sbooscripts - SimpleBox Probabilistic and Runoff improvements

Major enhancements include: - Using parallel computing for probabilistic application of SimpleBox - Add option to include correlation between distributions of input parameters - Several smaller fixes and improvements

Major breaking change: Runoff and outflow from w0 (lake) and w1 (river) is now calculated based on precipitation. This changes the outcome and needs to be considered when using this version of SimpleBox for existing scenario's. The change allows for more flexibility in changing landscape scenario's and dividing the watershed across scales.

What's Changed

• Cleaned up README to be shorter. by @MatthiasHofRIVM in https://github.com/rivm-syso/SBooScripts/pull/134
• Update getting started vignette by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/137
• LEON-T case study by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/133
• Update getting started vignette by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/138
• Added missing units and descriptions to Units.csv and reordered the csv's by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/139
• File organisation for casestudies by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/140
• Updated method for pulling LHS samples - pulls only one set of samples per variables and then scales to the different distributions given by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/151
• Fix frag dis aggr by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/149
• Recipe case study by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/144
• Solver update testing by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/157
• Verification acid by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/158
• Solver module update by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/147
• Update metadata by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/160
• update documentation quality document by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/161
• Added selection of default substance again by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/165
• Correlation Latin Hypercube Sampling by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/166
• Solve in parallel by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/154
• Used this for testing fix to k_Sedimentation by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/169
• Momentum measurement comparison by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/170
• Update of advection flows by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/167
• Installation without version control by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/173
• Correlation for LHS documentation by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/175

Full Changelog: https://github.com/rivm-syso/SBooScripts/compare/2024.11.1...2025.10.alpha1

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Published by jormercury 6 months ago

sbooscripts - 2025.04.0

First public release of SimpleBox object oriented in R

This SimpleBox implementation in R replaces the previous ones in spreadsheet format. To get started see the Readme in SBooScripts and the getting started.

What's new

• In this release, the SolverModule was updated. As much of the code needed for solving was transferred from the solver function files to the SolverModule. All solver function files were removed, and the ODE functions were moved to a new file: fGeneral.R. Solving steady state deterministically, steady state probabilistically, dynamic deterministically and dynamic probabilistically now happens inside the SolverModule.
• The ConcentrationModule was deleted, instead there is a function that is called from the solver module which calculates concentrations.
• Standard plot functions were added to SBcore, reachable via: World$PlotConcentration() and World$PlotSolution(). A suitable plot function was created for all solvers.
• The existing solver vignettes were deleted. Instead, there is one solver vignette: Solver use.rmd (link)
• The getting started vignette was updated to work with the updates to SBoo.

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Published by anne-hids 10 months ago

sbooscripts - 2024.11.2

What's Changed

• Update fragmentation and deaggregation process, specific for TRWP and microplastics
• Restructuring of documentation (more to come)
• Case study work described, LEON-T, SUNSHINE, ReCiPe.

Full Changelog: https://github.com/rivm-syso/SBooScripts/compare/2024.11.0...2024.11.2

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Published by jormercury about 1 year ago

sbooscripts - 2024.11.1

This release contains the LEON-T case study files, but is not a final release. It will be merged with the development branch with some clean-up of the code in order to be released.

Important changes relate to: - Added TRWP as particle in the substance list - Changed k_Fragmentation to a species process across A/P to S species. - Default kfrag data now added to SubstanceSubCompartSpeciesData.csv for TRWP and microplastic.

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Published by jormercury about 1 year ago

sbooscripts - 2024.11.0

• Work in DynamicUncertain solver (work with init scripts)
• Documentation, guidance updated
• Some work on case studies
• Fixes

Full Changelog: https://github.com/rivm-syso/SBooScripts/compare/2024.8.0a...2024.8.1

What's Changed

• Vr ah jaap test by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/114
• Ah emission test by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/116
• Vr trapped solver by @valeriederijk in https://github.com/rivm-syso/SBooScripts/pull/117
• Cleaned verified2 by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/119
• Main by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/121
• kdeg for microplastics update by @valeriederijk in https://github.com/rivm-syso/SBooScripts/pull/122
• bug fix microplastic by @valeriederijk in https://github.com/rivm-syso/SBooScripts/pull/123
• Ah vr concentration function by @valeriederijk in https://github.com/rivm-syso/SBooScripts/pull/124
• Vr updatepubscripts2 by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/125
• Solver explanation by @valeriederijk in https://github.com/rivm-syso/SBooScripts/pull/120
• small notes by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/126
• Ah uncertain solver by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/127
• Created vignette explaining the use of the steady state uncertain solver by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/128
• Created testscript for uncertain dynamic solver and testscript for mutatevar. Small updates to other test scripts by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/129
• Guidance document by @MatthiasHofRIVM in https://github.com/rivm-syso/SBooScripts/pull/130
• intro and text edits by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/131
• LEON-T case study, solver and concentration module testing by @anne-hids in https://github.com/rivm-syso/SBooScripts/pull/132
• Cleaned up README to be shorter. by @MatthiasHofRIVM in https://github.com/rivm-syso/SBooScripts/pull/134
• Solvers and Case Studies by @jormercury in https://github.com/rivm-syso/SBooScripts/pull/135

Full Changelog: https://github.com/rivm-syso/SBooScripts/compare/2024.8.0a...2024.8.1

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Published by jormercury over 1 year ago

sbooscripts - SB4xlsx port

This version was verified to not have differences between the spreadsheet and R implementation of SimpleBox of more than 0.1%. The only aspect not ported yet is that of dissolution of particles, so change of species from solid to unbound. This is part of further work https://github.com/rivm-syso/SBoo/issues/148 and will be tested in future updates.

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Published by jormercury over 1 year ago

sbooscripts - SB4xlsx port

Initial release of verified R implementation of SimpleBox. The verification results in <0.1% differences from excel calculations. See verification vignettes.

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Published by jormercury over 1 year ago