Package: BLMEngineInR 0.1.7

Kelly Croteau

BLMEngineInR: Biotic Ligand Model Engine

A chemical speciation and toxicity prediction model for the toxicity of metals to aquatic organisms. The Biotic Ligand Model (BLM) engine was originally programmed in 'PowerBasic' by Robert Santore and others. The main way the BLM can be used is to predict the toxicity of a metal to an organism with a known sensitivity (i.e., it is known how much of that metal must accumulate on that organism's biotic ligand to cause a physiological effect in a certain percentage of the population, such as a 20% loss in reproduction or a 50% mortality rate). The second way the BLM can be used is to estimate the chemical speciation of the metal and other constituents in water, including estimating the amount of metal accumulated to an organism's biotic ligand during a toxicity test. In the first application of the BLM, the amount of metal associated with a toxicity endpoint, or regulatory limit will be predicted, while in the second application, the amount of metal is known and the portions of that metal that exist in various forms will be determined. This version of the engine has been re-structured to perform the calculations in a different way that will make it more efficient in R, while also making it more flexible and easier to maintain in the future. Because of this, it does not currently match the desktop model exactly, but we hope to improve this comparability in the future.

Authors:Robert Santore [aut], Kelly Croteau [aut, cre]

BLMEngineInR_0.1.7.tar.gz
BLMEngineInR_0.1.7.tar.gz(r-4.7-arm64)BLMEngineInR_0.1.7.tar.gz(r-4.7-x86_64)BLMEngineInR_0.1.7.tar.gz(r-4.6-arm64)BLMEngineInR_0.1.7.tar.gz(r-4.6-x86_64)
BLMEngineInR_0.1.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
BLMEngineInR/json (API)
NEWS

# Install 'BLMEngineInR' in R:
install.packages('BLMEngineInR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblascpp

1.70 score 1 scripts 503 downloads 37 exports 6 dependencies

Last updated from:b9fd33d5e7. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK207
linux-devel-x86_64OK200
source / vignettesOK219
linux-release-arm64OK203
linux-release-x86_64OK191
wasm-releaseOK178

Exports:AddComponentsAddCriticalValuesAddDefCompsAddInCompsAddInLabsAddInVarsAddMassCompartmentsAddPhasesAddSpecialDefsAddSpeciesBlankProblemBlankWHAMBLMCheckBLMObjectCHESSConvertWHAMVThermoFileConvertWindowsParamFileDefineProblemDefineWHAMGetDataListCATMatchInputsToProblemReadInputsFromFileRemoveComponentsRemoveCriticalValuesRemoveDefCompsRemoveInCompsRemoveInLabsRemoveInVarsRemoveMassCompartmentsRemovePhasesRemoveSpecialDefsRemoveSpeciesWriteDetailedFileWriteInputFileWriteParamFileWriteWHAMFile

Dependencies:cliopenxlsxRcppRcppArmadillostringizip

Readme and manuals

Help Manual

Help pageTopics
All NIST_20170203.dbs reactionsAll_NIST20170203_reactions
All WATER23.dbs reactionsAll_WATER23_reactions
Make a blank input problem list objectBlankProblem
Make a blank WHAM parameter list objectBlankWHAM
Run the Biotic Ligand ModelBLM
Carbonate system problemcarbonate_system_problem
Check an object for use in the BLMEngineInR packageCheckBLMObject
CHemical Equilibria in Soils and SolutionsCHESS
Common Parameter DefinitionsCommonParameterDefinitions
Add or remove components in the problemAddComponents AddDefComps AddInComps Components RemoveComponents RemoveDefComps RemoveInComps
Convert from a WHAM V thermodynamic database fileConvertWHAMVThermoFile
Convert From a Windows BLM Parameter FileConvertWindowsParamFile
Edit Critical Values TableAddCriticalValues CriticalValues RemoveCriticalValues
Cu problem with only inorganic componentsCu_full_inorganic_problem
Copper problem with WHAM V organic matterCu_full_organic_problem
Define the speciation problemDefineProblem
Read a WHAM file and make a WHAM listDefineWHAM
Get data from the input fileGetData
Add or remove input labels in a problemAddInLabs InLabs RemoveInLabs
Add or remove a input variables in a problemAddInVars InVars RemoveInVars
List Critical Accumulation TableListCAT
Add or remove mass compartments in a problemAddMassCompartments MassCompartments RemoveMassCompartments
Match Inputs to ProblemMatchInputsToProblem
Molecular and atomic weightsMW
Ni problem with WHAM V organic matterNi_full_organic_problem
Ni problem with WHAM V organic matter and NiHCO3 toxicNi_HCO3_full_organic_problem
Add or remove phase reactions in a problemAddPhases Phases RemovePhases
Read a BLM Input FileReadInputsFromFile
Add or remove species definitionsAddSpecialDefs RemoveSpecialDefs SpecialDefs
Add or remove a species reactions in a problemAddSpecies RemoveSpecies Species
Water mass compartment only problemwater_MC_problem
Water-only problemwater_problem
Write a VERY Detailed Output FileWriteDetailedFile
Write a BLM input fileWriteInputFile
Write a BLM Parameter FileWriteParamFile
Write a WHAM Parameter FileWriteWHAMFile