Changelog

Source: NEWS.md

mcmodule (development version)

New features

• agg_variates() now accepts custom aggregation functions through agg_func. It also warns when automatic probability aggregation is applied to values greater than one (#98).

• eval_module() now accepts a list of previous mcmodule objects, allowing an expression to use nodes from multiple modules. Conflicting node names must be resolved beforehand, for example with add_prefix().

• create_mcnodes() now supports namespace-qualified distribution functions and functions with required arguments. Bare rpert now resolves explicitly to mc2d::rpert(), with a warning when it is masked by the freedom package (#45).

• mc_network(), visNetwork_nodes(), and get_node_table() gain a percentages argument. Count and time nodes, and stochastic nodes with values exceeding one, are displayed numerically, percentage formatting can also be disabled entirely (#41).

• Added data-raw/water_example.R, which generates the water-supply quantitative microbial risk assessment example data, node specifications, data keys, and pathway expressions.

Bug fixes and improvements

• at_least_one() now combines nodes directly when every input comes from sample_design, avoiding unnecessary key matching (#96).

• create_mcnodes() now constructs mcdata and mcstoc nodes directly instead of generating and parsing R code. Configured transformation expressions continue to be evaluated as R code.

• eval_module() now reports clearer errors for unnamed or duplicated expression blocks and unsupported expression statements.

• Input nodes that match columns in multiple datasets now produce an informative error instead of being assigned to a dataset implicitly.

• mc_filter() and mc_compare() now use name exactly as supplied. suffix is appended only when a name is generated automatically from mc_name (#93).

• mc_network() now provides clearer legend labels and node tooltips and omits duplicated parameter and dependency information (#41).

• mc_summary() now applies digits and sep_keys consistently when returning stored summaries.

• mc_summary() now returns summaries with sequential row names (#94).

• trial_totals() now creates non-sampled input nodes from mctable or module data when sample_design is supplied (#95).

• Added data-raw/imports_example.R to document and standardise generation of the existing imports example datasets and related package objects.

mcmodule 1.3.1

CRAN release: 2026-09-02

Lifecycle

• agg_totals() is now deprecated in favour of agg_variates(). agg_totals() remains available for backwards compatibility, but now issues a lifecycle warning.

Bug fixes

• mc_plot() now draws boxplots above scatter points (#86).

• get_node_list() now uses node_name instead of param_names when filtering in_nodes (#84).

• optim_ndvar() no longer produces warnings related to empty mctable handling (#87).

• mcmodule_converg() tests are now reproducible on CRAN. Tests for non-convergence now set a random seed, because false negatives are expected when using a very limited number of simulations (#87).

Documentation

• Updated the sensitivity analysis vignette and added references.

• Updated README installation instructions to recommend pak::pak() instead of devtools::install_github().

mcmodule 1.3.0

CRAN release: 2026-05-25

New features

• Added support for sensitivity-analysis workflows based on sampling designs (Morris and Sobol), including new helpers mctable_bounds() and mctable_sobol_matrices() (#49).

• eval_module() now supports creating modules using a sampling design (#49).

• Added set_sampling_design() to register a sampling design for use across the workflow (#49).

• Other package functions (mc_keys(), mc_match(), mc_match_data(), trial_totals()) adapted to handle nodes created from sampling designs (#49).

• Added a tornado plot for correlation analysis via mcmodule_tornado() (#49).

• Added mcnode_null_rm() to replace absent nodes by an specific value (similar to mcnode_na_rm()) (#66).

• Added a experimental function to optimize the number of iterations needed for uncertainty convergence optim_ndvar() (#82).

• Improved convergence diagnostics in mcmodule_converg(), including clearer summaries and reporting of non-converged nodes (#49).

• Improved mcmodule_info(), now returns the number of nodes by type and handles more complex module–expression combinations (#70).

Bug fixes

• Fixed a bug in mc_compare() when comparing a total mcnode with multiple data_names (#71).

• Fixed an add_prefix() bug where totals node names were not correctly prefixed (#68).

• Fixed a bug in eval_module() when package::function() nomenclature was used within expressions (#32).

• Renamed filter_suffix to suffix (#77).

Documentation

• Expanded the main package vignette, including sensitivity analysis examples (#49, #70).

• Added sensitivity analysis vignette (#49, #70).

• Expanded mc_compare() documentation with align_uncertainty explanation (#65).

• Updated the package citation and README details (#57, #69).

mcmodule 1.2.0

CRAN release: 2026-03-02

Breaking changes

• create_mcnodes() no longer automatically calculates rpert() mode when not provided. This was not widely used and lacked transparency.

New features

• New mc_filter() filters mcnodes and metadata within mcmodules or using mcnode and data (#53).

• New mc_plot() visualises Monte Carlo results with support for filters and color mapping. This function is experimental and may change in future versions (#4).

• New mcmodule_info() provides comprehensive information about mcmodule structure (#43).

• New mcmodule_corr() calculates correlation matrices for mcmodule variates (#48).

• New mcmodule_converg() assesses convergence of Monte Carlo simulations (#50).

• New mcmodule_to_matrices() converts mcmodules to matrix format (#3).

• New mcmodule_to_mc() adapts mcmodules to mc2d mc objects with optional aggregation of variates (#3).

• eval_module() now supports mcstoc() and mcdata() calls directly within expressions, with proper nvariates handling (#32, #42).

• New which_mcnode() function, with specific wrapers for NA (which_mcnode_na()) and Inf ()which_mcnode_inf()) detection (#35).

Minor improvements and bug fixes

• add_prefix() no longer has issues when mcmodule uses pipes (#51).

• add_prefix() and combine_modules() now handle absent module metadata in nodes.

• create_mcnodes() now handles argument ordering and issues warnings for multiple column matches (#34).

• eval_module() improves handling of mcnode creation from data when nodes are not in mctable or prev_mcmodule (#32).

• get_node_list() now uses custom AST traversal parser and improves mcnode ordering for better network visualization(#39, #40).

• mc_network() fixes bug related to unprefixed inputs in trial_totals output nodes.

• trial_totals() now combines keys from all inputs, not just the main mc_name.

• eval_module()and set_mctable()now can use sensi_baseline and sensi_variation to perfrom One-At-a-Time sensitivity analysis. This will be further developed in future releases (#49).

• Not exported functions mc_summary_keys() and node_list_summary() have been removed.

• The distinction between “exp” and “module” terminology has been clarified throughout the package.

• Function documentation has been extended and harmonised.

• Documentation updated to clarify use of mcstoc() and mcdata() within expressions in eval_module() (#32, #42).

• Vignettes updated to document new analysis functions and features (#3, #4, #32, #48, #49, #50).

• Website links updated to https://nataliaciria.com/mcmodule/.

mcmodule 1.1.1

CRAN release: 2025-11-25

• eval_module() gains keys and overwrite_keys arguments to add keys that aren’t in data_keys or replace existing keys (#23).

• keys_match() now returns early when keys already match, improving performance and fixing occasional bugs (#28).

• Core functions (eval_module(), trial_totals(), dim_match(), at_least_one(), mc_match(), create_mcnodes(), get_node_list()) now support mcnodes with multiple data names, with clear messages indicating defaults (#19).

• create_mcnodes() and eval_module() provide clearer error messages for invalid or missing data (#18).

• mc_match() and mc_match_data() include improved scenario baseline checks and error messages.

mcmodule 1.1.0

CRAN release: 2025-10-22

• Re-submission to CRAN. Removed unexported function examples.

• eval_module() gains match_keys parameter for flexible data-mcnode matching.

• eval_module() now supports multiple prev_mcmodule data names.

• eval_module() improves R function handling within mcmodule expressions.

• trial_totals() now supports agg_suffix skipping.

• at_least_one() improves agg_keys combination.

• Fixed missing agg_suffix handling.

• Fixed dimension matching for aggregated nodes.

• Fixed prefix issues in combined probability nodes.

• NA removal added in key columns.

• Added tests for totals custom names and various dimension matching scenarios.

mcmodule 1.0.1

• Re-submission to CRAN. Removed unexported function examples, replaced dontrun with donttest, added vignette link to DESCRIPTION, and included citation file.

mcmodule 1.0.0

• Initial CRAN submission.