Log Message:
(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).