MCRA Documentation
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User guide
Introduction to MCRA
User interface
Welcome page
Registering
Logging in
Setting up two-factor authentication
Authenticator apps
Google Authenticator
Microsoft Authenticator
Windows app: 2Fast Authenticator
Request an authenticator QR code
Main user interface
Data and calculation model
Modular design
Nominal run and uncertainty analysis
Variability diagnostics
Retain & Refine and tiered approaches
Uncertainty
Uncertainty due to limited sampled data
Empirical method, resampling
Parametric methods
Uncertainty due to missing data
Uncertainty due to modelling approach
Data repository
Creating and uploading data files
Moving repositories and data sources
Repository access levels
Linking remote data repositories
Workspaces and actions
Workspace browser
Workspace overview page
Action area
Scoping: entity selection
Implicit versus explicit scoping
Comparing new data to set scopes
Standard action area
Creating a standard action
Standard action reports
Converting a standard action to a full action
Action zip files
MCRA web and core
MCRA core
MCRA web
Running MCRA core using the command line interface
Results panel
Examples
Cumulative dietary exposure assessment
Introduction
Preparation
Example 1
Example 2
Example 3
TDS-based exposure and risk assessment
Standard actions
Aggregate exposure assessment
Introduction
Preparation
Example 1
Example 2
Hazard characterisations from PoDs
Introduction
Preparation
Example 1
Health impact estimates
Introduction
Preparation
Example 1
Assessment group membership probabilities
Introduction
Preparation
Example 1
Example 2
Reference Manual
Modules
Primary entity modules
Effects
Effects from data
Effects calculation
Effects data formats
Effects settings
Selection settings
Foods
Foods from data
Foods data formats
Food coding systems
Food classification: FoodEx1
Food code definition
Food codes in consumption surveys
Food codes in concentration data
Food processing
Recipes and food translation
Market shares and brand loyalty
Supertypes
Maximum Residue Levels
MCRA food code conversion algorithm
Food classification: FoodEx2
Foods and food hierarchies
Facets and facet descriptors
Implicit facets
Foods as facets
The FoodEx 2 coding system
FoodEx2
Reading and dealing with FoodEx 2 codes
Reading and dealing with facets data
Reading facets data
Dealing with facets
Facets in food conversion
Using facets that reveal processing data
Food hierarchies
Reading and dealing with food hierarchy data
Reading food hierarchy data
Using food hierarchies for food conversion
Using hierarchy data in the output
Food unit weights
Non-dietary exposure sources
Non-dietary exposure sources from data
Non-dietary exposure sources data formats
Populations
Populations from data
Populations calculation
Population definition from dietary surveys
Populations data selection
Populations data formats
Populations settings
Selection settings
Responses
Responses from data
Responses data formats
Responses settings
Selection settings
Substances
Substances from data
Substances data formats
Substances settings
Selection settings
Test systems
Test systems from data
Test systems data formats
Consumption modules
Consumptions
Consumptions from data
Consumptions calculation
Consumption population definition
Multiple surveys
Consumptions data formats
Consumptions settings
Selection settings
Uncertainty settings
Consumptions tiers
Overview
Retrospective dietary CRA (EC 2018) - Acute / Tier I
Retrospective dietary CRA (EC 2018) - Chronic / Tier I
Retrospective dietary CRA (EC 2018) - Acute / Tier II
Retrospective dietary CRA (EC 2018) - Chronic / Tier II
Retrospective dietary CRA (EFSA 2022) - Acute / Tier I
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier I
Retrospective dietary CRA (EFSA 2022) - Acute / Tier II
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier II
Prospective dietary CRA (EFSA 2023) - Acute / Tier II
Prospective dietary CRA (EFSA 2023) - Chronic / Tier II
Consumptions uncertainty
Food recipes
Food recipes from data
Food recipes data formats
Market shares
Market shares from data
Market shares data formats
Market shares and brand loyalty
Single value consumptions
Single value consumptions from data
Single value consumptions calculation
Single value consumptions data formats
Single value consumptions settings
Calculation settings
Occurrence modules
Concentration distributions
Concentration distributions from data
Concentration distributions data formats
Concentration limits
Concentration limits from data
Concentration limits data formats
Concentration models
Concentration models calculation
Concentration model types
Empirical model
Censored spike lognormal model
Censored-Spike Truncated lognormal model
Censored Lognormal model
Zero-spike censored lognormal model
Censored spike MRL model
Summary statistics model
Concentration models
Mixture zero spike and censored lognormal
Censored lognormal
Mixture censored spike and truncated lognormal
Mixture censored spike and lognormal
Imputation of non-detect measurements
No imputation
Impute all censored values by factor times LOQ
Impute censored values based on authorized uses
No imputation except for authorized uses
Deriving the variance of TDS samples from monitoring
Concentration models settings
Calculation settings
Uncertainty settings
Concentration models tiers
Overview
Retrospective dietary CRA (EC 2018) - Acute / Tier I
Retrospective dietary CRA (EC 2018) - Chronic / Tier I
Retrospective dietary CRA (EC 2018) - Acute / Tier II
Retrospective dietary CRA (EC 2018) - Chronic / Tier II
Retrospective dietary CRA (EFSA 2012) - Optimistic
Retrospective dietary CRA (EFSA 2012) - Acute / Pessimistic
Retrospective dietary CRA (EFSA 2012) - Chronic / Pessimistic
Retrospective dietary CRA (EFSA 2022) - Acute / Tier I
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier I
Retrospective dietary CRA (EFSA 2022) - Acute / Tier II
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier II
Prospective dietary CRA (EFSA 2023) - Acute / Tier II
Prospective dietary CRA (EFSA 2023) - Chronic / Tier II
Concentration models uncertainty
Concentrations
Concentrations from data
Concentrations calculation
Filter samples exceeding the concentration limits
Substance conversion
Use of substance authorisations in substance conversion
Multiple allocations of the same active substance in one sample
Food extrapolation
1. Substance-specific imputation of missing values by extrapolated measurements
1. Extrapolation of complete samples for multiple substances
Imputation of water concentrations
Focal commodity scenario analysis
Replace samples with focal commodity samples
Append focal commodity samples
Replace measurements of focal food/substance combinations
Remove measurements of focal food/substance combinations
Filter samples by specific sample properties
Concentrations data formats
Concentrations settings
Selection settings
Uncertainty settings
Concentrations tiers
Overview
Retrospective dietary CRA (EC 2018) - Acute / Tier I
Retrospective dietary CRA (EC 2018) - Chronic / Tier I
Retrospective dietary CRA (EC 2018) - Acute / Tier II
Retrospective dietary CRA (EC 2018) - Chronic / Tier II
Retrospective dietary CRA (EFSA 2012) - Acute / Pessimistic
Retrospective dietary CRA (EFSA 2012) - Chronic / Pessimistic
Retrospective dietary CRA (EFSA 2022) - Acute / Tier I
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier I
Retrospective dietary CRA (EFSA 2022) - Acute / Tier II
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier II
Prospective dietary CRA (EFSA 2023) - Acute / Tier II
Prospective dietary CRA (EFSA 2023) - Chronic / Tier II
Concentrations uncertainty
Deterministic substance conversion factors
Deterministic substance conversion factors from data
Deterministic substance conversion factors data formats
Focal food concentrations
Focal food concentrations from data
Focal food concentrations data formats
Focal food concentrations settings
Selection settings
Calculation settings
Food extrapolations
Food extrapolations from data
Food extrapolations data formats
Modelled foods
Modelled foods calculation
Modelled foods settings
Calculation settings
Occurrence frequencies
Occurrence frequencies from data
Occurrence frequencies calculation
Occurrence frequencies data formats
Occurrence frequencies Settings
Selection settings
Occurrence patterns
Occurrence patterns from data
Occurrence patterns calculation
Occurrence patterns data formats
Occurrence patterns settings
Selection settings
Calculation settings
Uncertainty settings
Occurrence patterns tiers
Overview
Retrospective dietary CRA (EC 2018) - Acute / Tier I
Retrospective dietary CRA (EC 2018) - Chronic / Tier I
Retrospective dietary CRA (EC 2018) - Acute / Tier II
Retrospective dietary CRA (EC 2018) - Chronic / Tier II
Retrospective dietary CRA (EFSA 2022) - Acute / Tier I
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier I
Retrospective dietary CRA (EFSA 2022) - Acute / Tier II
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier II
Prospective dietary CRA (EFSA 2023) - Acute / Tier II
Prospective dietary CRA (EFSA 2023) - Chronic / Tier II
Processing factors
Processing factors from data
Processing factors calculation
Processing factors fixed or distribution based
Nonnegative processing factors
Processing factors between 0 and 1
Processing factors data formats
Processing factors settings
Uncertainty settings
Processing factors uncertainty
Single value concentrations
Single value concentrations from data
Single value concentrations calculation
Single value concentrations data formats
Single value concentrations settings
Selection settings
Substance authorisations
Substance authorisations from data
Substance authorisations data formats
Substance approvals
Substance approvals from data
Substance approvals data formats
Substance conversions
Substance conversions from data
Substance conversions data formats
Total diet study sample compositions
Total diet study sample compositions from data
Total diet study sample compositions data formats
Unit variability factors
Unit variability factors from data
Unit variability factors data formats
Exposure modules
Consumptions by modelled food
Consumptions by modelled food calculation
Consumptions by modelled food
Calculation settings
Dietary exposures
Dietary exposures calculation
Acute exposure assessment
Modelling unit-to-unit variation
Estimation of intake values using the concept of unit variability
Beta distribution
Lognormal distribution
Bernoulli distribution
Chronic exposure assessment
Chronic exposure models
Observed individual means (OIM)
Model based and model assisted
Betabinomial-Normal model (BBN)
Logisticnormal-Normal model (LNN with and without correlation)
Discrete/semi-parametric model (ISUF)
Model-Then-Add
Chronic exposure as a function of covariates
Total Diet Study
Model-Then-Add
The Model step
The Add step
Chronic exposure as a function of covariates
Total Diet Study
TDS reduction to limit scenario analysis
Substance concentrations generation
Sample-based concentrations generation
Substance-based concentrations generation
Processing correction
Chronic exposure assessment, daily consumed foods
Model based usual intake
Model based usual intake on the transformed scale
Model based using a logarithmic transformation
Model based using a power transformation
Model assisted usual intake on the transformed scale
Model assisted using a logarithmic transformation
Model assisted using a power transformation
Chronic exposure assessment, episodically consumed foods
Beta-Binomial model for frequencies (BBN)
Model based frequencies for usual intake
Model assisted frequencies for usual intake
Logistic-Normal model for frequencies (LNN0)
Model based frequencies for usual intake
Model assisted frequencies for usual intake
Logistic-Normal model for frequencies correlated with amounts (LNN)
Model based usual intake
Model assisted usual intake
Dietary exposures settings
Calculation settings
Output settings
Uncertainty settings
Dietary exposures tiers
Overview
Retrospective dietary CRA (EC 2018) - Acute / Tier I
Retrospective dietary CRA (EC 2018) - Chronic / Tier I
Retrospective dietary CRA (EC 2018) - Acute / Tier II
Retrospective dietary CRA (EC 2018) - Chronic / Tier II
Retrospective dietary CRA (EFSA 2012) - Optimistic
Retrospective dietary CRA (EFSA 2012) - Acute / Pessimistic
Retrospective dietary CRA (EFSA 2012) - Chronic / Pessimistic
Retrospective dietary CRA (EFSA 2022) - Acute / Tier I
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier I
Retrospective dietary CRA (EFSA 2022) - Acute / Tier II
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier II
Prospective dietary CRA (EFSA 2023) - Acute / Tier II
Prospective dietary CRA (EFSA 2023) - Chronic / Tier II
High exposure food substance combinations
High exposure food substance combinations calculation
Screening calculation for large Cumulative Assessment Groups
Statistical model for the screening step (acute exposure)
Statistical model for the screening step (chronic exposure)
High exposure food substance combinations settings
Calculation settings
Exposures
Exposures calculation
Combining dietary and non-dietary exposures
Example 1
Example 2
Example 3
Internal exposures calculation
Calculation of internal concentrations using absorption factors
Calculation of internal concentrations using kinetic models
Dosing patterns
Non-stationary period
Counting of co-exposure
Maximum Cumulative Ratio
Risk based, standardised or unweighted exposures
Exposures settings
Calculation settings
Output settings
Uncertainty settings
Exposure mixtures
Exposure mixtures calculation
Risk based, standardised or unweighted exposures
Sparse nonnegative matrix underapproximation
Exposure matrix
Mechanisms to influence sparsity
Substance contributions to components
Component exposures in population and subgroups
Network analysis
Exposure mixtures settings
Calculation settings
Food conversions
Food conversions calculation
Substance independent conversion
Substance dependent conversion
Food conversion settings
Calculation settings
Biological matrix concentration comparisons
Biological matrix concentration comparisons calculation
Biological matrix concentration comparisons settings
Calculation settings
Exposure biomarker conversions
Exposure biomarker conversions from data
Uniform distribution
Lognormal distribution
Beta distribution
Exposure biomarker conversions data formats
Exposure biomarker conversions
Calculation settings
Human monitoring analysis
Human monitoring analysis calculation
Imputation of censored values
Imputation of missing values
Standardise blood for lipid content
Standardise/normalise urine for creatinine or specific gravity
Combine urine from different sampling methods
Filter for complete cases
Apply exposure biomarker conversion of substance concentrations
Apply kinetic conversion of substance concentrations from other biological matrices
Calculation of acute human monitoring concentrations
Calculation of chronic human monitoring concentrations
Human monitoring analysis settings
Calculation settings
Output settings
Human monitoring data
Human monitoring data from data
Selection on sampling method
Filter on repeated measurements
Excluded substances from sampling method
Use complete analysed samples
Use sampling weights
Human monitoring data data formats
PARC harmonised HBM data format
Human monitoring data settings
Selection settings
Output settings
Uncertainty settings
Non-dietary exposures
Non-dietary exposures from data
Non-dietary exposures data formats
Non-dietary exposures settings
Uncertainty settings
Non-dietary exposures uncertainty
Single value dietary exposures
Single value dietary exposures calculation
Acute single value dietary exposure assessment
IESTI (International Estimated Short-Term Intake)
Alternative IESTI-styled assessments
IESTI special cases
Chronic single value dietary exposure assessment
TMDI (Theoretical Maximum Dietary Intake)
IEDI (International Estimated Dietary Intake)
NEDI (National Estimated Dietary Intake): Rees-Day model (I)
NEDI (National Estimated Dietary Intake): Rees-Day model (II)
Alternative TMDI-, IEDI- or NEDI-styled assessments
Single value dietary exposures data formats
Single value dietary exposures settings
Selection settings
Calculation settings
Single value non-dietary exposures
Single value non-dietary exposures from data
Single value non-dietary exposures calculation
Acute single value non-dietary exposure assessment
Chronic single value non-dietary exposure assessment
Single value non-dietary exposures data formats
Single value non-dietary exposures settings
Selection settings
Calculation settings
Hazard modules
Active substances
Active substances from data
Active substances calculation
Active substances data formats
Active substances settings
Calculation settings
Uncertainty settings
AOP networks
AOP networks from data
AOP Networks calculation
AOP networks data formats
AOP networks settings
Selection settings
Dose response data
Dose response data from data
Dose response data data formats
Dose response data settings
Selection settings
Dose response models
Dose response models from data
Dose response models calculation
Proast models
Dose response models data formats
Dose response models settings
Calculation settings
Uncertainty settings
Effect representations
Effect representations from data
Effect representations data formats
Effect representations data formats
Hazard characterisations
Hazard characterisations from data
Hazard characterisations calculation
Hazard characterisation type extrapolation
Inter-species extrapolation
Intra-species extrapolation of hazard characterisations
Additional assessment factors
In-vitro in-vivo extrapolation (IVIVE)
IVIVE for calculating internal hazard characterisations
IVIVE for calculating external hazard characterisations
Kinetic conversion of hazard characterisations
Extrapolation from external to internal hazard characterisations
Calculation of internal doses using absorption factors
Calculation of internal doses using human PBPK models
Calculation of internal doses using animal PBPK models
Extrapolation from internal to external hazard characterisations
Hazard characterisation imputation
Munro P5 (TTC approach)
Munro central value
Available hazard characterisations distribution P5
Available hazard characterisations distribution central value
Aggregation over multiple available hazard characterisations
Hazard characterisations data formats
Hazard characterisations settings
Selection settings
Calculation settings
Uncertainty settings
Inter-species conversions
Inter-species conversions from data
Inter-species conversions data formats
Inter-species conversions settings
Selection settings
Uncertainty settings
Intra species factors
Intra species factors from data
Intra species factors calculation
Intra-species factors data formats
Intra species factors settings
Selection settings
Points of departure
Points of departure from data
Points of departure data formats
Points of departure settings
Uncertainty settings
Relative potency factors
Relative potency factors from data
Relative potency factors calculation
Relative potency factors data formats
Relative potency factors settings
Calculation settings
Uncertainty settings
In-silico modules
Molecular docking models
Molecular docking models from data
Molecular docking models data formats
QSAR membership models
QSAR membership models from data
QSAR membership models data formats
Kinetic modules
Kinetic models
Kinetic models from data
Kinetic models data formats
Kinetic models settings
Calculation settings
Uncertainty settings
Available kinetic models
EuroMix Generic PBK (v1)
EuroMix Bisphenols PBPK model (v1)
EuroMix Bisphenols PBPK model (v2)
EuroMix Generic PBTK model (v5)
EuroMix Generic PBTK model (v6)
PBK model chlorpyrifos (v1)
EuroMix generic PBK model
Bisphenol model
Risk modules
Risks
Risks calculation
Risk metric calculation type
Inverse distribution
Risk by food
Risks settings
Calculation settings
Output settings
Risks tiers
Overview
Retrospective dietary CRA (EC 2018) - Acute / Tier I
Retrospective dietary CRA (EC 2018) - Chronic / Tier I
Retrospective dietary CRA (EC 2018) - Acute / Tier II
Retrospective dietary CRA (EC 2018) - Chronic / Tier II
Retrospective dietary CRA (EFSA 2012) - Optimistic
Retrospective dietary CRA (EFSA 2012) - Acute / Pessimistic
Retrospective dietary CRA (EFSA 2012) - Chronic / Pessimistic
Retrospective dietary CRA (EFSA 2022) - Acute / Tier I
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier I
Retrospective dietary CRA (EFSA 2022) - Acute / Tier II
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier II
Prospective dietary CRA (EFSA 2023) - Acute / Tier II
Prospective dietary CRA (EFSA 2023) - Chronic / Tier II
Single value risks
Single value risks calculation
Combining single value exposures and hazard characterisations
Single value risks from individual risks
Adjustment factors and uncertainty specification
Background-only adjustment factor
Single value risks settings
Calculation settings
Single value risks tiers
Overview
Retrospective dietary CRA (EC 2018) - Acute / Tier I
Retrospective dietary CRA (EC 2018) - Chronic / Tier I
Retrospective dietary CRA (EC 2018) - Acute / Tier II
Retrospective dietary CRA (EC 2018) - Chronic / Tier II
Retrospective dietary CRA (EFSA 2022) - Acute / Tier I
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier I
Retrospective dietary CRA (EFSA 2022) - Acute / Tier II
Retrospective dietary CRA (EFSA 2022) - Chronic / Tier II
Prospective dietary CRA (EFSA 2023) - Acute / Tier II
Prospective dietary CRA (EFSA 2023) - Chronic / Tier II
Standard actions
Chronic mixture risk assessment of metals
Chronic cumulative exposure assessment PA
Chronic cumulative exposure assessment PFAS
Demo acute cumulative risk assessment
Acute single substance dietary exposure assessment of carbofuran or chlorpyrifos
Chronic single substance dietary exposure assessment of lead or atropine
Demo Human Monitoring Analysis bisphenols
TDS-based long term dietary exposure and risk assessment
Long-term dietary exposure and risk of nickel for the Belgian population
TDS-based long-term exposure and risk assessment of methylmercury for German children
Introduction
Standard action options
Standard action data
Acute Cumulative Risk Assessment Craniofacial Alterations (EFSA 2022)
EU acute cumulative exposure assessment (2018) Tier I and Tier II
EU chronic cumulative exposure assessment (2018) Tier I and Tier II
EU Prospective Dietary Cumulative Risk Assessment (2023)
EU Retrospective Dietary Cumulative Risk Assessment (2023)
Risk steatosis from imazalil
Training prospective risk assessment acute Tier II
Training prospective risk assessment chronic Tier II
Training substance prioritisation acute neuro
Type and Unit definitions
Adjustment factor distribution method types
Assessment group membership calculation methods
Benchmark response type
Biological matrix
Biological organisation type
Biomarker conversion distribution type
Body weight unit
Boolean type
Cluster method type
Combination method membership info and PoD presence types
Concentration limit value type
Concentration model types
Concentration unit
Concentration value type
Consumption intake unit
Consumption unit
Consumption value type
Covariate model types
Dietary exposures details level types
Dose response model type
Dose unit
Estimates nature types
Exposure approach types
Exposure calculation method
Exposure method types
Exposure path type
Exposure route
Exposure type
Expression type
External exposure unit
Focal commodity replacement method types
Function types
Gender type
Harvest application type
Hazard characterisation type
Hazard dose imputation method types
Health effect types
Individual property type
Individual subset types
Intake model types
Internal model type
Isced type
Job task type
Left-censored data handling methods
Mean value correction types
Measurement result type
Missing value imputation method types
Modelled foods calculation source types
Month type
Multiple substance handling method types
Network analysis type
Nondetect imputation method types
Point of departure type
Point of departure types
Probability distribution type
Processing distribution type
Property level type
Response type
Risk characterisation ratio
Riskmetric calculation types
Single value dietary exposures calculation method types
Single value risk calculation method types
Standardise blood methods
Standardise/normalise urine concentration method
Substance group selection method types
Substance translation allocation method types
Target dose selection method types
Target doses calculation method types
Target level type
Test system type
Testing method types
Time unit
Transform types
Uncertainty types
Unit variability correlation types
Unit variability model types
Unit variability types
Unit weight value type
Value qualifier
Application Programming Interface (API)
Command Line Interface (CLI)
Introduction
Action template structure
Create a new action template
Run an action
Output files and folder structure
Appendices
NOAEL collection of Munro et al.
Box-Cox power transformation
Gauss-Hermite Integration
One-dimensional Gauss-Hermite integration
Two-dimensional Gauss-Hermite integration
Maximum likelihood for the LNN model with two-dimensional Gauss-Hermite integration
Glossary
Bibliography
Publications using MCRA
References
Colophon
Contributors to MCRA
Change Log
Version 10.0.15 (2024-06-21)
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Version 10.0.14 (2024-06-18)
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Version 10.0.13 (2024-05-28)
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Version 10.0.6 (2024-01-26)
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Version 10.0.5 (2023-12-21)
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Version 10.0.2 (2023-10-26)
Version 10.0.1 (2023-10-23)
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Version 10.0.0 (2023-06-23)
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Version 9.2.10 (2023-06-01)
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Version 9.2.8 (2023-04-25)
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Version 9.2.7 (2023-04-03)
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Version 9.2.4 (2023-02-03)
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Version 9.2.3 (2023-01-16)
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Version 9.2.2 (2022-12-20)
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MCRA Documentation
Modules
Hazard modules
AOP networks
AOP networks from data
AOP networks from data