Quantification Rules Design

Document Type: Rule Design (Tier 2) Domain: RULES-QUANT Domain Character: Algorithmic SRS Reference: rule-rquant.md, rule-quant-validation.md, rule-stdqt.md, rule-linear-regression-validation.md, rule-standard-curve-validation.md, rule-managing-quantities.md, rule-quantity-weight.md, rule-notts-quant-multiply.md, rule-reporting-qual.md, rule-reporting-quant-as-qual.md Status: Draft Last Updated: 2026-01-25

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1. Overview

1.0 Rule Summary

Property	Value
Intent	Calculate, validate, format, and report quantities from PCR analysis using standard curve quantification, linear regression parameters, and configurable reporting thresholds. Supports tiered quantity formatting, specimen-type-specific configurations, and qualitative/quantitative outcome determination.
Inputs	Well observations (CT, quantity, classification), Standard curve parameters (slope, intercept, R2, efficiency), Quantification settings (thresholds, ranges), Reporting configurations (groups, boundaries, specimen types), Tissue weight, Concentration factor
Outputs	Calculated quantities, Formatted reporting quantities, LIMS status codes (DETECTED, NOT DETECTED, DETECTED_QUANT, DETECTED_LOQ), Error codes (UNABLE_TO_QUANTIFY, RQUANT_LIMITS_MISSED, BAD_R2, BAD_GRADIENT, etc.)
Precedence	QUANT_VALIDATION and LINEAR_REGRESSION_VALIDATION run early (during import); STDQT after CT calculation; RQUANT/RQUANTASQUAL/RQUAL after quantification; TISSUE_WEIGHT and NOTES_QUANT_MULTIPLY during analysis

1.1 Purpose

The Quantification Rules cluster handles all aspects of PCR quantity calculation, validation, formatting, and reporting. This encompasses:

1. Standard Curve Validation - Validates CT values and R-squared correlation against standard curve parameters
2. Linear Regression Validation - Calculates and validates regression parameters (slope, intercept, R2, efficiency) from standard controls
3. Quantity Validation - Assigns known quantities to observations, validates standard controls, performs CT range validation
4. Standard Quantity Calculation (STDQT) - Calculates patient sample quantities using standard curve parameters
5. Quantity Formatting (RQUANT) - Applies tiered formatting rules (Groups 2-9) to quantities for LIMS export
6. Qualitative Reporting (RQUAL) - Determines Detected/Not Detected outcomes by CT vs cutoff comparison
7. Quant-as-Qual Reporting (RQUANTASQUAL) - Converts quantitative results to qualitative outcomes using LoD thresholds
8. Quantity Weight Normalization (TISSUE_WEIGHT) - Normalizes quantities by tissue weight
9. Quantity Multiplier (NOTES_QUANT_MULTIPLY) - Applies concentration factor as quantity multiplier
10. Placeholder Substitution (Managing Quantities) - Substitutes {LOQ} and {QUANT} placeholders in LIMS messages

1.2 Requirements Covered

REQ ID	Title	Priority	Source Rule
REQ-RULES-RQUANT-001	Evaluate and Format Sample Quantities	Must	RQUANT
REQ-RULES-RQUANT-002	Handle Missing Configuration	Must	RQUANT
REQ-RULES-RQUANT-003	Select Reporting Configuration by Specimen Type	Should	RQUANT
REQ-RULES-QUANTVAL-001	Assign Known Quantities to Observations	Must	QUANT_VALIDATION
REQ-RULES-QUANTVAL-002	Exclude Non-Quantifiable Observations	Must	QUANT_VALIDATION
REQ-RULES-QUANTVAL-003	Calculate Linear Regression Parameters	Must	QUANT_VALIDATION
REQ-RULES-QUANTVAL-004	Validate Standard Controls Against Thresholds	Must	QUANT_VALIDATION
REQ-RULES-QUANTVAL-005	Validate CT Values Against Range Bounds	Must	QUANT_VALIDATION
REQ-RULES-QUANTVAL-006	Support Error Resolution	Should	QUANT_VALIDATION
REQ-RULES-LINREG-001	Calculate Linear Regression Parameters	Must	LINEAR_REGRESSION_VALIDATION
REQ-RULES-LINREG-002	Exclude Error Wells from Regression Calculation	Must	LINEAR_REGRESSION_VALIDATION
REQ-RULES-LINREG-003	Classify Insufficient Standard Control Errors	Must	LINEAR_REGRESSION_VALIDATION
REQ-RULES-LINREG-004	Apply Resolutions to Linear Regression Errors	Should	LINEAR_REGRESSION_VALIDATION
REQ-RULES-LINREG-005	Propagate Series-Level Resolutions	Should	LINEAR_REGRESSION_VALIDATION
REQ-RULES-LINREG-006	Exclude Wells from Regression via Resolution	Should	LINEAR_REGRESSION_VALIDATION
REQ-RULES-STDQT-001	Calculate Standard Quantity	Must	STDQT
REQ-RULES-STDQT-002	Apply Quantity Multiplier	Should	STDQT
REQ-RULES-STDQT-003	Use Fallback Standard Controls	Should	STDQT
REQ-RULES-STDQT-004	Propagate Run Target Quantification Errors	Must	STDQT
REQ-RULES-STDQT-005	Configure Well Failure Scope	Should	STDQT
REQ-RULES-STDCURVE-001	Validate CT Values Against Standard Curve	Must	STDQT
REQ-RULES-QTYWEIGHT-001	Normalize Quantity Using Tissue Weight	Must	TISSUE_WEIGHT
REQ-RULES-QTYWEIGHT-002	Generate Error for Invalid Tissue Weight	Must	TISSUE_WEIGHT
REQ-RULES-NOTTSQM-001	Set Quantity Multiplier from Concentration Factor	Must	NOTES_QUANT_MULTIPLY
REQ-RULES-QUANTITIES-001	Support Quantity Placeholders in LIMS Export	Must	RQUANTASQUAL
REQ-RULES-RQUAL-001	Qualitative Reporting Outcome Determination	Must	RQUAL
REQ-RULES-RQUAL-002	Specimen-Specific Reporting Configuration Selection	Should	RQUAL
REQ-RULES-RQUANTQUAL-001	Report Quantitative Results as Qualitative Outcomes	Must	RQUANTASQUAL
REQ-RULES-RQUANTQUAL-002	Select LoD Threshold Based on Specimen Type	Should	RQUANTASQUAL

1.3 Constraints

Tier 2 Constraint: This document describes ownership, patterns, and design rationale. It links to reference docs for full schemas.

1.4 Dependencies

Direction	Component	Purpose
Consumes	Well + Observations	CT values, classifications, quantities
	Kit Configuration	Standard curves, reporting configs, thresholds
	Runfile Data	Machine quantities, tissue weights
Related	WDCLS Rule	Classification for eligibility checks
	Combined Outcome Rule	May set outcomes before RQUANT
Precedes	LIMS Export	Formatted quantities exported

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2. Component Architecture

2.1 Component Diagram

2.2 Component Responsibilities

Component	File	Responsibility	REQ Trace
QuantValidationRule	Analyzer/Rules/QuantValidationRule.php	Known quantity assignment, CT range validation	QUANTVAL-001 to 006
LinearRegressionValidationRule	Analyzer/Rules/LinearRegressionValidationRule.php	Regression calculation and validation	LINREG-001 to 006
StdqtRule	Analyzer/Rules/StdqtRule.php	Patient quantity calculation	STDQT-001 to 005
RquantRule	Analyzer/Rules/RquantRule.php	Tiered quantity formatting	RQUANT-001 to 003
RqualRule	Analyzer/Rules/RqualRule.php	Qualitative outcome determination	RQUAL-001, 002
RquantasqualRule	Analyzer/Rules/RquantasqualRule.php	Quant-to-qual conversion	RQUANTQUAL-001, 002
QuantityWeightRule	Analyzer/Rules/QuantityWeightRule.php	Tissue weight normalization	QTYWEIGHT-001, 002
NotesQuantMultiplyRule	Analyzer/Rules/NotesQuantMultiplyRule.php	Concentration factor multiplier	NOTTSQM-001
FillObservationQuantity	Concerns/QuantValidationRule/FillObservationQuantity.php	Assigns known quantities	QUANTVAL-001
ValidateCT	Concerns/QuantValidationRule/ValidateCT.php	CT range validation	QUANTVAL-005
ValidateCoordinates	Concerns/QuantValidationRule/ValidateCoordinates.php	Standard control count validation	LINREG-002, 003
ValidateSlope	Concerns/QuantValidationRule/ValidateSlope.php	Slope range validation	LINREG-001
ValidateR2	Concerns/QuantValidationRule/ValidateR2.php	R-squared threshold validation	LINREG-001
ValidateEfficiency	Concerns/QuantValidationRule/ValidateEfficiency.php	PCR efficiency validation	LINREG-001
LinearRegressionGenerator	Support/LinearRegressionGenerator.php	Math: slope, intercept, R2 calculation	LINREG-001
CalculateQuantityUsingInterceptAndSlope	Concerns/CalculateQuantityUsingInterceptAndSlope.php	Math: quantity from CT	STDQT-001
SetErrorToSeriesWells	Concerns/QuantValidationRule/SetErrorToSeriesWells.php	Error propagation to series	QUANTVAL-004, LINREG-003
HandleResolutions	Concerns/QuantValidationRule/HandleResolutions.php	Resolution management	QUANTVAL-006, LINREG-004 to 006

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3. Data Design

3.1 Entities

Entity	Owner	Read/Write	Fields Used
wells	RUNRPT	Read/Write	observations, error_code, lims_status, reporting_quantity, quantity_multiplier, tissue_weight, concentration_factor
observations	RUNRPT	Read/Write	final_ct, final_cls, quantity, target_id, role
run_targets	RUNRPT	Read/Write	slope, intercept, r2, efficiency
known_quantities	KITCFG	Read	target_id, role, known_quantity
calculated_quantification_settings	KITCFG	Read	target, role, min_controls, min_r2, min_slope, max_slope, min_efficiency, max_efficiency
curve_control_range_settings	KITCFG	Read	low_bound, upper_bound
reportings	KITCFG	Read	group_id, upper_boundary, specimen_type

See Database Reference for full schema.

3.2 Key Data Structures

// Linear Regression Parameters
interface LinearRegression {
  slope: number;           // Gradient of log(qty) vs CT
  intercept: number;       // Y-intercept
  r2: number;              // Correlation coefficient (0-1)
  efficiency: number;      // PCR efficiency: -1 + 10^(-1/slope)
}

// Quantity Group Configuration (RQUANT)
interface ReportingGroup {
  group_id: number;        // 1-9
  upper_boundary: number;  // Quantity threshold
  specimen_type?: string;  // Optional specimen filter
  last_modified: Date;     // For fallback selection
}

// Quantification Settings
interface QuantificationSettings {
  target_id: string;
  role: string;
  min_controls: number;    // Default: 2
  min_r2: number;          // R2 threshold
  min_slope: number;       // Slope range lower bound
  max_slope: number;       // Slope range upper bound
  min_efficiency: number;  // Efficiency range lower bound
  max_efficiency: number;  // Efficiency range upper bound
}

// Standard Control Coordinate
interface Coordinate {
  quantity: number;        // Known quantity (log scale)
  ct: number;              // Cycle threshold
}

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4. Interface Design

4.1 Rule Interface

All quantification rules implement AnalyzerRuleContract:

interface AnalyzerRuleContract {
    public function handle(
        ConfigurationRepository $config,
        AnalyzableObservation $observation,
        RunMix $runMix,
        RunTarget $runTarget,
        AnalyzableWell $well,
        WellCollection $wells,
        PatientWellCollection $previousPatientWells,
        PecWellCollection $previousPecWells,
        RunTargetsCollection $runTargets
    ): void;
}

4.2 Internal APIs

Method	Class	Purpose
shouldNotBeQuantified(obs)	QuantValidationRule	Check IC target, negative CLS, non-quant role
mapCoordinatesFromQuantitativeObservations(obs)	WellCollection	Extract coordinates for regression
generate(coordinates)	LinearRegressionGenerator	Calculate slope, intercept, R2
calculateEfficiency(runTarget)	LinearRegressionValidationRule	Compute PCR efficiency from slope
roundFromSignificant(number, sigFigs)	RquantRule	Round to N significant figures
getAllGroupReportingsForObservation(obs)	ConfigurationRepository	Get reporting groups
getFirstGroupReportingForObservation(obs)	ConfigurationRepository	Get LoD threshold

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5. Behavioral Design

5.1 Standard Quantity Calculation (REQ-RULES-STDQT-001)

Algorithm: Calculate Standard Quantity

Inputs:
- ct: number - Well's final CT value
- intercept: number - Standard curve intercept
- slope: number - Standard curve slope (gradient)
- multiplier: number - Quantity multiplier (default: 1)

Outputs:
- quantity: number - Calculated quantity

Assumptions:
- Slope and intercept are non-null and valid
- CT is a valid numeric value
- Slope is non-zero (prevents division by zero)

Steps:
1. Calculate log quantity: log_qty = (ct - intercept) / slope
2. Calculate base quantity: base_qty = 10^log_qty
3. Apply multiplier: final_qty = base_qty * multiplier
4. Return final_qty

Notes:
- Slope is typically negative (higher CT = lower quantity)
- Example: CT=27, intercept=33, slope=-1 yields 10^((27-33)/-1) = 10^6 = 1,000,000

5.2 Linear Regression Calculation (REQ-RULES-LINREG-001)

Algorithm: Calculate Linear Regression Parameters

Inputs:
- coordinates: Coordinate[] - Array of {quantity, ct} from standard controls

Outputs:
- slope: number - Regression slope
- intercept: number - Regression intercept
- r2: number - R-squared correlation coefficient

Assumptions:
- Coordinates use log(quantity) as X, CT as Y
- At least 2 valid coordinates exist

Steps:
1. Calculate means:
   - x_mean = sum(log(qty)) / n
   - y_mean = sum(ct) / n

2. Calculate slope:
   - numerator = sum((log(qty) - x_mean) * (ct - y_mean))
   - denominator = sum((log(qty) - x_mean)^2)
   - slope = numerator / denominator

3. Calculate intercept:
   - intercept = y_mean - slope * x_mean

4. Calculate R-squared:
   - SS_res = sum((ct - predicted_ct)^2)  where predicted_ct = slope * log(qty) + intercept
   - SS_tot = sum((ct - y_mean)^2)
   - R2 = 1 - (SS_res / SS_tot)

5. Return {slope, intercept, r2}

Notes:
- Efficiency is calculated separately: efficiency = -1 + 10^(-1/slope)
- Typical R2 threshold is 0.99 for high-quality standard curves

5.3 RQUANT Tiered Formatting (REQ-RULES-RQUANT-001)

Algorithm: Format Quantity for LIMS Export

Inputs:
- quantity: number - Calculated quantity
- reportings: ReportingGroup[] - Sorted by group_id ascending

Outputs:
- reporting_quantity: string - Formatted quantity
- lims_status: string - LIMS status code

Steps:
1. IF negative classification: RETURN status = 'NOT DETECTED'

2. IF no reportings configured: SET error = 'RQUANT_LIMITS_MISSED', RETURN

3. Iterate through groups (sorted by group_id):

   Group 1 (LoD):
   - IF quantity < upper_boundary: RETURN status = 'NOT DETECTED'

   Group 2 (LOQ):
   - IF quantity < upper_boundary:
     - reporting_quantity = format(upper_boundary)
     - RETURN status = 'DETECTED_LOQ'

   Group 3 (No Rounding):
   - IF quantity < upper_boundary:
     - reporting_quantity = format(quantity)
     - RETURN status = 'DETECTED_QUANT'

   Group 4 (Boundary Value):
   - IF quantity < upper_boundary:
     - reporting_quantity = format(upper_boundary)
     - RETURN status = 'DETECTED_QUANT'

   Group 5 (1 Sig Fig):
   - IF quantity < upper_boundary:
     - reporting_quantity = roundSignificant(quantity, 1)
     - RETURN status = 'DETECTED_QUANT'

   Group 6 (2 Sig Figs):
   - IF quantity < upper_boundary:
     - reporting_quantity = roundSignificant(quantity, 2)
     - RETURN status = 'DETECTED_QUANT'

   Group 7 (3 Sig Figs):
   - IF quantity < upper_boundary:
     - reporting_quantity = roundSignificant(quantity, 3)
     - RETURN status = 'DETECTED_QUANT'

   Group 8 (2 Sig Figs):
   - IF quantity < upper_boundary:
     - reporting_quantity = roundSignificant(quantity, 2)
     - RETURN status = 'DETECTED_QUANT'

   Group 9 (Scientific):
   - IF quantity < upper_boundary:
     - reporting_quantity = scientific(quantity, 2)
     - RETURN status = 'DETECTED_QUANT'
   - IF quantity >= upper_boundary:
     - reporting_quantity = scientific(upper_boundary, 2)
     - RETURN status = 'DETECTED_HIQ'

5.3.1 RQUANT Group Decision Table

Group	Condition	Rounding	Format	Example Input	Example Output
1 (LoD)	qty < threshold	N/A	N/A	50 < 100	NOT DETECTED
2 (LOQ)	qty < threshold	None	threshold	150 < 200	"200"
3	qty < threshold	None	raw	250	"250"
4	qty < threshold	None	threshold	400	"500"
5	qty < threshold	1 sig	rounded	1,040	"1,000"
6	qty < threshold	2 sig	rounded	2,123	"2,100"
7	qty < threshold	3 sig	rounded	12,927	"12,900"
8	qty < threshold	2 sig	rounded	1,565,323	"1,600,000"
9	qty < threshold	2 sig	scientific	9,982,000	"1.00E+07"
9+	qty >= threshold	2 sig	scientific	15,000,000	">1.00E+07"

Precedence: Groups evaluated in ascending order (1 through 9); first match wins. Default: If quantity exceeds all thresholds, Group 9+ applies.

5.4 Tissue Weight Normalization (REQ-RULES-QTYWEIGHT-001)

Algorithm: Normalize Quantity by Tissue Weight

Inputs:
- quantity: number|null - Observation quantity
- tissue_weight: number|null|string - Well tissue weight

Outputs:
- quantity: number|null - Normalized quantity (or unchanged)

Steps:
1. IF tissue_weight is null: RETURN original quantity (skip)
2. IF tissue_weight is non-numeric: SET error = 'INVALID_TISSUE_WEIGHT', RETURN
3. IF tissue_weight == 0: RETURN original quantity (skip, avoid division by zero)
4. IF quantity is null: RETURN null (skip)
5. normalized_quantity = quantity / (2 * tissue_weight)
6. RETURN normalized_quantity

Notes:
- Multiplier of 2 is a fixed domain-specific constant
- Example: quantity=100, tissue_weight=0.1 yields 100/(2*0.1) = 500

5.5 Qualitative Outcome Determination (REQ-RULES-RQUAL-001)

Algorithm: Determine Qualitative Outcome (RQUAL)

Inputs:
- ct: number - Well's CT value
- cutoff: number - Upper boundary from reporting config
- use_sample_type: boolean - Whether to match by specimen type

Outputs:
- lims_status: string - 'DETECTED' or 'NOT DETECTED'

Steps:
1. Select reporting configuration:
   - IF use_sample_type enabled: match by specimen type
   - ELSE: use most recently modified reporting config

2. Get cutoff from selected reporting's upper_boundary

3. Compare CT against cutoff:
   - IF ct < cutoff: RETURN 'NOT DETECTED' (error condition)
   - IF ct >= cutoff: RETURN 'DETECTED'

Notes:
- Counter-intuitive: lower CT indicates NOT DETECTED
- Boundary is inclusive (ct == cutoff yields DETECTED)

5.6 Standard Control Validation Decision Logic (REQ-RULES-LINREG-003)

Valid Well Count	min_controls Config	Error Code
count = 1	Any	ONE_STANDARD_CONTROL
1 < count < min_controls	e.g., 3	INSUFFICIENT_STANDARD_CONTROLS
count >= min_controls	e.g., 3	No error (proceed)

Precedence: Evaluated before regression calculation. Default: min_controls defaults to 2. Note: ONE_STANDARD_CONTROL is NOT resolvable; INSUFFICIENT_STANDARD_CONTROLS is resolvable.

5.7 Error Propagation from Run Target (REQ-RULES-STDQT-004)

Run Target Error	Patient Well Effect
INSUFFICIENT_STANDARD_CONTROLS	UNABLE_TO_QUANTIFY
STANDARD_WITHOUT_QUANT	UNABLE_TO_QUANTIFY
BAD_R2	UNABLE_TO_QUANTIFY
BAD_GRADIENT	UNABLE_TO_QUANTIFY
BAD_EFFICIENCY	UNABLE_TO_QUANTIFY

Scope: Configurable via only_fail_positive_wells:

• true: Only positive-classified wells receive error
• false: All patient wells receive error

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6. Error Handling

Condition	Detection	Response	Resolvable
No reporting configuration	reportings.isEmpty()	RQUANT_LIMITS_MISSED	No
Target ID null	observation.getTargetId() == null	RQUANT_LIMITS_MISSED	No
Missing known quantity	No config match for target/role	STANDARD_WITHOUT_QUANT	No
Below min controls (count=1)	coordinates.length == 1	ONE_STANDARD_CONTROL	No
Below min controls (count>1)	coordinates.length < min_controls	INSUFFICIENT_STANDARD_CONTROLS	Yes
R2 below threshold	r2 < min_r2	BAD_R2	Yes
Slope outside range	slope < min_slope OR slope > max_slope	BAD_GRADIENT	Yes
Efficiency outside range	eff < min_eff OR eff > max_eff	BAD_EFFICIENCY	Yes
CT outside bounds	ct < low_bound OR ct > upper_bound	STANDARD_OUTSIDE_CT_RANGE	Yes
Missing slope/intercept	slope == null OR intercept == null	UNABLE_TO_QUANTIFY	No
Non-numeric tissue weight	!is_numeric(tissue_weight)	INVALID_TISSUE_WEIGHT	No

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7. Configuration

Setting	Path	Default	Effect	REQ
min_controls	Calculated Quantification Settings	2	Minimum standard controls	LINREG-003
min_r2	Calculated Quantification Settings	-	R2 threshold	LINREG-001
min_slope / max_slope	Calculated Quantification Settings	-	Slope range	LINREG-001
min_efficiency / max_efficiency	Calculated Quantification Settings	-	Efficiency range	LINREG-001
low_bound / upper_bound	Curve Control Range Settings	-	CT validation bounds	QUANTVAL-005
use_sample_type	System Settings	false	Specimen-type-specific reporting	RQUANT-003, RQUAL-002
use_fallback_shared_controls	System Settings	false	Backup controls from alternate mixes	STDQT-003
only_fail_positive_wells	System Settings	true	Limit error propagation scope	STDQT-005
round_ninth_reporting_group	System Settings	false	Round Group 9 scientific notation	RQUANT-001

See Configuration Reference for full documentation.

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8. Implementation Mapping

8.1 Code Locations

Component	Path
QUANT_VALIDATION Entry	Analyzer/Rules/QuantValidationRule.php
LINEAR_REGRESSION_VALIDATION Entry	Analyzer/Rules/LinearRegressionValidationRule.php
STDQT Entry	Analyzer/Rules/StdqtRule.php
RQUANT Entry	Analyzer/Rules/RquantRule.php
RQUAL Entry	Analyzer/Rules/RqualRule.php
RQUANTASQUAL Entry	Analyzer/Rules/RquantasqualRule.php
TISSUE_WEIGHT Entry	Analyzer/Rules/QuantityWeightRule.php
NOTES_QUANT_MULTIPLY Entry	Analyzer/Rules/NotesQuantMultiplyRule.php
Fill Quantity	Analyzer/Rules/Concerns/QuantValidationRule/FillObservationQuantity.php
CT Validation	Analyzer/Rules/Concerns/QuantValidationRule/ValidateCT.php
Coordinate Validation	Analyzer/Rules/Concerns/QuantValidationRule/ValidateCoordinates.php
Slope Validation	Analyzer/Rules/Concerns/QuantValidationRule/ValidateSlope.php
R2 Validation	Analyzer/Rules/Concerns/QuantValidationRule/ValidateR2.php
Efficiency Validation	Analyzer/Rules/Concerns/QuantValidationRule/ValidateEfficiency.php
Regression Math	Support/LinearRegressionGenerator.php
Quantity Calculation	Analyzer/Rules/Concerns/CalculateQuantityUsingInterceptAndSlope.php
Resolution Handling	Analyzer/Rules/Concerns/QuantValidationRule/HandleResolutions.php
Series Error Setting	Analyzer/Rules/Concerns/QuantValidationRule/SetErrorToSeriesWells.php

8.2 Requirement Traceability

REQ ID	Design Section	Primary Code
REQ-RULES-RQUANT-001	§5.3	RquantRule.php
REQ-RULES-RQUANT-002	§6	RquantRule.php:56-60
REQ-RULES-RQUANT-003	§5.3	ConfigurationRepository.getAllGroupReportingsForObservation()
REQ-RULES-QUANTVAL-001	§5.1	FillObservationQuantity.php
REQ-RULES-QUANTVAL-002	§2.2	QuantValidationRule.shouldNotBeQuantified()
REQ-RULES-QUANTVAL-003	§5.2	LinearRegressionGenerator.php
REQ-RULES-QUANTVAL-004	§6	SetErrorToSeriesWells.php
REQ-RULES-QUANTVAL-005	§5.4	ValidateCT.php
REQ-RULES-QUANTVAL-006	§6	HandleResolutions.php
REQ-RULES-LINREG-001	§5.2	LinearRegressionValidationRule.php, LinearRegressionGenerator.php
REQ-RULES-LINREG-002	§5.6	ValidateCoordinates.php
REQ-RULES-LINREG-003	§5.6	ValidateCoordinates.php
REQ-RULES-LINREG-004	§6	HandleResolutions.php
REQ-RULES-LINREG-005	§6	HandleResolutions.updateAllWellsWithSeriesResolution()
REQ-RULES-LINREG-006	§6	HandleResolutions.php
REQ-RULES-STDQT-001	§5.1	StdqtRule.php, CalculateQuantityUsingInterceptAndSlope.php
REQ-RULES-STDQT-002	§5.1	StdqtRule.php:68-71
REQ-RULES-STDQT-003	§2.2	StdqtRule.getMatchingRunTarget()
REQ-RULES-STDQT-004	§5.7	StdqtRule.hasQuantificationError()
REQ-RULES-STDQT-005	§5.7	StdqtRule.shouldGetError()
REQ-RULES-STDCURVE-001	§5.2, §5.5	ValidateCT.php, StdqtRule.php
REQ-RULES-QTYWEIGHT-001	§5.4	QuantityWeightRule.php
REQ-RULES-QTYWEIGHT-002	§6	QuantityWeightRule.php
REQ-RULES-NOTTSQM-001	§2.2	NotesQuantMultiplyRule.php
REQ-RULES-QUANTITIES-001	§5.3	RquantRule.php (placeholder in reporting)
REQ-RULES-RQUAL-001	§5.5	RqualRule.php
REQ-RULES-RQUAL-002	§5.5	ConfigurationRepository.getFirstGroupReportingForObservation()
REQ-RULES-RQUANTQUAL-001	§5.5	RquantasqualRule.php
REQ-RULES-RQUANTQUAL-002	§5.5	ConfigurationRepository.getFirstGroupReportingForObservation()

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9. Design Decisions

Decision	Rationale	Alternatives Considered
Separate validation and calculation rules	Clear separation of concerns; validation can fail independently	Single monolithic rule (rejected: too complex)
Series-level error propagation	Standard curve issues affect all wells using that curve	Per-well errors only (rejected: misleading)
Tiered formatting with 9 groups	Lab-specific precision requirements vary by magnitude	Single format (rejected: insufficient precision control)
Specimen-type config selection	Different sample matrices have different detection thresholds	Single config per target (rejected: insufficient flexibility)
Fixed 2x multiplier in tissue weight	Domain-specific constant from assay protocol	Configurable multiplier (rejected: no business need)
Resolvable vs non-resolvable errors	Some errors can be manually overridden; others cannot	All resolvable (rejected: ONE_STANDARD_CONTROL is fundamentally unresolvable)

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10. Performance Considerations

Scenario	Concern	Mitigation
Large number of standard controls	Regression calculation overhead	Linear time algorithm O(n)
Many reporting groups	Iteration overhead	Early exit on first match
Series-level resolution propagation	Well collection iteration	Filtered iteration on target match
Historical run lookups (fallback controls)	Database queries	Indexed queries, limited to run-level data

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11. Related Documents

Document	Relevant Sections
SRS: rule-rquant.md	RQUANT requirements
SRS: rule-quant-validation.md	QUANT_VALIDATION requirements
SRS: rule-linear-regression-validation.md	LINEAR_REGRESSION_VALIDATION requirements
SRS: rule-stdqt.md	STDQT requirements
SRS: rule-standard-curve-validation.md	Standard curve validation
SRS: rule-reporting-qual.md	RQUAL requirements
SRS: rule-reporting-quant-as-qual.md	RQUANTASQUAL requirements
SRS: rule-quantity-weight.md	TISSUE_WEIGHT requirements
SRS: rule-notts-quant-multiply.md	NOTES_QUANT_MULTIPLY requirements
SRS: rule-managing-quantities.md	Placeholder substitution
SDS: Rules Engine	Framework overview
SDS: Classification Rules	Classification inputs to quantification