline", knots: [{ value: 2e3 }, { value: 12e3 }, { value: 24e3 }] } }
+          ]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    const numOfKnots = regression.Inner.state.config.independent[0].q.knots.length;
+    const $id = tid2$id("aaclassic_5", regression);
+    const knotLines = regDom.inputs.selectAll(".sjpp-vp-violinDiv .sjpp-vp-line").nodes();
+    test.equal(knotLines.length, numOfKnots, `Should render 3 lines over the independent variable violin plot`);
+    let tableLabel, table, results;
+    const splinePlot = regDom.results.select('div[name^="Cubic spline plots"] img').node();
+    test.ok(splinePlot, `Should render a cubic spline plot`);
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    test.equal(
+      Object.keys(data.coefficients.terms[$id].categories).length,
+      numOfKnots - 1,
+      `Should pass data for ${numOfKnots - 1} spline functions`
+    );
+    for (const [i, tr] of table.entries()) {
+      if (i < 2 || i == table.length - 1) continue;
+      if (i == 2) {
+        results = checkOnlyRowValues(
+          Array.from(tr.childNodes).slice(1),
+          getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[1].innerText])
+        );
+        test.equal(results, true, `Should render all ${tr.childNodes[1].innerText} data in ${tableLabel}`);
+      } else {
+        results = checkOnlyRowValues(
+          Array.from(tr.childNodes),
+          getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[0].innerText])
+        );
+        test.equal(results, true, `Should render all ${tr.childNodes[0].innerText} data in ${tableLabel}`);
+      }
+    }
+    tableLabel = "nonlinearity table";
+    table = regDom.results.selectAll('div[name^="Nonlinearity statistics"] table tr').nodes();
+    test.ok(table.length, `Should render ${tableLabel} for a cubic spline variable`);
+    results = checkTableRow(table, 0, data.nonlinearity.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    results = checkTableRow(table, 1, data.nonlinearity.terms[$id]);
+    test.equal(results, true, `Should render all spline variable data in ${tableLabel}`);
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Linear: continuous outcome = "agedx", independents = "sex" * "aaclassic_5"', (test) => {
+  test.timeoutAfter(5e3);
+  test.plan(2);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "linear",
+          outcome: {
+            id: "agedx"
+          },
+          independent: [
+            { id: "sex", interactions: ["aaclassic_5"] },
+            { id: "aaclassic_5", q: { mode: "continuous" }, interactions: ["sex"] }
+          ]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    let tableLabel, table, results;
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    const interactionRow = table[4];
+    test.equal(
+      interactionRow.childNodes[0].innerText,
+      "Sex :\nCumulative Alkylating Agents (Cyclo ...",
+      "Should render interaction term name"
+    );
+    const values2check = Array.from(interactionRow.childNodes).slice(3);
+    const sex$id = tid2$id("sex", regression);
+    const aaclassic_5$id = tid2$id("aaclassic_5", regression);
+    const interaction = data.coefficients.interactions.find(
+      (interaction2) => interaction2.term1 == sex$id && interaction2.term2 == aaclassic_5$id
+    );
+    if (!interaction) throw "interaction not found";
+    interaction.categories[0].lst;
+    results = checkOnlyRowValues(values2check, getCoefData(interaction.categories[0].lst));
+    test.equal(results, true, `Should render all interaction data in ${tableLabel}`);
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Linear: continuous outcome = "agedx", geneVariant independent = "TP53"', (test) => {
+  test.timeoutAfter(5e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "linear",
+          outcome: {
+            id: "agedx"
+          },
+          independent: [{ term: { type: "geneVariant", gene: "TP53" }, q: { type: "predefined-groupset" } }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    let tableLabel, table, results;
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    const $id = tid2$id("TP53", regression);
+    for (const [i, tr] of table.entries()) {
+      if (i < 2 || i == table.length - 1) continue;
+      if (i == 2) {
+        const checkValues = getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[1].innerText]);
+        results = checkOnlyRowValues(Array.from(tr.childNodes).slice(1), checkValues);
+        test.equal(results, true, `Should render all ${tr.childNodes[1].innerText} data in ${tableLabel}`);
+      } else {
+        const checkValues = getCoefData(data.coefficients.terms[$id].categories[tr.childNodes[0].innerText]);
+        results = checkOnlyRowValues(Array.from(tr.childNodes), checkValues);
+        test.equal(results, true, `Should render all ${tr.childNodes[0].innerText} data in ${tableLabel}`);
+      }
+    }
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Logistic: continuous outcome = "hrtavg", continuous independent = "agedx"', (test) => {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "logistic",
+          outcome: {
+            id: "hrtavg",
+            isAtomic: true
+          },
+          independent: [{ id: "agedx", q: { mode: "continuous" } }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    let tableLabel, table, results, testTerm;
+    const sampleSizeDiv = regDom.results.selectAll('div[name^="Sample size"] span').nodes().filter((d) => d.innerText == data.sampleSize);
+    test.ok(
+      regDom.results.node().querySelector('div[name^="Sample size"]') && sampleSizeDiv,
+      `Should render "Sample size: ${data.sampleSize}"`
+    );
+    tableLabel = "Deviance residuals table";
+    table = regDom.results.selectAll('table[name^="sjpp-residuals-table"] tr').nodes();
+    results = checkTableRow(table, 1, data.residuals.rows);
+    test.equal(results, true, `Should render all residuals data in ${tableLabel}`);
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    const coefHeader = structuredClone(data.coefficients.header);
+    coefHeader.splice(3, 2, "95% CI");
+    coefHeader[2] = coefHeader[2] + String.fromCharCode(160) + "\u24D8";
+    results = checkTableRow(table, 0, coefHeader);
+    test.equal(results, true, `Should render all coefficient headers in ${tableLabel}`);
+    const logHeaders = coefHeader.filter((d) => d === "Odds ratio" + String.fromCharCode(160) + "\u24D8");
+    test.equal(logHeaders.length, 1, `Should render headers specific to logistic regression`);
+    const coefIntercept = [data.coefficients.intercept[0], data.coefficients.intercept[1]];
+    coefIntercept.push(...getCoefData(data.coefficients.intercept.slice(2)));
+    results = checkTableRow(table, 1, coefIntercept);
+    test.equal(results, true, `Should render all intercept data in ${tableLabel}`);
+    testTerm = "Age (years) at Cancer Diagnosis";
+    const checkValues1 = [testTerm, "(continuous)"];
+    checkValues1.push(...getCoefData(data.coefficients.terms[tid2$id("agedx", regression)].fields));
+    results = checkTableRow(table, 2, checkValues1);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "type3 table";
+    table = regDom.results.selectAll('div[name^="Type III statistics"] table tr').nodes();
+    results = checkTableRow(table, 0, data.type3.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    results = checkTableRow(table, 1, data.type3.intercept);
+    test.equal(results, true, `Should render all intercept data in ${tableLabel}`);
+    const checkValues2 = [testTerm];
+    data.type3.terms[tid2$id("agedx", regression)].forEach((d) => checkValues2.push(d));
+    results = checkTableRow(table, 2, checkValues2);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "other summary statistics table";
+    table = regDom.results.selectAll('div[name^="Other summary statistics"] table tr').nodes();
+    for (const [i, header] of data.other.header.entries()) {
+      results = checkTableRow(table, i, [header, data.other.rows[i]]);
+      test.equal(results, true, `Should render all ${header} data in ${tableLabel}`);
+    }
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Logistic: categorical outcome = "diaggrp", continuous independent = "agedx"', (test) => {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "logistic",
+          outcome: {
+            id: "diaggrp",
+            isAtomic: true
+          },
+          independent: [{ id: "agedx", q: { mode: "continuous" } }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    let tableLabel, table, results, testTerm;
+    const sampleSizeDiv = regDom.results.selectAll('div[name^="Sample size"] span').nodes().filter((d) => d.innerText == data.sampleSize);
+    test.ok(
+      regDom.results.node().querySelector('div[name^="Sample size"]') && sampleSizeDiv,
+      `Should render "Sample size: ${data.sampleSize}"`
+    );
+    tableLabel = "Deviance residuals table";
+    table = regDom.results.selectAll('table[name^="sjpp-residuals-table"] tr').nodes();
+    results = checkTableRow(table, 1, data.residuals.rows);
+    test.equal(results, true, `Should render all residuals data in ${tableLabel}`);
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    const coefHeader = structuredClone(data.coefficients.header);
+    coefHeader.splice(3, 2, "95% CI");
+    coefHeader[2] = coefHeader[2] + String.fromCharCode(160) + "\u24D8";
+    results = checkTableRow(table, 0, coefHeader);
+    test.equal(results, true, `Should render all coefficient headers in ${tableLabel}`);
+    const logHeaders = coefHeader.filter((d) => d === "Odds ratio" + String.fromCharCode(160) + "\u24D8");
+    test.equal(logHeaders.length, 1, `Should render headers specific to logistic regression`);
+    const coefIntercept = [data.coefficients.intercept[0], data.coefficients.intercept[1]];
+    coefIntercept.push(...getCoefData(data.coefficients.intercept.slice(2)));
+    results = checkTableRow(table, 1, coefIntercept);
+    test.equal(results, true, `Should render all intercept data in ${tableLabel}`);
+    testTerm = "Age (years) at Cancer Diagnosis";
+    const checkValues1 = [testTerm, "(continuous)"];
+    checkValues1.push(...getCoefData(data.coefficients.terms[tid2$id("agedx", regression)].fields));
+    results = checkTableRow(table, 2, checkValues1);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "type3 table";
+    table = regDom.results.selectAll('div[name^="Type III statistics"] table tr').nodes();
+    results = checkTableRow(table, 0, data.type3.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    results = checkTableRow(table, 1, data.type3.intercept);
+    test.equal(results, true, `Should render all intercept data in ${tableLabel}`);
+    const checkValues2 = [testTerm];
+    data.type3.terms[tid2$id("agedx", regression)].forEach((d) => checkValues2.push(d));
+    results = checkTableRow(table, 2, checkValues2);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "other summary statistics table";
+    table = regDom.results.selectAll('div[name^="Other summary statistics"] table tr').nodes();
+    for (const [i, header] of data.other.header.entries()) {
+      results = checkTableRow(table, i, [header, data.other.rows[i]]);
+      test.equal(results, true, `Should render all ${header} data in ${tableLabel}`);
+    }
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Cox: graded outcome = "Arrhythmias", continuous independent = "agedx"', (test) => {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "cox",
+          outcome: {
+            id: "Arrhythmias"
+          },
+          independent: [{ id: "agedx", q: { mode: "continuous" } }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    let tableLabel, table, results, testTerm;
+    const sampleSizeDiv = regDom.results.selectAll('div[name^="Sample size"] span').nodes().filter((d) => d.innerText == data.sampleSize);
+    test.ok(
+      regDom.results.node().querySelector('div[name^="Sample size"]') && sampleSizeDiv,
+      `Should render "Sample size: ${data.sampleSize}"`
+    );
+    const numOfEventsDiv = regDom.results.selectAll('div[name^="Number of events"] span').nodes().filter((d) => d.innerText == data.eventCnt);
+    test.ok(
+      regDom.results.node().querySelector('div[name^="Number of events"]') && numOfEventsDiv,
+      `Should render "Number of events: ${data.eventCnt}"`
+    );
+    test.ok(
+      !regDom.results.select('table[name^="sjpp-residuals-table"]').node(),
+      `Should not render residuals table in cox regression`
+    );
+    const $id = tid2$id("agedx", regression);
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    const coefHeader = structuredClone(data.coefficients.header);
+    coefHeader.splice(2, 2);
+    coefHeader.splice(3, 2, "95% CI");
+    coefHeader[2] = coefHeader[2] + String.fromCharCode(160) + "\u24D8";
+    results = checkTableRow(table, 0, coefHeader);
+    test.equal(results, true, `Should render all coefficient headers in ${tableLabel}`);
+    const coxHeaders = coefHeader.filter((d) => d === "HR" + String.fromCharCode(160) + "\u24D8");
+    test.equal(coxHeaders.length, 1, `Should render headers specific to cox regression in ${tableLabel}`);
+    testTerm = "Age (years) at Cancer Diagnosis";
+    const checkValues1 = [testTerm, "(continuous)"];
+    data.coefficients.terms[$id].fields.splice(0, 2);
+    checkValues1.push(...getCoefData(data.coefficients.terms[$id].fields));
+    results = checkTableRow(table, 1, checkValues1);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "type3 table";
+    table = regDom.results.selectAll('div[name^="Type III statistics"] table tr').nodes();
+    results = checkTableRow(table, 0, data.type3.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    const checkValues2 = [testTerm];
+    data.type3.terms[$id].forEach((d) => checkValues2.push(d));
+    results = checkTableRow(table, 1, checkValues2);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "Statistical tests table";
+    table = regDom.results.selectAll('div[name^="Statistical tests"] table tr').nodes();
+    results = checkTableRow(table, 0, data.tests.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    for (const [i, row] of data.tests.rows.entries()) {
+      results = checkTableRow(table, i + 1, row);
+      test.equal(results, true, `Should render all ${row} data in ${tableLabel}`);
+    }
+    tableLabel = "other summary statistics table";
+    table = regDom.results.selectAll('div[name^="Other summary statistics"] table tr').nodes();
+    for (const [i, header] of data.other.header.entries()) {
+      results = checkTableRow(table, i, [header, data.other.rows[i]]);
+      test.equal(results, true, `Should render all ${header} data in ${tableLabel}`);
+    }
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Cox: survival outcome, continuous independent = "agedx"', (test) => {
+  test.timeoutAfter(3e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "cox",
+          outcome: {
+            id: "os"
+          },
+          independent: [{ id: "agedx", q: { mode: "continuous" } }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    const $id = tid2$id("agedx", regression);
+    let tableLabel, table, results, testTerm;
+    const sampleSizeDiv = regDom.results.selectAll('div[name^="Sample size"] span').nodes().filter((d) => d.innerText == data.sampleSize);
+    test.ok(
+      regDom.results.node().querySelector('div[name^="Sample size"]') && sampleSizeDiv,
+      `Should render "Sample size: ${data.sampleSize}"`
+    );
+    const numOfEventsDiv = regDom.results.selectAll('div[name^="Number of events"] span').nodes().filter((d) => d.innerText == data.eventCnt);
+    test.ok(
+      regDom.results.node().querySelector('div[name^="Number of events"]') && numOfEventsDiv,
+      `Should render "Number of events: ${data.eventCnt}"`
+    );
+    test.ok(
+      !regDom.results.select('table[name^="sjpp-residuals-table"]').node(),
+      `Should not render residuals table in cox regression`
+    );
+    tableLabel = "coefficients table";
+    table = regDom.results.selectAll('div[name^="Coefficients"] table tr').nodes();
+    const coefHeader = structuredClone(data.coefficients.header);
+    coefHeader.splice(2, 2);
+    coefHeader.splice(3, 2, "95% CI");
+    coefHeader[2] = coefHeader[2] + String.fromCharCode(160) + "\u24D8";
+    results = checkTableRow(table, 0, coefHeader);
+    test.equal(results, true, `Should render all coefficient headers in ${tableLabel}`);
+    const coxHeaders = coefHeader.filter((d) => d === "HR" + String.fromCharCode(160) + "\u24D8");
+    test.equal(coxHeaders.length, 1, `Should render headers specific to cox regression in ${tableLabel}`);
+    testTerm = "Age (years) at Cancer Diagnosis";
+    const checkValues1 = [testTerm, "(continuous)"];
+    data.coefficients.terms[$id].fields.splice(0, 2);
+    checkValues1.push(...getCoefData(data.coefficients.terms[$id].fields));
+    results = checkTableRow(table, 1, checkValues1);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "type3 table";
+    table = regDom.results.selectAll('div[name^="Type III statistics"] table tr').nodes();
+    results = checkTableRow(table, 0, data.type3.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    const checkValues2 = [testTerm];
+    data.type3.terms[$id].forEach((d) => checkValues2.push(d));
+    results = checkTableRow(table, 1, checkValues2);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "Statistical tests table";
+    table = regDom.results.selectAll('div[name^="Statistical tests"] table tr').nodes();
+    results = checkTableRow(table, 0, data.tests.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    for (const [i, row] of data.tests.rows.entries()) {
+      results = checkTableRow(table, i + 1, row);
+      test.equal(results, true, `Should render all ${row} data in ${tableLabel}`);
+    }
+    tableLabel = "other summary statistics table";
+    table = regDom.results.selectAll('div[name^="Other summary statistics"] table tr').nodes();
+    for (const [i, header] of data.other.header.entries()) {
+      results = checkTableRow(table, i, [header, data.other.rows[i]]);
+      test.equal(results, true, `Should render all ${header} data in ${tableLabel}`);
+    }
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)('Cox: survival outcome, cubic spline independent = "agedx"', (test) => {
+  test.timeoutAfter(9e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "regression",
+          regressionType: "cox",
+          outcome: {
+            id: "os"
+          },
+          independent: [{ id: "agedx", q: { mode: "spline", knots: [{ value: 3 }, { value: 8 }, { value: 13 }] } }]
+        }
+      ]
+    },
+    regression: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(regression) {
+    const data = await getData(regression);
+    const regDom = regression.Inner.dom;
+    const $id = tid2$id("agedx", regression);
+    const testTerm = "Age (years) at Cancer Diagnosis";
+    let tableLabel, table, results;
+    tableLabel = "nonlinearity table";
+    table = regDom.results.selectAll('div[name^="Nonlinearity statistics"] table tr').nodes();
+    test.ok(table.length, `Should render ${tableLabel} for a cubic spline variable`);
+    results = checkTableRow(table, 0, data.nonlinearity.header);
+    test.equal(results, true, `Should render all header data in ${tableLabel}`);
+    const checkValues = [testTerm];
+    data.nonlinearity.terms[$id].forEach((d) => checkValues.push(d));
+    results = checkTableRow(table, 1, checkValues);
+    test.equal(results, true, `Should render all ${testTerm} data in ${tableLabel}`);
+    tableLabel = "other summary statistics table";
+    table = regDom.results.selectAll('div[name^="Other summary statistics"] table tr').nodes();
+    test.ok(data.other.header.includes("AIC"), `Should report AIC in ${tableLabel}`);
+    for (const [i, header] of data.other.header.entries()) {
+      results = checkTableRow(table, i, [header, data.other.rows[i]]);
+      test.equal(results, true, `Should render all ${header} data in ${tableLabel}`);
+    }
+    if (test._ok) regression.Inner.app.destroy();
+    test.end();
+  }
+});
+var runpp = getRunPp("mass", {
+  state: {
+    nav: {
+      header_mode: "hide_search",
+      activeTab: 1
+    },
+    vocab: {
+      dslabel: "TermdbTest",
+      genome: "hg38-test"
+    }
+  },
+  debug: 1
+});
+async function getData(regression) {
+  const data = await regression.Inner.app.Inner.api.vocabApi.getRegressionData(getDataRequestOpts(regression));
+  function getDataRequestOpts(regression2) {
+    const c = regression2.Inner.config;
+    const opts = {
+      regressionType: c.regressionType,
+      outcome: c.outcome,
+      independent: c.independent
+    };
+    opts.filter = regression2.Inner.inputs.parent.filter;
+    return opts;
+  }
+  return data.resultLst[0].data;
+}
+function checkTableRow(table, idx, dataArray) {
+  const checkArray = [];
+  let issuesFound = 0;
+  table[idx].childNodes.forEach((t) => {
+    checkArray.push(t.innerText);
+  });
+  dataArray.forEach((d) => {
+    if (!checkArray.some((t) => t == d)) {
+      ++issuesFound;
+    }
+  });
+  if (issuesFound === 0) return true;
+  else return false;
+}
+function checkOnlyRowValues(valueNodes, dataArray) {
+  const checkArray = [];
+  let issuesFound = 0;
+  valueNodes.forEach((t) => {
+    checkArray.push(t.innerText);
+  });
+  dataArray.forEach((d) => {
+    if (!checkArray.some((t) => t == d)) {
+      ++issuesFound;
+    }
+  });
+  if (issuesFound === 0) return true;
+  else return false;
+}
+function getCoefData(in_data) {
+  const out_data = structuredClone(in_data);
+  out_data.splice(1, 2, `${out_data[1]} \u2013 ${out_data[2]}`);
+  return out_data;
+}
+function tid2$id(tid, regression) {
+  const t = regression.Inner.inputs.independent.inputLst.find((i) => {
+    const id = i.term.id || i.term.term.id || i.term.term.name;
+    return id == tid;
+  });
+  if (t) return t.term.$id;
+  throw "unknown " + tid;
+}
+//# sourceMappingURL=regression.integration.spec-BKM5UI7H.js.map