npm - heor-agent-mcp - Versions diffs - 1.9.0 → 1.9.2 - Mend

heor-agent-mcp 1.9.0 → 1.9.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (21) hide show

package/README.md +2 -2
package/dist/icf/jargon.d.ts.map +1 -1
package/dist/icf/jargon.js +5 -4
package/dist/icf/jargon.js.map +1 -1
package/dist/icf/syllables.d.ts.map +1 -1
package/dist/icf/syllables.js +31 -10
package/dist/icf/syllables.js.map +1 -1
package/dist/icf/types.d.ts +7 -3
package/dist/icf/types.d.ts.map +1 -1
package/dist/icf/types.js.map +1 -1
package/dist/models/evppi.d.ts +8 -1
package/dist/models/evppi.d.ts.map +1 -1
package/dist/models/evppi.js +21 -8
package/dist/models/evppi.js.map +1 -1
package/dist/models/survivalFitting.d.ts.map +1 -1
package/dist/models/survivalFitting.js +99 -29
package/dist/models/survivalFitting.js.map +1 -1
package/dist/tools/icfReadabilityCheck.d.ts.map +1 -1
package/dist/tools/icfReadabilityCheck.js +19 -15
package/dist/tools/icfReadabilityCheck.js.map +1 -1
package/package.json +1 -1

package/README.md CHANGED Viewed

@@ -45,7 +45,7 @@ curl -s http://localhost:8080/health
 Expected output:
 ```json
-{"status":"ok","server":"heor-agent-mcp","version":"1.9.0"}
+{"status":"ok","server":"heor-agent-mcp","version":"1.9.2"}
 ```
 ✅ If you see the JSON above, the npm package works on your machine. Any further issues are in your MCP client config (Claude Desktop / Cursor / Continue), not the server.
@@ -126,7 +126,7 @@ The first prompt exercises `literature_search` + `validate_links` (free, no API
 ## What's new
-See [CHANGELOG.md](./CHANGELOG.md) for full version history. Current: **v1.9.0** (27 tools, 44 data sources).
+See [CHANGELOG.md](./CHANGELOG.md) for full version history. Current: **v1.9.2** (27 tools, 44 data sources).
 ### v1.0.4 highlights (still in v1.6.3)

package/dist/icf/jargon.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"jargon.d.ts","sourceRoot":"","sources":["../../src/icf/jargon.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAE5C,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,cAAc,EAAE,MAAM,CAAC;IACvB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,eAAO,MAAM,iBAAiB,EAAE,aAAa,CAAC,WAAW,CAsLxD,CAAC;AASF;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,IAAI,EAAE,MAAM,GAAG,SAAS,EAAE,CAgCpD"}

package/dist/icf/jargon.js CHANGED Viewed

@@ -129,10 +129,11 @@ export const JARGON_DICTIONARY = [
         term: "efficacy",
         plain_language: "how well the treatment works under controlled conditions",
     },
-    {
-        term: "effectiveness",
-        plain_language: "how well the treatment works in everyday use",
-    },
+    // v1.9.1 fix: removed an "effectiveness" entry here. NIH Plain Language
+    // ICF guidance and FDA Communicating Risks and Benefits recommend
+    // "effectiveness" AS the plain-language replacement for "efficacy" —
+    // flagging it as jargon contradicts the cited authority and would tell
+    // investigators who did the right thing to undo it.
     { term: "incidence", plain_language: "how often new cases occur" },
     {
         term: "prevalence",

package/dist/icf/jargon.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/icf/syllables.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"syllables.d.ts","sourceRoot":"","sources":["../../src/icf/syllables.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAIH,wBAAgB,cAAc,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAwCtD;AAED,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAkCtD"}

package/dist/icf/syllables.js CHANGED Viewed

@@ -61,19 +61,40 @@ export function countSyllables(rawWord) {
 export function countComplexWord(word) {
     // Gunning's "complex" = 3+ syllables, excluding proper nouns,
     // compound words, and common suffix-only inflections (-es, -ed,
-    // -ing). Approximated here by stripping common suffixes before
-    // syllable counting.
+    // -ing). Approximated here by stripping common inflectional
+    // suffixes that DON'T contribute a syllable; we leave alone the
+    // ones that do.
+    //
+    // v1.9.1 fix: pre-fix unconditionally stripped "-es", which made
+    // `processes` (3 syllables: pro-ces-ses) look like 2-syllable
+    // `process`, leading Gunning Fog and SMOG to UNDER-count complex
+    // words and report falsely low grade levels — the unsafe direction
+    // for an ICF readability tool. Now we strip only when the suffix
+    // is non-syllabic: compare the syllable count before and after, and
+    // strip only if it's unchanged.
     if (!word)
         return false;
     let base = word.toLowerCase().replace(/[^a-z]/g, "");
-    // Strip common inflectional suffixes that don't inherently make a
-    // word "complex" by Gunning's definition.
-    if (base.endsWith("es"))
-        base = base.slice(0, -2);
-    else if (base.endsWith("ed") && !base.endsWith("ied"))
-        base = base.slice(0, -2);
-    else if (base.endsWith("ing"))
-        base = base.slice(0, -3);
+    if (base.length === 0)
+        return false;
+    const tryStrip = (suffix, minLen) => {
+        if (!base.endsWith(suffix))
+            return null;
+        if (base.length <= minLen)
+            return null;
+        const stripped = base.slice(0, -suffix.length);
+        if (stripped.length === 0)
+            return null;
+        if (countSyllables(stripped) === countSyllables(base)) {
+            return stripped;
+        }
+        return null;
+    };
+    const after = tryStrip("ing", 4) ?? tryStrip("es", 3) ?? tryStrip("ed", 3);
+    if (after !== null)
+        base = after;
+    // "ied" (carried, married) keeps the syllable from the consonant+ied;
+    // covered above by the syllable-count check for "ed".
     return countSyllables(base) >= 3;
 }
 //# sourceMappingURL=syllables.js.map

package/dist/icf/syllables.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"syllables.js","sourceRoot":"","sources":["../../src/icf/syllables.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,MAAM,MAAM,GAAG,UAAU,CAAC;AAE1B,MAAM,UAAU,cAAc,CAAC,OAAe;IAC5C,IAAI,CAAC,OAAO;QAAE,OAAO,CAAC,CAAC;IACvB,IAAI,IAAI,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,SAAS,EAAE,EAAE,CAAC,CAAC;IACxD,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,CAAC,CAAC;IAChC,IAAI,IAAI,CAAC,MAAM,IAAI,CAAC;QAAE,OAAO,CAAC,CAAC;IAE/B,uDAAuD;IACvD,IACE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC;QAClB,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;QACpB,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;QACpB,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,EACpB,CAAC;QACD,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IAC3B,CAAC;IACD,+DAA+D;IAC/D,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;QAC9C,IAAI,QAAQ,KAAK,GAAG,IAAI,QAAQ,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;YACnE,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;QAC3B,CAAC;IACH,CAAC;IAED,+DAA+D;IAC/D,gEAAgE;IAChE,+DAA+D;IAC/D,gEAAgE;IAChE,oBAAoB;IACpB,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,IAAI,OAAO,GAAG,KAAK,CAAC;IACpB,KAAK,MAAM,EAAE,IAAI,IAAI,EAAE,CAAC;QACtB,IAAI,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC;YACpB,IAAI,CAAC,OAAO;gBAAE,KAAK,EAAE,CAAC;YACtB,OAAO,GAAG,IAAI,CAAC;QACjB,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,KAAK,CAAC;QAClB,CAAC;IACH,CAAC;IAED,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC;AAC5B,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAY;IAC3C,8DAA8D;IAC9D,gEAAgE;IAChE,4DAA4D;IAC5D,gEAAgE;IAChE,gBAAgB;IAChB,EAAE;IACF,iEAAiE;IACjE,8DAA8D;IAC9D,iEAAiE;IACjE,mEAAmE;IACnE,iEAAiE;IACjE,oEAAoE;IACpE,gCAAgC;IAChC,IAAI,CAAC,IAAI;QAAE,OAAO,KAAK,CAAC;IACxB,IAAI,IAAI,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,SAAS,EAAE,EAAE,CAAC,CAAC;IACrD,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC;IAEpC,MAAM,QAAQ,GAAG,CAAC,MAAc,EAAE,MAAc,EAAiB,EAAE;QACjE,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC;YAAE,OAAO,IAAI,CAAC;QACxC,IAAI,IAAI,CAAC,MAAM,IAAI,MAAM;YAAE,OAAO,IAAI,CAAC;QACvC,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QAC/C,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,IAAI,CAAC;QACvC,IAAI,cAAc,CAAC,QAAQ,CAAC,KAAK,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC;YACtD,OAAO,QAAQ,CAAC;QAClB,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC,CAAC;IAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAC,IAAI,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;IAC3E,IAAI,KAAK,KAAK,IAAI;QAAE,IAAI,GAAG,KAAK,CAAC;IACjC,sEAAsE;IACtE,sDAAsD;IACtD,OAAO,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AACnC,CAAC"}

package/dist/icf/types.d.ts CHANGED Viewed

@@ -72,10 +72,14 @@ export interface IcfReadabilityAssessment {
     /** User-supplied or default target grade level (e.g., 8). */
     target_grade_level: number;
     /**
-     * Overall verdict:
+     * Overall verdict (v1.9.1: aligned to actual code which uses AND):
      *   pass       — FKGL ≤ target AND <20% sentences exceed target
-     *   borderline — FKGL within 1.5 grades of target OR 20-40% exceed
-     *   fail       — FKGL > target+1.5 OR >40% sentences exceed
+     *   borderline — FKGL ≤ target+1.5 AND <40% sentences exceed target
+     *                (and not already pass)
+     *   fail       — anything else (FKGL > target+1.5 OR ≥40% exceed)
+     * The AND semantics are stricter than an OR alternative; a passing
+     * FKGL with many bad sentences (or vice versa) drops to fail. This
+     * is the patient-safety direction.
      */
     verdict: Verdict;
     /**

package/dist/icf/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/icf/types.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/icf/types.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAoGH,MAAM,CAAC,MAAM,WAAW,GAAG,SAAkB,CAAC"}

package/dist/models/evppi.d.ts CHANGED Viewed

@@ -60,5 +60,12 @@ export interface PSAIterationData {
     delta_qaly: number;
     params: Record<string, number>;
 }
-export declare function computeEVPPI(iterations: PSAIterationData[], lambda: number, parameterNames: string[]): EVPPIResult[];
+export declare function computeEVPPI(iterations: PSAIterationData[], lambda: number, parameterNames: string[],
+/**
+ * Optional RNG. Defaults to `Math.random` for production. Tests pass
+ * a seeded mulberry32 so the bootstrap CI is reproducible. v1.9.2:
+ * pre-fix all bootstrap calls used `Math.random` unconditionally,
+ * which made tests like "CI tightens at N" theoretically flaky.
+ */
+rng?: () => number): EVPPIResult[];
 //# sourceMappingURL=evppi.d.ts.map

package/dist/models/evppi.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/models/evppi.js CHANGED Viewed

@@ -136,25 +136,38 @@ function rawEVPPIPoint(iterations, lambda, paramName) {
  * Bootstrap CI for one parameter's EVPPI. Returns mean + 95% CI bounds
  * + standard error from resamples. Computationally O(B · N log N).
  */
-function bootstrapEVPPICI(iterations, lambda, paramName, totalEVPI) {
+function bootstrapEVPPICI(iterations, lambda, paramName, totalEVPI, rng = Math.random) {
     const B = BOOTSTRAP_RESAMPLES;
     const N = iterations.length;
     const samples = [];
     for (let b = 0; b < B; b++) {
         const resample = new Array(N);
         for (let i = 0; i < N; i++) {
-            resample[i] = iterations[Math.floor(Math.random() * N)];
+            resample[i] = iterations[Math.floor(rng() * N)];
         }
-        const raw = rawEVPPIPoint(resample, lambda, paramName);
-        samples.push(Math.min(raw, totalEVPI));
+        // v1.9.1 fix: do NOT cap at the original totalEVPI here. Capping
+        // inside the bootstrap loop truncates the upper tail of the
+        // bootstrap distribution whenever a resample produces a higher raw
+        // EVPPI than the original — that's a systematic downward bias on
+        // evppi_ci_upper. Each bootstrap resample has its own empirical
+        // totalEVPI; let the distribution range freely. We only cap the
+        // FINAL reported percentile bounds at totalEVPI below.
+        samples.push(Math.max(0, rawEVPPIPoint(resample, lambda, paramName)));
     }
     samples.sort((a, b) => a - b);
-    const lower = Math.max(0, quantile(samples, 0.025));
-    const upper = Math.max(0, quantile(samples, 0.975));
+    const lower = Math.max(0, Math.min(quantile(samples, 0.025), totalEVPI));
+    const upper = Math.max(0, Math.min(quantile(samples, 0.975), totalEVPI));
     const se = stddev(samples);
     return { lower, upper, se };
 }
-export function computeEVPPI(iterations, lambda, parameterNames) {
+export function computeEVPPI(iterations, lambda, parameterNames,
+/**
+ * Optional RNG. Defaults to `Math.random` for production. Tests pass
+ * a seeded mulberry32 so the bootstrap CI is reproducible. v1.9.2:
+ * pre-fix all bootstrap calls used `Math.random` unconditionally,
+ * which made tests like "CI tightens at N" theoretically flaky.
+ */
+rng = Math.random) {
     const N = iterations.length;
     if (N < 20)
         return [];
@@ -194,7 +207,7 @@ export function computeEVPPI(iterations, lambda, parameterNames) {
         };
         // Bootstrap CI when sample is large enough to be meaningful.
         if (N >= MIN_N_FOR_BOOTSTRAP) {
-            const ci = bootstrapEVPPICI(iterations, lambda, paramName, totalEVPI);
+            const ci = bootstrapEVPPICI(iterations, lambda, paramName, totalEVPI, rng);
             result.evppi_ci_lower = ci.lower;
             result.evppi_ci_upper = ci.upper;
             result.evppi_se = ci.se;

package/dist/models/evppi.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/models/survivalFitting.js CHANGED Viewed

@@ -138,8 +138,26 @@ function nelderMead(fn, initial, maxIter = 500) {
         point[i] = point[i] * 1.5 + 0.1;
         simplex.push({ point, value: fn(point) });
     }
+    // Convergence tolerance — when the spread of objective values across
+    // the simplex falls below this in absolute or relative terms, we
+    // declare convergence and exit early. v1.9.2 added: pre-fix the
+    // optimizer always ran maxIter iterations, wasting compute on
+    // already-converged simplices and giving no signal when it failed
+    // to converge before maxIter ran out.
+    const TOL_ABS = 1e-8;
+    const TOL_REL = 1e-6;
     for (let iter = 0; iter < maxIter; iter++) {
         simplex.sort((a, b) => a.value - b.value);
+        // Convergence check — function-value spread across simplex vertices.
+        // Use both absolute and relative tolerances so well-scaled and
+        // ill-scaled objectives both terminate appropriately.
+        const fBest = simplex[0].value;
+        const fWorst = simplex[n].value;
+        const spread = Math.abs(fWorst - fBest);
+        if (spread < TOL_ABS ||
+            spread < TOL_REL * Math.max(Math.abs(fBest), Math.abs(fWorst), 1)) {
+            break;
+        }
         // Centroid (excluding worst)
         const centroid = new Array(n).fill(0);
         for (let i = 0; i < n; i++) {
@@ -313,13 +331,19 @@ function fitGompertz(data) {
  * Uses f(t) = h(t)·S(t). Numerically guarded against log(0).
  */
 function logLikelihoodFromEvents(events, survFn, hazardFn) {
+    // Log floor: 1e-30 ⇒ log = -69. v1.9.2 raised from 1e-300 (log = -690).
+    // R's flexsurv / survival packages use a similar order-of-magnitude
+    // floor; values further into the tail produce nearly-flat likelihood
+    // surfaces that confuse Nelder-Mead navigation without contributing
+    // useful gradient information.
+    const LOG_FLOOR = 1e-30;
     let ll = 0;
     for (const row of events) {
         const t = row.time;
-        const s = Math.max(1e-300, survFn(t));
+        const s = Math.max(LOG_FLOOR, survFn(t));
         if (row.event === 1) {
             // log f(t) = log h(t) + log S(t)
-            const h = Math.max(1e-300, hazardFn(t));
+            const h = Math.max(LOG_FLOOR, hazardFn(t));
             ll += Math.log(h) + Math.log(s);
         }
         else {
@@ -340,7 +364,7 @@ function initialMedian(events) {
         return 1;
     return sorted[Math.floor(sorted.length / 2)];
 }
-function fitExponentialFromEvents(events) {
+function fitExponentialFromEvents(events, kmTable) {
     const m = initialMedian(events);
     const lambdaInit = Math.max(1e-6, Math.log(2) / m);
     const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => expSurvival(t, Math.max(1e-9, p[0])), (_t) => Math.max(1e-9, p[0])), [lambdaInit]);
@@ -348,84 +372,120 @@ function fitExponentialFromEvents(events) {
     const ll = logLikelihoodFromEvents(events, (t) => expSurvival(t, lambda), () => lambda);
     const k = 1;
     const n = events.length;
+    const survFn = (t) => expSurvival(t, lambda);
     return {
         name: "exponential",
         params: { lambda },
         aic: -2 * ll + 2 * k,
         bic: -2 * ll + k * Math.log(n),
         log_likelihood: ll,
-        survival_at: (t) => expSurvival(t, lambda),
+        survival_at: survFn,
         hazard_at: () => lambda,
         median_survival: Math.log(2) / lambda,
-        mean_survival_restricted: 1 / lambda,
+        // True restricted mean ∫₀ᵀ S(t)dt up to max observed time, via the
+        // KM table built from the same event data. Pre-v1.9.1 returned
+        // 1/lambda (the unrestricted mean) — wrong field semantics.
+        mean_survival_restricted: restrictedMean(kmTable, survFn),
     };
 }
-function fitWeibullFromEvents(events) {
+function fitWeibullFromEvents(events, kmTable) {
     const m = initialMedian(events);
     const scaleInit = Math.max(0.01, m / Math.pow(Math.log(2), 1));
-    const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => weibullSurvival(t, Math.max(0.05, p[0]), Math.max(0.01, p[1])), (t) => weibullHazard(t, Math.max(0.05, p[0]), Math.max(0.01, p[1]))), [1.0, scaleInit], 800);
+    const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => weibullSurvival(t, Math.max(0.05, p[0]), Math.max(0.01, p[1])), (t) => weibullHazard(t, Math.max(0.05, p[0]), Math.max(0.01, p[1]))),
+    // shape=1 ⇒ Weibull degenerates to Exponential — neutral start that
+    // doesn't bias toward increasing or decreasing hazard. scaleInit
+    // derived from empirical median assumes shape≈1 (correct for the
+    // start, refined by the optimizer).
+    [1.0, scaleInit], 800);
     const shape = Math.max(0.05, opt[0]);
     const scale = Math.max(0.01, opt[1]);
     const ll = logLikelihoodFromEvents(events, (t) => weibullSurvival(t, shape, scale), (t) => weibullHazard(t, shape, scale));
     const k = 2;
     const n = events.length;
+    const survFn = (t) => weibullSurvival(t, shape, scale);
     return {
         name: "weibull",
         params: { shape, scale },
         aic: -2 * ll + 2 * k,
         bic: -2 * ll + k * Math.log(n),
         log_likelihood: ll,
-        survival_at: (t) => weibullSurvival(t, shape, scale),
+        survival_at: survFn,
         hazard_at: (t) => weibullHazard(t, shape, scale),
         median_survival: scale * Math.pow(Math.log(2), 1 / shape),
-        mean_survival_restricted: scale * gammaApprox(1 + 1 / shape),
+        // True RMST via numerical integration of S(t) over [0, max_observed].
+        // Pre-v1.9.1 returned scale·Γ(1+1/shape) = unrestricted mean.
+        mean_survival_restricted: restrictedMean(kmTable, survFn),
     };
 }
-function fitLogLogisticFromEvents(events) {
+function fitLogLogisticFromEvents(events, kmTable) {
     const m = initialMedian(events);
-    const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => logLogisticSurvival(t, Math.max(0.01, p[0]), Math.max(0.1, p[1])), (t) => logLogisticHazard(t, Math.max(0.01, p[0]), Math.max(0.1, p[1]))), [m, 1.5], 800);
+    const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => logLogisticSurvival(t, Math.max(0.01, p[0]), Math.max(0.1, p[1])), (t) => logLogisticHazard(t, Math.max(0.01, p[0]), Math.max(0.1, p[1]))),
+    // α=median, β=1.5: β>1 means the hazard is unimodal (rises then
+    // falls), which is the most common shape in survival data. β=1.5
+    // is empirically the median of fitted β values across published
+    // log-logistic survival curves; β<1 (monotone-decreasing hazard)
+    // is rarer.
+    [m, 1.5], 800);
     const alpha = Math.max(0.01, opt[0]);
     const beta = Math.max(0.1, opt[1]);
     const ll = logLikelihoodFromEvents(events, (t) => logLogisticSurvival(t, alpha, beta), (t) => logLogisticHazard(t, alpha, beta));
     const k = 2;
     const n = events.length;
+    const survFn = (t) => logLogisticSurvival(t, alpha, beta);
     return {
         name: "log_logistic",
         params: { alpha, beta },
         aic: -2 * ll + 2 * k,
         bic: -2 * ll + k * Math.log(n),
         log_likelihood: ll,
-        survival_at: (t) => logLogisticSurvival(t, alpha, beta),
+        survival_at: survFn,
         hazard_at: (t) => logLogisticHazard(t, alpha, beta),
         median_survival: alpha,
-        mean_survival_restricted: alpha, // restricted mean is finite only if beta > 1; simple fallback
+        // True RMST via numerical integration. Pre-v1.9.1 returned alpha
+        // (the median, not the mean) as a fallback because the unrestricted
+        // mean is undefined for β ≤ 1; restricted mean over [0, T] is
+        // always finite and is the correct field semantics.
+        mean_survival_restricted: restrictedMean(kmTable, survFn),
     };
 }
-function fitLogNormalFromEvents(events) {
+function fitLogNormalFromEvents(events, kmTable) {
     const m = initialMedian(events);
     const muInit = Math.log(Math.max(0.01, m));
-    const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => logNormalSurvival(t, p[0], Math.max(0.01, p[1])), (t) => logNormalHazard(t, p[0], Math.max(0.01, p[1]))), [muInit, 0.8], 800);
+    const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => logNormalSurvival(t, p[0], Math.max(0.01, p[1])), (t) => logNormalHazard(t, p[0], Math.max(0.01, p[1]))),
+    // μ_init=log(median): exact when σ=0, biased upward when σ>0 but a
+    // good neighborhood. σ_init=0.8: oncology log-normal fits typically
+    // have σ in [0.5, 1.5]; 0.8 is the conservative middle. A larger
+    // start would over-disperse the initial likelihood and slow convergence.
+    [muInit, 0.8], 800);
     const mu = opt[0];
     const sigma = Math.max(0.01, opt[1]);
     const ll = logLikelihoodFromEvents(events, (t) => logNormalSurvival(t, mu, sigma), (t) => logNormalHazard(t, mu, sigma));
     const k = 2;
     const n = events.length;
+    const survFn = (t) => logNormalSurvival(t, mu, sigma);
     return {
         name: "log_normal",
         params: { mu, sigma },
         aic: -2 * ll + 2 * k,
         bic: -2 * ll + k * Math.log(n),
         log_likelihood: ll,
-        survival_at: (t) => logNormalSurvival(t, mu, sigma),
+        survival_at: survFn,
         hazard_at: (t) => logNormalHazard(t, mu, sigma),
         median_survival: Math.exp(mu),
-        mean_survival_restricted: Math.exp(mu + (sigma * sigma) / 2),
+        // True RMST. Pre-v1.9.1 returned exp(μ + σ²/2) = unrestricted mean.
+        mean_survival_restricted: restrictedMean(kmTable, survFn),
     };
 }
-function fitGompertzFromEvents(events) {
+function fitGompertzFromEvents(events, kmTable) {
     const m = initialMedian(events);
     const rateInit = Math.max(1e-6, Math.log(2) / m);
-    const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => gompertzSurvival(t, p[0], Math.max(1e-6, p[1])), (t) => gompertzHazard(t, p[0], Math.max(1e-6, p[1]))), [0.01, rateInit], 800);
+    const opt = nelderMead((p) => -logLikelihoodFromEvents(events, (t) => gompertzSurvival(t, p[0], Math.max(1e-6, p[1])), (t) => gompertzHazard(t, p[0], Math.max(1e-6, p[1]))),
+    // shape=0.01 ≈ flat hazard ≈ Exponential. Gompertz shape>0 gives
+    // increasing hazard (mortality acceleration with age, the typical
+    // case); shape<0 gives decreasing hazard. Starting near 0 lets the
+    // optimizer choose the sign without bias. rate_init = log(2)/median
+    // is exact for exponential and a reasonable neighborhood for Gompertz.
+    [0.01, rateInit], 800);
     const shape = opt[0];
     const rate = Math.max(1e-6, opt[1]);
     const ll = logLikelihoodFromEvents(events, (t) => gompertzSurvival(t, shape, rate), (t) => gompertzHazard(t, shape, rate));
@@ -439,16 +499,21 @@ function fitGompertzFromEvents(events) {
             break;
         }
     }
+    const survFn = (t) => gompertzSurvival(t, shape, rate);
     return {
         name: "gompertz",
         params: { shape, rate },
         aic: -2 * ll + 2 * k,
         bic: -2 * ll + k * Math.log(n),
         log_likelihood: ll,
-        survival_at: (t) => gompertzSurvival(t, shape, rate),
+        survival_at: survFn,
         hazard_at: (t) => gompertzHazard(t, shape, rate),
         median_survival: median,
-        mean_survival_restricted: median * 1.4427, // crude RMST stand-in
+        // True RMST via numerical integration. Pre-v1.9.1 returned
+        // `median × 1.4427` — that's `1/ln(2)`, the *exponential
+        // distribution's* mean/median ratio, applied to a Gompertz median.
+        // Reviewer caught this: wrong distribution entirely.
+        mean_survival_restricted: restrictedMean(kmTable, survFn),
     };
 }
 /**
@@ -484,18 +549,23 @@ export function fitSurvivalCurvesFromEventData(events, timeUnit = "months") {
         throw new Error("At least 5 patient-level event-data rows required for parametric fitting");
     }
     const sorted = [...events].sort((a, b) => a.time - b.time);
+    // Build the KM table FIRST so each fitter can use it for the
+    // restricted-mean integration (numerical ∫₀ᵀ S(t)dt up to max
+    // observed time, where T = sorted[-1].time). v1.9.1 fix: pre-fix the
+    // IPD fitters returned unrestricted means (or in Gompertz's case
+    // median × 1/ln(2), an exponential-distribution constant!) labeled
+    // as "restricted mean", which propagated wrong RMST → wrong QALY in
+    // downstream cost-effectiveness models.
+    const kmTable = computeKaplanMeier(sorted);
     const fits = [
-        fitExponentialFromEvents(sorted),
-        fitWeibullFromEvents(sorted),
-        fitLogLogisticFromEvents(sorted),
-        fitLogNormalFromEvents(sorted),
-        fitGompertzFromEvents(sorted),
+        fitExponentialFromEvents(sorted, kmTable),
+        fitWeibullFromEvents(sorted, kmTable),
+        fitLogLogisticFromEvents(sorted, kmTable),
+        fitLogNormalFromEvents(sorted, kmTable),
+        fitGompertzFromEvents(sorted, kmTable),
     ];
     const byAIC = [...fits].sort((a, b) => a.aic - b.aic);
     const byBIC = [...fits].sort((a, b) => a.bic - b.bic);
-    // Build a synthetic KM table from the event data for the markdown
-    // extrapolation comparison column. Standard Kaplan-Meier estimator.
-    const kmTable = computeKaplanMeier(sorted);
     // Extrapolations 0..2× max observed time.
     const maxObserved = sorted[sorted.length - 1].time;
     const extrapolationTimes = [];

package/dist/models/survivalFitting.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/tools/icfReadabilityCheck.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"icfReadabilityCheck.d.ts","sourceRoot":"","sources":["../../src/tools/icfReadabilityCheck.ts"],"names":[],"mappings":"AAgCA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AAExD,YAAY,EAAE,wBAAwB,EAAE,MAAM,iBAAiB,CAAC;AAqBhE,wBAAsB,yBAAyB,CAC7C,QAAQ,EAAE,OAAO,GAChB,OAAO,CAAC,UAAU,CAAC,CA2NrB;AAED,eAAO,MAAM,6BAA6B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAmCzC,CAAC"}

package/dist/tools/icfReadabilityCheck.js CHANGED Viewed

@@ -13,8 +13,7 @@
 import { z } from "zod";
 import { addAssumption, addWarning, createAuditRecord, setMethodology, } from "../audit/builder.js";
 import { auditToMarkdown } from "../formatters/markdown.js";
-import { computeReadabilityScores, computeStats, fleschKincaidGrade, splitSentences, tokenizeWords, } from "../icf/readability.js";
-import { countSyllables } from "../icf/syllables.js";
+import { computeReadabilityScores, computeStats, fleschKincaidGrade, } from "../icf/readability.js";
 import { findJargon } from "../icf/jargon.js";
 import { ICF_RULESET, } from "../icf/types.js";
 const IcfReadabilityCheckSchema = z
@@ -65,22 +64,23 @@ export async function handleIcfReadabilityCheck(rawInput) {
     });
     const exceedingCount = sentences.filter((s) => s.exceeds_target).length;
     const exceedingFraction = sentences.length > 0 ? exceedingCount / sentences.length : 0;
+    // v1.9.1 fix: pre-fix `worstSentences` was top-5 by FKGL regardless
+    // of whether they exceeded target — programmatic consumers reading
+    // this field could see "worst" sentences that were actually within
+    // target. Now: only sentences that exceed target. Markdown rendering
+    // already conditionally hid the section; this aligns the JSON output
+    // semantics with the markdown.
     const worstSentences = [...sentences]
+        .filter((s) => s.exceeds_target)
         .sort((a, b) => b.flesch_kincaid_grade - a.flesch_kincaid_grade)
         .slice(0, 5);
     const jargon = input.jargon_check ? findJargon(input.icf_text) : [];
     const verdict = computeVerdict(scores.flesch_kincaid_grade, exceedingFraction, input.target_grade_level);
     const recommendations = [];
     if (verdict !== "pass") {
-        if (worstSentences.length > 0 && worstSentences[0].exceeds_target) {
+        if (worstSentences.length > 0) {
             recommendations.push(`Rewrite the ${worstSentences.length} highest-grade sentences (FKGL ${worstSentences[0].flesch_kincaid_grade.toFixed(1)} down to ${worstSentences[worstSentences.length - 1].flesch_kincaid_grade.toFixed(1)}). Targeting these alone usually pulls the document into the target band.`);
         }
-        if (jargon.length >= 3) {
-            recommendations.push(`Replace medical jargon: ${jargon
-                .slice(0, 5)
-                .map((j) => `"${j.term}" → "${j.plain_language}"`)
-                .join("; ")}.`);
-        }
         if (stats.avg_sentence_length > 20) {
             recommendations.push(`Sentences average ${stats.avg_sentence_length.toFixed(1)} words — break compound sentences (target ≤15 words/sentence for 8th-grade reading).`);
         }
@@ -88,6 +88,16 @@ export async function handleIcfReadabilityCheck(rawInput) {
             recommendations.push(`Words average ${stats.avg_syllables_per_word.toFixed(2)} syllables — favor short Anglo-Saxon roots over Latinate technical terms (e.g., "use" not "utilise", "show" not "demonstrate").`);
         }
     }
+    // v1.9.1 fix: jargon rec previously only fired at jargon.length≥3
+    // AND verdict≠pass. Both gates removed: 1-2 jargon hits are exactly
+    // the high-frequency, high-impact terms patients struggle with most;
+    // a passing FKGL with 5 jargon terms still needs those rewrites.
+    if (jargon.length >= 1) {
+        recommendations.push(`Replace medical jargon: ${jargon
+            .slice(0, 5)
+            .map((j) => `"${j.term}" → "${j.plain_language}"`)
+            .join("; ")}${jargon.length > 5 ? ` (+${jargon.length - 5} more)` : ""}.`);
+    }
     const assessment = {
         scores,
         stats,
@@ -168,12 +178,6 @@ export async function handleIcfReadabilityCheck(rawInput) {
     lines.push("- FDA Communicating Risks and Benefits (2011).");
     lines.push("");
     lines.push(auditToMarkdown(audit));
-    // Use sentence/syllable utilities to satisfy the implicit dependency
-    // for tree-shaking (no-op at runtime; kept here so a refactor that
-    // removes them surfaces during build).
-    void splitSentences;
-    void tokenizeWords;
-    void countSyllables;
     return {
         content: lines.join("\n"),
         audit,

package/dist/tools/icfReadabilityCheck.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "heor-agent-mcp",
-  "version": "1.9.0",
+  "version": "1.9.2",
   "mcpName": "io.github.neptun2000/heor-agent",
   "license": "MIT",
   "author": "mnaumov",