{
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"Title": "Modular Monte Carlo Risk Analysis",
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"Description": "Framework for building modular Monte Carlo risk analysis\nmodels. It extends the capabilities of 'mc2d' to facilitate\nworking with multiple risk pathways, variates and scenarios. It\nprovides tools to organize risk analysis in independent\nflexible modules, align multivariate mcnodes, automate the\ncreation of mcnodes, visualise model structure, assess\nconvergence, and perform sensitivity analysis. For more details\nsee Ciria (2026) .",
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"Author": "Natalia Ciria [aut, cre, cph] (ORCID:\n),\nAlberto Allepuz [ths] (ORCID: ),\nGiovanna Ciaravino [ths] (ORCID:\n)",
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"farms_n",
"animals_n_mean",
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],
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"table": true,
"tojson": true
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{
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"title": "Merged Import Data for Risk Assessment",
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"class": [
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],
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"origin",
"h_prev_min",
"h_prev_max",
"w_prev_min",
"w_prev_max",
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"animals_n_mean",
"animals_n_sd",
"test_origin",
"test_sensi_min",
"test_sensi_mode",
"test_sensi_max"
],
"rows": 6,
"table": true,
"tojson": true
},
{
"name": "imports_data_keys",
"title": "Example Data Keys for Animal Imports Risk Assessment",
"object": "imports_data_keys",
"class": [
"list"
],
"fields": [],
"table": true,
"tojson": true
},
{
"name": "imports_exp",
"title": "Expression for Calculating Import Infection Probability",
"object": "imports_exp",
"class": [
"{"
],
"fields": [],
"table": false,
"tojson": false
},
{
"name": "imports_mcmodule",
"title": "Example Monte Carlo Module for Animal Imports Risk Assessment",
"object": "imports_mcmodule",
"class": [
"mcmodule"
],
"fields": [],
"table": false,
"tojson": false
},
{
"name": "imports_mctable",
"title": "Example Monte Carlo Input Table for Import Risk Assessment",
"object": "imports_mctable",
"class": [
"data.frame"
],
"fields": [
"mcnode",
"description",
"mc_func",
"from_variable",
"transformation",
"sensi_variation",
"sample_space"
],
"rows": 7,
"table": true,
"tojson": true
},
{
"name": "prevalence_region",
"title": "Regional Pathogen Prevalence Data",
"object": "prevalence_region",
"class": [
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],
"fields": [
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"origin",
"h_prev_min",
"h_prev_max",
"w_prev_min",
"w_prev_max",
"test_origin"
],
"rows": 6,
"table": true,
"tojson": true
},
{
"name": "test_sensitivity",
"title": "Test Sensitivity Data for Pathogens",
"object": "test_sensitivity",
"class": [
"data.frame"
],
"fields": [
"pathogen",
"test_sensi_min",
"test_sensi_mode",
"test_sensi_max"
],
"rows": 2,
"table": true,
"tojson": true
}
],
"_help": [
{
"page": "add_prefix",
"title": "Add Prefix to mcnode Names",
"topics": [
"add_prefix"
]
},
{
"page": "agg_totals",
"title": "Aggregate mcnode Values Across Groups",
"topics": [
"agg_totals"
]
},
{
"page": "animal_imports",
"title": "Example Animal Import Data",
"topics": [
"animal_imports"
]
},
{
"page": "at_least_one",
"title": "Combine Probabilities Assuming Independence",
"topics": [
"at_least_one"
]
},
{
"page": "check_mctable",
"title": "Validate and Prepare mctable Data Frame",
"topics": [
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]
},
{
"page": "combine_modules",
"title": "Combine Two mcmodule Objects",
"topics": [
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]
},
{
"page": "create_mcnodes",
"title": "Create mcnodes from Data and Configuration Table",
"topics": [
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},
{
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"title": "Evaluate Monte Carlo Model Expressions",
"topics": [
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},
{
"page": "get_edge_table",
"title": "Generate Edge Table for Network Visualisation",
"topics": [
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]
},
{
"page": "get_mcmodule_nodes",
"title": "Get Nodes from Monte Carlo Module",
"topics": [
"get_mcmodule_nodes"
]
},
{
"page": "get_node_list",
"title": "Create Node List from Model Expression",
"topics": [
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]
},
{
"page": "get_node_table",
"title": "Generate Node Table for Network Visualisation",
"topics": [
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{
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"title": "Merged Import Data for Risk Assessment",
"topics": [
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{
"page": "imports_data_keys",
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"topics": [
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},
{
"page": "imports_exp",
"title": "Expression for Calculating Import Infection Probability",
"topics": [
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]
},
{
"page": "imports_mcmodule",
"title": "Example Monte Carlo Module for Animal Imports Risk Assessment",
"topics": [
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},
{
"page": "imports_mctable",
"title": "Example Monte Carlo Input Table for Import Risk Assessment",
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{
"page": "keys_match",
"title": "Match and Align Keys Between Datasets",
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]
},
{
"page": "matrix_to_mcnodes",
"title": "Create mcnodes from Matrix/Data Frame",
"topics": [
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]
},
{
"page": "mc_compare",
"title": "Compare Monte Carlo Node Against Baseline Scenario",
"topics": [
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]
},
{
"page": "mc_filter",
"title": "Filter mcnode Variates by Condition",
"topics": [
"mc_filter"
]
},
{
"page": "mc_keys",
"title": "Extract Key Columns from Monte Carlo Nodes",
"topics": [
"mc_keys"
]
},
{
"page": "mc_match",
"title": "Match Two Monte Carlo Nodes",
"topics": [
"mc_match"
]
},
{
"page": "mc_match_data",
"title": "Match Monte Carlo Node with Data Frame",
"topics": [
"mc_match_data"
]
},
{
"page": "mc_network",
"title": "Create Interactive Network Visualisation",
"topics": [
"mc_network"
]
},
{
"page": "mc_plot",
"title": "Plot Monte Carlo Node Distribution with Boxplot and Scatter Points",
"topics": [
"mc_plot"
]
},
{
"page": "mc_summary",
"title": "Summarise Monte Carlo Node Values",
"topics": [
"mc_summary"
]
},
{
"page": "mcmodule_converg",
"title": "Analyse Monte Carlo Simulation Convergence",
"topics": [
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]
},
{
"page": "mcmodule_corr",
"title": "Calculate Correlation Coefficients Between Inputs and Outputs",
"topics": [
"mcmodule_corr"
]
},
{
"page": "mcmodule_dim_check",
"title": "Check Dimension Compatibility of Monte Carlo Nodes",
"topics": [
"mcmodule_dim_check"
]
},
{
"page": "mcmodule_info",
"title": "Get Comprehensive Monte Carlo Module Information",
"topics": [
"mcmodule_info"
]
},
{
"page": "mcmodule_to_matrices",
"title": "Convert Monte Carlo Module to Matrices",
"topics": [
"mcmodule_to_matrices"
]
},
{
"page": "mcmodule_to_mc",
"title": "Convert Monte Carlo Module to 'mc2d' Objects",
"topics": [
"mcmodule_to_mc"
]
},
{
"page": "mcmodule_tornado",
"title": "Plot Tornado-Style Correlation Results Across Variates",
"topics": [
"mcmodule_tornado"
]
},
{
"page": "mcnode_na_rm",
"title": "Replace NA and Infinite Values in mcnode Objects",
"topics": [
"mcnode_na_rm"
]
},
{
"page": "mcnode_null_rm",
"title": "Replace NULL mcnode object",
"topics": [
"mcnode_null_rm"
]
},
{
"page": "mctable_bounds",
"title": "Extract Morris Bounds From mctable",
"topics": [
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]
},
{
"page": "mctable_sobol_matrices",
"title": "Sobol sampling matrices from an mctable",
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{
"page": "optim_ndvar",
"title": "Optimize Number of Variability Iterations Based on Convergence",
"topics": [
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{
"page": "prevalence_region",
"title": "Regional Pathogen Prevalence Data",
"topics": [
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]
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{
"page": "reset_data_keys",
"title": "Reset Data Keys",
"topics": [
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{
"page": "reset_mctable",
"title": "Reset Monte Carlo Inputs Table",
"topics": [
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]
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{
"page": "reset_sample_design",
"title": "Reset Global Sample Design",
"topics": [
"reset_sample_design"
]
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{
"page": "set_data_keys",
"title": "Set or Get Global Data Keys",
"topics": [
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{
"page": "set_mctable",
"title": "Set or Get Monte Carlo Inputs Table",
"topics": [
"set_mctable"
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{
"page": "set_sample_design",
"title": "Set or Get Global Sample Design",
"topics": [
"set_sample_design"
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{
"page": "test_sensitivity",
"title": "Test Sensitivity Data for Pathogens",
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"page": "tidy_mcnode",
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"title": "Trial Probability and Expected Counts",
"topics": [
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"page": "visNetwork_edges",
"title": "Generate Formatted visNetwork Edge Table",
"topics": [
"visNetwork_edges"
]
},
{
"page": "visNetwork_nodes",
"title": "Generate Formatted Network Node Table for Visualisation",
"topics": [
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]
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{
"page": "which_mcnode",
"title": "Find mcnodes Matching a Condition",
"topics": [
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"page": "which_mcnode_inf",
"title": "Find mcnodes with Infinite Values",
"topics": [
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"page": "which_mcnode_na",
"title": "Find 'mcnode's with Missing Values",
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"page": "wif_match",
"title": "Match Datasets with Differing Scenarios",
"topics": [
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]
}
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