Package: nimble
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
    compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
    and do basic R-style math, and compiling both models and nimbleFunctions via
    custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte Carlo
    Expectation Maximization, and some other tools. The nimbleFunction system makes
    it easy to do things like implement new MCMC samplers from R, customize the
    assignment of samplers to different parts of a model from R, and compile the
    new samplers automatically via C++ alongside the samplers 'NIMBLE' provides.
    'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New
    distributions and functions can be added, including as calls to external
    compiled code. Although most people think of MCMC as the main goal of the
    'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing
    arbitrary other kinds of model-generic algorithms as well. A full User Manual is
    available at <https://r-nimble.org>.
Version: 1.0.1
Date: 2023-06-15
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Authors@R: c(
    person("Perry", "de Valpine", role = "aut"),
    person("Christopher", "Paciorek", , "paciorek@stat.berkeley.edu", role = c("aut", "cre")),
    person("Daniel", "Turek", role = "aut"),
    person("Nick", "Michaud", role = "aut"),
    person("Cliff", "Anderson-Bergman", role = "aut"),
    person("Fritz", "Obermeyer", role = "aut"),
    person("Claudia", "Wehrhahn Cortes", role = "aut", comment = "Bayesian nonparametrics system"),
    person("Abel", "Rodr\u00edguez", role = "aut", comment = "Bayesian nonparametrics system"),
    person("Duncan", "Temple Lang", role = "aut", comment = "packaging configuration"),
    person("Wei", "Zhang", role = "aut", comment = "Laplace approximation"),
    person("Sally", "Paganin", role = "aut", comment = "reversible jump MCMC"),
    person("Joshua", "Hug", role = "aut", comment = "WAIC"),
    person("Wei", "Zhang", role = "aut", comment = "Laplace approximation"),
    person("Jagadish", "Babu", role = "ctb", comment = "code for the compilation system for an early version of NIMBLE"),
    person("Lauren", "Ponisio", role = "ctb", comment = "contributions to the cross-validation code"),
    person("Peter", "Sujan", role = "ctb", comment = "multivariate t distribution code")
    )
Depends: R (>= 3.1.2)
Imports: methods,igraph,coda,R6,pracma,numDeriv
Suggests: testthat
URL: https://r-nimble.org, https://github.com/nimble-dev/nimble
BugReports: https://github.com/nimble-dev/nimble/issues
SystemRequirements: GNU make
License: BSD_3_clause + file LICENSE | GPL (>= 2)
Copyright: See COPYRIGHTS file.
Note: For convenience, the package includes the necessary header files
        for the Eigen distribution. (This is all that is needed to use
        that functionality.) You can use an alternative installation of
        Eigen on your system or the one we provide. The license for the
        Eigen code is very permissive and allows us to distribute it
        with this package. See <http://eigen.tuxfamily.org/index.php?
        title=Main_Page> and also the License section on that page.
Encoding: UTF-8
Collate: config.R all_utils.R options.R distributions_inputList.R
        distributions_processInputList.R
        distributions_implementations.R BUGS_BUGSdecl.R BUGS_contexts.R
        BUGS_nimbleGraph.R BUGS_modelDef.R BUGS_model.R
        BUGS_graphNodeMaps.R BUGS_readBUGS.R BUGS_macros.R
        BUGS_testBUGS.R BUGS_getDependencies.R BUGS_utils.R
        BUGS_mathCompatibility.R externalCalls.R genCpp_exprClass.R
        genCpp_operatorLists.R genCpp_RparseTree2exprClasses.R
        genCpp_initSizes.R genCpp_buildIntermediates.R
        genCpp_processSpecificCalls.R genCpp_sizeProcessing.R
        genCpp_toEigenize.R genCpp_insertAssertions.R genCpp_maps.R
        genCpp_liftMaps.R genCpp_eigenization.R genCpp_addDebugMarks.R
        genCpp_generateCpp.R RCfunction_core.R RCfunction_compile.R
        nimbleFunction_util.R nimbleFunction_core.R
        nimbleFunction_nodeFunction.R nimbleFunction_nodeFunctionNew.R
        nimbleFunction_Rderivs.R nimbleFunction_Rexecution.R
        nimbleFunction_compile.R nimbleFunction_keywordProcessing.R
        nimbleList_core.R types_util.R types_symbolTable.R
        types_modelValues.R types_modelValuesAccessor.R
        types_modelVariableAccessor.R types_nimbleFunctionList.R
        types_nodeFxnVector.R types_numericLists.R cppDefs_utils.R
        cppDefs_variables.R cppDefs_core.R cppDefs_namedObjects.R
        cppDefs_ADtools.R cppDefs_BUGSmodel.R cppDefs_RCfunction.R
        cppDefs_nimbleFunction.R cppDefs_nimbleList.R
        cppDefs_modelValues.R cppDefs_cppProject.R
        cppDefs_outputCppFromRparseTree.R cppInterfaces_utils.R
        cppInterfaces_models.R cppInterfaces_modelValues.R
        cppInterfaces_nimbleFunctions.R cppInterfaces_otherTypes.R
        nimbleProject.R initializeModel.R parameterTransform.R CAR.R
        Laplace.R MCMC_utils.R MCMC_configuration.R MCMC_build.R
        MCMC_run.R MCMC_samplers.R MCMC_conjugacy.R MCMC_autoBlock.R
        MCMC_RJ.R MCMC_WAIC.R MCEM_build.R crossValidation.R
        BNP_distributions.R BNP_samplers.R NF_utils.R miscFunctions.R
        makevars.R setNimbleInternalFunctions.R registration.R
        nimble-package.r zzz.R
RoxygenNote: 7.2.3
NeedsCompilation: yes
Packaged: 2023-06-15 14:51:41 UTC; paciorek
Author: Perry de Valpine [aut],
  Christopher Paciorek [aut, cre],
  Daniel Turek [aut],
  Nick Michaud [aut],
  Cliff Anderson-Bergman [aut],
  Fritz Obermeyer [aut],
  Claudia Wehrhahn Cortes [aut] (Bayesian nonparametrics system),
  Abel Rodríguez [aut] (Bayesian nonparametrics system),
  Duncan Temple Lang [aut] (packaging configuration),
  Wei Zhang [aut] (Laplace approximation),
  Sally Paganin [aut] (reversible jump MCMC),
  Joshua Hug [aut] (WAIC),
  Wei Zhang [aut] (Laplace approximation),
  Jagadish Babu [ctb] (code for the compilation system for an early
    version of NIMBLE),
  Lauren Ponisio [ctb] (contributions to the cross-validation code),
  Peter Sujan [ctb] (multivariate t distribution code)
Repository: CRAN
Date/Publication: 2023-06-15 19:50:03 UTC
Built: R 4.4.0; armv7--netbsdelf-eabihf; 2024-07-04 23:01:31 UTC; unix
