---
- branch: MAIN
  date: Sun Jun 11 03:24:46 UTC 2023
  files:
  - new: '1.7'
    old: '1.6'
    path: pkgsrc/math/R-nimble/Makefile
    pathrev: pkgsrc/math/R-nimble/Makefile@1.7
    type: modified
  - new: '1.7'
    old: '1.6'
    path: pkgsrc/math/R-nimble/distinfo
    pathrev: pkgsrc/math/R-nimble/distinfo@1.7
    type: modified
  id: 20230611T032446Z.9ccbd784765478f8569da629bf1b63c618b3d7fb
  log: |
    (math/R-nimble) Updated 0.13.1 to 1.0.0

    #                            CHANGES IN VERSION 1.0.0 (May 2023)

    This release introduces tools for automatic differentiation in NIMBLE.

    ## USER LEVEL CHANGES

    - Add tools for automatic differentiation. Functionality includes:

        -- The ability to differentiate nimbleFunctions with respect
        to input arguments in a flexible way.

        -- The ability to differentiate `model$calculate()` calls
        with respect to model node elements.

        -- Functionality that enables Hamiltonian Monte Carlo (provided in the
        `nimbleHMC` package).

        -- A parameter transformation system to work in unconstrained parameter
        spaces when model parameters have constrained domains.

    - Add Laplace approximation algorithm, allowing a user to approximate
    the marginal likelihood (integration/marginalizing over random effects/
    latent process values) and find the MLE.

    - Improve aspects of WAIC (PR #1256):

        -- Provide aggregate and per-chain WAIC when `perChainWAIC` is `TRUE`.

        -- Report number of `pWAIC` values greater than 0.4.

        -- Warn user if WAIC is enabled but not set to `TRUE` in `runMCMC`.

        -- Improve clarity in `help(WAIC)`.

    - Reduce the default adaptation interval for the `AF_slice` sampler to 200.

    - Improved control of `addSampler` method of MCMC
    configuration objects (PR #1293):

        -- `expandTarget` argument controls whether nodes specified in
           `target` undergo expansion via `expandNodeNames`, adding a
           separate sampler instance for each resulting node.

        -- When `expandTarget = TRUE`, the `scalarComponents` argument is
           passed as the `returnScalarComponents` argument to `expandNodeNames`.

        -- Removed `nodes` argument as redundant.  Target nodes are
           uniquely specified using the `target` argument.

    - Improve handling of resetting of scale when `adaptive=FALSE` (PR #1275).

    - Allow `dcat` to have a `prob` vector of length 1 (PR #1251).

    - Add error trapping for MCMC `thin` argument not positive and integer-valued
    (PR #1250).

    - Enhance discussion of MCMC initialization in the User Manual (issue #1247).

    - Enhance discussion of indexing in loops and variables in User Manual,
    including differences from JAGS.

    - Rework language in `help(buildMCMC)` to improve clarity.

    - Add information on predefined nimbleLists to the User Manual.

    - Improve error message when user-defined distribution has incorrect dimension
    for `x`.

    - Improve error message when mistakenly using `T()` in deterministic rather than
      stochastic model declaration.

    - Improve error-trapping when a loop index is incorrectly used in indexing
    a block of a variable (PR #1289).

    - Error trap use of reduction operations on scalars (PR #1281).

    - Error trap some cases of incorrect return type in user-defined simulation
    ('r') functions (PR #1280).

    - Error trap case where a variable name is also used as a loop index variable
    (PR #1278).

    - Error trap setting deterministic nodes as data in `setData` (PR #1269).

    - Better error trap of wrong size/dimensions of in `setInits` (PR #1260).

    - Export `clearCompiled`, allowing users to clear compiled objects and unload
    the shared library produced during nimble's compilation process (on non-Windows
    operating systems).

    ## BUG FIXES

    - Fix bug producing integer overflow in `getDependencyPathCountOneNode`
    and improve efficiency of checking maximum number of paths in conjugacy
    checking (PR #1322).

    - Fix long-standing memory leak in `dinvwish_chol` (PR #1320).

    - Fix bug giving incorrect results for `runCrossValidate`, when using the
    default MSE loss function and any user-defined loss functions,
    but not the 'predictive' loss function. Also, calculate loss when using
    the predictive loss using the compiled model rather than the uncompiled model.
    (PRs #1298, #1299).

    - Fix bug in conjugacy checking that caused incorrect identification of
    conjugate relationships with subsets and supersets of multivariate nodes,
    as well as inconsistent slices of multivariate nodes (PR #1290).

    - Fix `runMCMC` to reset the WAIC state when rerun (PR #1256).

    - Fix reset mechanism for WAIC so that one can get WAIC from all the samples
    in a chain that is created by multiple calls to the MCMC `$run` method even
    when `getWAIC` is called in the middle (PR #1310).

    - Fix bug affecting `d=2` case in uncompiled `RW_lkj_corr_cholesky` sampler
    (PR #1273).

    - Fix aliasing issue arising in assignment operations such as
    `nf$a <- nf$a[1:3]` (PR 1301).

    - Fix assignment into a block of a model variable (PR #1300).

    - Fix compilation error when using `nimSeq` with integers (PR #1282).

    - Fix scoping of argument evaluation for `replaceSamplers` method (PR #1287).

    - Fix a corner case where particular indexing in model code prevents model
    building (PR #1279).

    - Fix handling of right-hand side only nodes so not flagged as deterministic
    (issue #1269).

    - Error trap and fix a bug in handling particular cases in list-like subsetting
    (PR #1259).

    - Make optimDefaultControlList handle default values completely and with
      consistent compiled and uncompiled behavior.

    - make nimOptim respect parscale control parameter.

    - Update manual installation chapter and `INSTALL` links to gfortran on MacOS.

    ## DEVELOPER LEVEL CHANGES

    - Take `nimbleCppADbaseClass` out of `libnimble.a` and instead make a
    session-specific .o file from it to address AD-related crashes on some OSes. (PR
    #1318)

    - Remove `nimOptim_model` functionality. This fixes build warning on MacOS
      involving `nimOptim` (PR #1276).

    - Update `Eigen` copyright dates.

    - Fix invisible return of `NULL` in nimbleFunctions without explicit return
    statements (PR #1254).

    - Fix inconsistent use of offset in internal conversion functions (PR #1277).

    - Remove references to unsupported `trace` (issue #1262).

    #                            CHANGES IN VERSION 0.13.2 (May 2023)

    ## DEVELOPER LEVEL CHANGES

    - Remove code triggering Windows warnings about writing bytes into region of
      size 0 by modifying `setLength`.

    - Remove use of C++11 standard, per CRAN requirements. As part of this, replace
      use of `std::ptr_fun` (PR #1292).
  module: pkgsrc
  subject: 'CVS commit: pkgsrc/math/R-nimble'
  unixtime: '1686453886'
  user: mef