Package: RBaM 1.1.2

Benjamin Renard

RBaM: Bayesian Modeling: Estimate a Computer Model and Make Uncertain Predictions

An interface to the 'BaM' (Bayesian Modeling) engine, a 'Fortran'-based executable aimed at estimating a model with a Bayesian approach and using it for prediction, with a particular focus on uncertainty quantification. Classes are defined for the various building blocks of 'BaM' inference (model, data, error models, Markov Chain Monte Carlo (MCMC) samplers, predictions). The typical usage is as follows: (1) specify the model to be estimated; (2) specify the inference setting (dataset, parameters, error models...); (3) perform Bayesian-MCMC inference; (4) read, analyse and use MCMC samples; (5) perform prediction experiments. Technical details are available (in French) in Renard (2017) <https://hal.science/hal-02606929v1>. Examples of applications include Mansanarez et al. (2019) <doi:10.1029/2018WR023389>, Le Coz et al. (2021) <doi:10.1002/hyp.14169>, Perret et al. (2021) <doi:10.1029/2020WR027745>, Darienzo et al. (2021) <doi:10.1029/2020WR028607> and Perret et al. (2023) <doi:10.1061/JHEND8.HYENG-13101>.

Authors:Benjamin Renard [aut, cre, cph], INRAE [fnd], Ministère de la Transition Ecologique - SCHAPI [fnd]

RBaM_1.1.2.tar.gz
RBaM_1.1.2.zip(r-4.7-any)RBaM_1.1.2.zip(r-4.6-any)RBaM_1.1.2.zip(r-4.5-any)
RBaM_1.1.2.tgz(r-4.6-any)RBaM_1.1.2.tgz(r-4.5-any)
RBaM_1.1.2.tar.gz(r-4.7-any)RBaM_1.1.2.tar.gz(r-4.6-any)
RBaM_1.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RBaM/json (API)

# Install 'RBaM' in R:
install.packages('RBaM', repos = c('https://bam-tools.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bam-tools/rbam/issues

Datasets:

On CRAN:

Conda:

bayesian-inferencemodelingstatisticsuncertainty

4.63 score 1 stars 1 packages 47 scripts 365 downloads 39 exports 39 dependencies

Last updated from:5108898da7. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK157
source / vignettesOK201
linux-releaseOK145
macos-releaseOK174
macos-oldrelOK185
windows-develOK101
windows-releaseOK75
windows-oldrelOK93
wasm-releaseOK113

Exports:BaMblocDiagdatasetdensityPlotdownloadBaMgetAwPfromBathygetCataloguegetInitPargetNamesgetParNamesgetPathToBaMllfunk_iid_Gaussianllfunk_iLinear_GaussianlogLikelihood_BaMlogPosterior_BaMlogPosterior_BaM_wrappedlogPrior_FlatMCMC_AMMCMC_OAATmcmcCookingmcmcOptionsmcmcSummarymodelparameterparameter_VARpredictionreadMCMCremnantErrorModelresidualOptionsrunModelrunOptionssetInitParsetPathToBaMSPD_estimateSPD_getVARpropertiestracePlotviolinPlotwritePredInputsxtraModelInfo

Dependencies:clicpp11crayondplyrfarvergenericsggplot2gluegridExtragtablehmsisobandlabelinglifecyclemagrittrmvtnormpillarpkgconfigprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6RColorBrewerrjsonrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Run BaMBaM
Bloc-diagonal matrix constructorblocDiag
dataset object constructor.dataset
densityPlotdensityPlot
BaM downloaderdownloadBaM
Bathymetry interpretergetAwPfromBathy
BaM cataloguegetCatalogue
Get initial valuesgetInitPar
Get object namesgetNames
Get parameter namesgetParNames
Path to BaMgetPathToBaM
Log-likelihood function: iid Gaussianllfunk_iid_Gaussian
Log-likelihood function: independent-linear Gaussianllfunk_iLinear_Gaussian
BaM log-likelihoodlogLikelihood_BaM
BaM log-posteriorlogPosterior_BaM
BaM log-posteriorlogPosterior_BaM_wrapped
Log-prior function: improper flat priorlogPrior_Flat
Adaptive Metropolis samplerMCMC_AM
Adaptive One-At-A-Time Metropolis samplerMCMC_OAAT
mcmcCooking constructor.mcmcCooking
mcmcOptions object constructor.mcmcOptions
mcmcSummary constructor.mcmcSummary
Meyras GaugingsMeyrasGaugings
model object constructor.model
parameter object constructor.parameter
Varying parameter object constructor.parameter_VAR
prediction object constructor.prediction
MCMC ReaderreadMCMC
remnantErrorModel object constructor.remnantErrorModel
residualOptions constructor.residualOptions
Run ModelrunModel
runOptions constructor.runOptions
Sauze GaugingsSauzeGaugings
Set initial valuessetInitPar
Path to BaMsetPathToBaM
Estimation of a BaRatin-SPD modelSPD_estimate
Properties of VAR parametersSPD_getVARproperties
dataset to stringtoString.dataset
mcmcCooking to stringtoString.mcmcCooking
mcmcOptions to stringtoString.mcmcOptions
mcmcSummary to stringtoString.mcmcSummary
model to stringtoString.model
parameter to stringtoString.parameter
parameter_VAR to stringtoString.parameter_VAR
prediction to stringtoString.prediction
remnantErrorModel to stringtoString.remnantErrorModel
residualOptions to stringtoString.residualOptions
runOptions to stringtoString.runOptions
MCMC reportingtracePlot
Evolution of two populationstwoPopulations
violinPlotviolinPlot
Write prediction inputswritePredInputs
xtraModelInfo constructor.xtraModelInfo