diagcalc 3.2.0

package/lib/diagcalc-core.js

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+(function (root, factory) {
+  if (typeof module === "object" && module.exports) {
+    module.exports = factory();
+    return;
+  }
+
+  root.DiagcalcCore = factory();
+}(typeof globalThis !== "undefined" ? globalThis : this, () => {
+  function validateInputs({ tp, fp, fn, tn, preTestProb }) {
+    const inputs = [tp, fp, fn, tn];
+    if (inputs.some((value) => Number.isNaN(value) || value < 0)) {
+      return { valid: false, message: "Enter non-negative integers for all confusion matrix cells." };
+    }
+
+    if (inputs.some((value) => !Number.isInteger(value))) {
+      return { valid: false, message: "Use whole numbers for TP, FP, FN, and TN." };
+    }
+
+    if (Number.isNaN(preTestProb)) {
+      return { valid: false, message: "Enter a valid pre-test probability." };
+    }
+
+    if (preTestProb < 0 || preTestProb >= 100) {
+      return { valid: false, message: "Pre-test probability must be between 0 and 99.9%." };
+    }
+
+    if (tp + fn === 0) {
+      return { valid: false, message: "Sensitivity is indeterminate: add cases with disease (TP or FN)." };
+    }
+
+    if (tn + fp === 0) {
+      return { valid: false, message: "Specificity is indeterminate: add cases without disease (TN or FP)." };
+    }
+
+    if (tp + fp === 0) {
+      return { valid: false, message: "PPV is indeterminate: at least one positive test result is required." };
+    }
+
+    if (tn + fn === 0) {
+      return { valid: false, message: "NPV is indeterminate: at least one negative test result is required." };
+    }
+
+    return { valid: true };
+  }
+
+  function calculateMetrics({ tp, fp, fn, tn, preTestProb }) {
+    const totals = {
+      diseased: tp + fn,
+      nonDiseased: tn + fp,
+      positives: tp + fp,
+      negatives: tn + fn,
+    };
+
+    const preTest = preTestProb / 100;
+    const sensitivity = tp / totals.diseased;
+    const specificity = tn / totals.nonDiseased;
+    const ppv = tp / totals.positives;
+    const npv = tn / totals.negatives;
+    const lrPositive = calculateRatio(sensitivity, 1 - specificity);
+    const lrNegative = calculateRatio(1 - sensitivity, specificity);
+    const preTestOdds = calculateOdds(preTest);
+    const postTestOddsPositive = multiplyOdds(preTestOdds, lrPositive);
+    const postTestOddsNegative = multiplyOdds(preTestOdds, lrNegative);
+    const postTestProbPositive = probabilityFromOdds(postTestOddsPositive);
+    const postTestProbNegative = probabilityFromOdds(postTestOddsNegative);
+
+    return {
+      sensitivity: {
+        label: "Sensitivity",
+        value: sensitivity,
+        ci: calcWilsonInterval(tp, totals.diseased),
+        note: buildSensitivityNote(sensitivity),
+      },
+      specificity: {
+        label: "Specificity",
+        value: specificity,
+        ci: calcWilsonInterval(tn, totals.nonDiseased),
+        note: buildSpecificityNote(specificity),
+      },
+      ppv: {
+        label: "Positive predictive value (PPV)",
+        value: ppv,
+        ci: calcWilsonInterval(tp, totals.positives),
+        note: "Probability of disease given a positive result.",
+      },
+      npv: {
+        label: "Negative predictive value (NPV)",
+        value: npv,
+        ci: calcWilsonInterval(tn, totals.negatives),
+        note: "Probability of no disease given a negative result.",
+      },
+      lrPositive: {
+        label: "Positive likelihood ratio (LR+)",
+        value: lrPositive,
+        formatter: formatLikelihood,
+        note: interpretLRPositive(lrPositive),
+      },
+      lrNegative: {
+        label: "Negative likelihood ratio (LR-)",
+        value: lrNegative,
+        formatter: formatLikelihood,
+        note: interpretLRNegative(lrNegative),
+      },
+      preTestProbability: {
+        label: "Pre-test probability",
+        value: preTest,
+        note: "Estimated starting point before the test result.",
+      },
+      postTestPositive: {
+        label: "Post-test probability (positive result)",
+        value: postTestProbPositive,
+        note: "Updated probability of disease after a positive test.",
+      },
+      postTestNegative: {
+        label: "Post-test probability (negative result)",
+        value: postTestProbNegative,
+        note: "Updated probability of disease after a negative test.",
+      },
+    };
+  }
+
+  function calcWilsonInterval(successes, total) {
+    if (total === 0) {
+      return null;
+    }
+
+    const z = 1.96;
+    const phat = successes / total;
+    const denominator = 1 + (z ** 2) / total;
+    const center = phat + (z ** 2) / (2 * total);
+    const margin = z * Math.sqrt((phat * (1 - phat) + (z ** 2) / (4 * total)) / total);
+    const lower = Math.max(0, (center - margin) / denominator);
+    const upper = Math.min(1, (center + margin) / denominator);
+    return { lower, upper };
+  }
+
+  function calculateRatio(numerator, denominator) {
+    if (denominator === 0) {
+      return Infinity;
+    }
+    if (numerator === 0) {
+      return 0;
+    }
+    return numerator / denominator;
+  }
+
+  function calculateOdds(probability) {
+    if (probability === 1) {
+      return Infinity;
+    }
+    if (probability === 0) {
+      return 0;
+    }
+    return probability / (1 - probability);
+  }
+
+  function multiplyOdds(odds, ratio) {
+    if (odds === 0 || ratio === 0) {
+      return 0;
+    }
+    if (!Number.isFinite(odds) || !Number.isFinite(ratio)) {
+      return Infinity;
+    }
+    return odds * ratio;
+  }
+
+  function probabilityFromOdds(odds) {
+    if (odds === Infinity) {
+      return 1;
+    }
+    if (odds === 0) {
+      return 0;
+    }
+    return odds / (1 + odds);
+  }
+
+  function formatValue(value, customFormatter) {
+    if (typeof customFormatter === "function") {
+      return customFormatter(value);
+    }
+    return formatPercentage(value);
+  }
+
+  function formatPercentage(value) {
+    if (!Number.isFinite(value)) {
+      return "—";
+    }
+    return `${(value * 100).toFixed(1)}%`;
+  }
+
+  function normaliseDecimal(value) {
+    if (typeof value !== "string") {
+      return "";
+    }
+    return value.replace(",", ".").trim();
+  }
+
+  function safeParseInt(value) {
+    if (typeof value !== "string") {
+      return NaN;
+    }
+    const trimmed = value.trim();
+    if (trimmed === "") {
+      return NaN;
+    }
+    if (!/^\d+$/.test(trimmed)) {
+      return NaN;
+    }
+    return parseInt(trimmed, 10);
+  }
+
+  function formatLikelihood(value) {
+    if (!Number.isFinite(value)) {
+      return "∞";
+    }
+    if (value === 0) {
+      return "0";
+    }
+    return value >= 10 ? value.toFixed(1) : value.toFixed(2);
+  }
+
+  function clamp(value, min, max) {
+    return Math.min(Math.max(value, min), max);
+  }
+
+  function buildSensitivityNote(value) {
+    if (value >= 0.9) {
+      return "Captures most cases with disease. Useful for screening.";
+    }
+    if (value >= 0.7) {
+      return "Moderate sensitivity: consider alongside clinical context.";
+    }
+    return "Low sensitivity: consider additional tests to reduce false negatives.";
+  }
+
+  function buildSpecificityNote(value) {
+    if (value >= 0.9) {
+      return "Few false positives. Suitable for confirming diagnoses.";
+    }
+    if (value >= 0.7) {
+      return "Moderate specificity: confirm with other laboratory or clinical data.";
+    }
+    return "Low specificity: beware of false positives and their impact on treatment decisions.";
+  }
+
+  function interpretLRPositive(value) {
+    if (!Number.isFinite(value)) {
+      return "LR+ is very high: a positive result virtually confirms the disease.";
+    }
+    if (value >= 10) {
+      return "LR+ >= 10 indicates strong evidence in favour of disease.";
+    }
+    if (value >= 5) {
+      return "Moderate LR+: substantially increases the probability of disease.";
+    }
+    if (value >= 2) {
+      return "Low LR+: limited gain; combine with other data.";
+    }
+    return "LR+ close to 1: a positive result barely changes the probability of disease.";
+  }
+
+  function interpretLRNegative(value) {
+    if (!Number.isFinite(value)) {
+      return "LR- is infinite: a negative result does not reduce the probability of disease.";
+    }
+    if (value <= 0.1) {
+      return "LR- <= 0.1 indicates strong evidence against disease.";
+    }
+    if (value <= 0.2) {
+      return "Moderate LR-: reduces the probability of disease.";
+    }
+    if (value <= 0.5) {
+      return "Low LR-: limited impact; consider further evaluation.";
+    }
+    return "LR- close to 1: a negative result does not rule out disease.";
+  }
+
+  function buildProbabilityBar(value, width) {
+    const safeWidth = Number.isInteger(width) && width > 0 ? width : 20;
+    const safeValue = Number.isFinite(value) ? clamp(value, 0, 1) : 0;
+    const filled = Math.round(safeValue * safeWidth);
+    return `${"#".repeat(filled)}${"-".repeat(safeWidth - filled)}`;
+  }
+
+  return {
+    buildProbabilityBar,
+    buildSensitivityNote,
+    buildSpecificityNote,
+    calcWilsonInterval,
+    calculateMetrics,
+    calculateOdds,
+    calculateRatio,
+    clamp,
+    formatLikelihood,
+    formatPercentage,
+    formatValue,
+    interpretLRNegative,
+    interpretLRPositive,
+    multiplyOdds,
+    normaliseDecimal,
+    probabilityFromOdds,
+    safeParseInt,
+    validateInputs,
+  };
+}));

package/lib/diagcalc-datasets.js

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+(function (root, factory) {
+  if (typeof module === "object" && module.exports) {
+    module.exports = factory();
+    return;
+  }
+
+  root.DiagcalcDatasets = factory();
+}(typeof globalThis !== "undefined" ? globalThis : this, () => {
+  const datasets = {
+    screening: {
+      tp: 42,
+      fp: 58,
+      fn: 18,
+      tn: 882,
+      preTestProb: 6,
+      name: "Screening programme (low prevalence)",
+      description: "Generic population screening scenario with low prevalence.",
+      reference: null,
+    },
+    caseControl: {
+      tp: 92,
+      fp: 18,
+      fn: 8,
+      tn: 82,
+      preTestProb: 50,
+      name: "Case-control study",
+      description: "Typical case-control design with artificially balanced prevalence.",
+      reference: null,
+    },
+    clinic: {
+      tp: 75,
+      fp: 25,
+      fn: 10,
+      tn: 140,
+      preTestProb: 40,
+      name: "Specialist clinic",
+      description: "Specialist clinic setting with intermediate prevalence.",
+      reference: null,
+    },
+    ddimer: {
+      tp: 195,
+      fp: 87,
+      fn: 5,
+      tn: 413,
+      preTestProb: 28.6,
+      name: "D-dimer for pulmonary embolism",
+      description: "Low Wells score + D-dimer to rule out pulmonary embolism in the emergency department.",
+      reference: {
+        authors: "Righini M, et al.",
+        title: "Age-Adjusted D-Dimer Cutoff Levels to Rule Out Pulmonary Embolism",
+        journal: "JAMA. 2014;311(11):1117-1124",
+        doi: "10.1001/jama.2014.2135",
+        url: "https://jamanetwork.com/journals/jama/fullarticle/1839153",
+      },
+    },
+    troponin: {
+      tp: 289,
+      fp: 156,
+      fn: 11,
+      tn: 1544,
+      preTestProb: 15,
+      name: "High-sensitivity troponin for AMI",
+      description: "High-sensitivity troponin for diagnosis of acute myocardial infarction.",
+      reference: {
+        authors: "Reichlin T, et al.",
+        title: "Early Diagnosis of Myocardial Infarction with Sensitive Cardiac Troponin Assays",
+        journal: "N Engl J Med. 2009;361(9):858-867",
+        doi: "10.1056/NEJMoa0900428",
+        url: "https://www.nejm.org/doi/full/10.1056/NEJMoa0900428",
+      },
+    },
+    mammography: {
+      tp: 7,
+      fp: 93,
+      fn: 3,
+      tn: 897,
+      preTestProb: 1,
+      name: "Screening mammography",
+      description: "Mammographic screening in women aged 50-69 (aggregated data).",
+      reference: {
+        authors: "Kopans DB, et al.",
+        title: "Screening Mammography Performance Metrics",
+        journal: "Radiology. 2020;297(2):239-240",
+        doi: "10.1148/radiol.2020203635",
+        url: "https://pubs.rsna.org/doi/10.1148/radiol.2020203635",
+      },
+    },
+    covid_antigen: {
+      tp: 103,
+      fp: 8,
+      fn: 47,
+      tn: 192,
+      preTestProb: 42.9,
+      name: "Rapid COVID-19 antigen test",
+      description: "Rapid antigen test for SARS-CoV-2 in symptomatic patients (first 7 days).",
+      reference: {
+        authors: "Dinnes J, et al.",
+        title: "Rapid, Point-of-Care Antigen Tests for COVID-19",
+        journal: "Cochrane Database Syst Rev. 2022;7:CD013705",
+        doi: "10.1002/14651858.CD013705.pub3",
+        url: "https://www.cochranelibrary.com/cdsr/doi/10.1002/14651858.CD013705.pub3",
+      },
+    },
+    hiv_elisa: {
+      tp: 199,
+      fp: 1,
+      fn: 1,
+      tn: 9799,
+      preTestProb: 2,
+      name: "HIV ELISA",
+      description: "4th-generation ELISA for HIV screening in the general population.",
+      reference: {
+        authors: "Masciotra S, et al.",
+        title: "Performance of HIV Diagnostic Tests",
+        journal: "J Clin Microbiol. 2013;51(6):1694-1700",
+        doi: "10.1128/JCM.03552-12",
+        url: "https://journals.asm.org/doi/10.1128/JCM.03552-12",
+      },
+    },
+    strep_throat: {
+      tp: 142,
+      fp: 25,
+      fn: 18,
+      tn: 315,
+      preTestProb: 32,
+      name: "Rapid Streptococcus test",
+      description: "Rapid antigen test for streptococcal pharyngitis in children with fever and sore throat.",
+      reference: {
+        authors: "Cohen JF, et al.",
+        title: "Rapid Antigen Detection Test for Group A Streptococcus in Children",
+        journal: "Cochrane Database Syst Rev. 2016;7:CD010502",
+        doi: "10.1002/14651858.CD010502.pub2",
+        url: "https://www.cochranelibrary.com/cdsr/doi/10.1002/14651858.CD010502.pub2",
+      },
+    },
+    xray_pneumonia: {
+      tp: 168,
+      fp: 82,
+      fn: 32,
+      tn: 318,
+      preTestProb: 33.3,
+      name: "Chest X-ray for pneumonia",
+      description: "Chest X-ray for community-acquired pneumonia in symptomatic adults.",
+      reference: {
+        authors: "Hagaman JT, et al.",
+        title: "Admission Chest Radiograph Lacks Sensitivity in Pneumonia",
+        journal: "Am J Med Sci. 2009;337(4):236-240",
+        doi: "10.1097/MAJ.0b013e31818ad805",
+        url: "https://www.amjmedsci.org/",
+      },
+    },
+  };
+
+  function getDataset(key) {
+    if (!Object.prototype.hasOwnProperty.call(datasets, key)) {
+      return null;
+    }
+
+    return datasets[key];
+  }
+
+  function listDatasets() {
+    return Object.keys(datasets).map((key) => ({
+      key,
+      ...datasets[key],
+    }));
+  }
+
+  return {
+    datasets,
+    getDataset,
+    listDatasets,
+  };
+}));

package/package.json

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+{
+  "name": "diagcalc",
+  "version": "3.2.0",
+  "description": "Diagnostic calculator for the browser, terminal, and plain CLI.",
+  "license": "MIT",
+  "keywords": [
+    "diagnostics",
+    "bayes",
+    "clinical",
+    "cli",
+    "tui"
+  ],
+  "engines": {
+    "node": ">=18"
+  },
+  "files": [
+    "bin",
+    "lib",
+    "tui",
+    "index.html",
+    "script.js",
+    "styles.css",
+    "README.md",
+    "LICENSE"
+  ],
+  "bin": {
+    "diag": "bin/diagcalc.js",
+    "diagcalc": "bin/diagcalc.js"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "tui": "node bin/diagcalc.js --tui",
+    "cli": "node bin/diagcalc.js --help"
+  },
+  "dependencies": {
+    "blessed": "^0.1.81"
+  }
+}