Changes in version 1.1.4                        

  - Fixed the posterior mean of Sigma returned by uncollapsePibble(...,
    ret_mean = TRUE) to use the correct inverse-Wishart mean.
  - Fixed OpenMP sampling in the uncollapse routines so posterior draws
    are reproducible across ncores for a fixed seed and no longer depend
    on overlapping thread RNG streams.
  - Added input validation to the multinomial-Dirichlet bootstrap so
    Dirichlet concentration parameters must be positive and finite.

                        Changes in version 1.1.3                        

  - Replaced explicit integer sequences with seq_len() and seq_along()
    for improved robustness.

                 Changes in version 1.1.1 (2024-06-05)                  

  - Fixing a minor bug in the configure script

                 Changes in version 1.1.0 (2024-05-30)                  

  - Updating the basset model to allow for additive Gaussian processes.
  - Updating the random seed generation.
  - Removed maltipoo as an export. There were a few small changes to
    names of internal maltipoo functions (e.g., "verify.maltipoo" became
    "verify_maltipoo").
  - Updating the configure script to a compile but that occured when
    OpenMP is present but R is not configured to use it.
  - Fixed a few small bugs (predicting with one sample; wrong constant;
    etc.).

                 Changes in version 1.0.4 (2023-03-24)                  

  - changing default optimizer (lbfgs rather than adam), adam is more
    sensitive to random seed
  - adding new r2 methods for calculating Bayesian R2 for pibble and
    basset models
  - predict.bassetfit now accepts a newdata=NULL argument to predict on
    training set

bug fixes

  - fixing a few discrepancies with base R commands (print, summary,
    etc).

                 Changes in version 1.0.3 (2022-08-23)                  

bug fixes

  - Updating documentation under the newest version of R (4.2.1)

                 Changes in version 1.0.2 (2022-07-06)                  

bug fixes

  - Removing a timing test because it is irrelevant and can fail under
    certain set-ups.

                 Changes in version 1.0.1 (2022-05-17)                  

bug fixes

  - Changing phyloseq from imports to depends, was causing issues
    installing from CRAN.
  - Fixing bug in configure.ac that was causing openmp parallelization
    to not work on some machines.

                 Changes in version 1.0.0 (2022-02-16)                  

More changes to make the final push for CRAN! Changes include:

  - Updating the description file to match CRAN's standards
  - Removing the dependency to driver
  - Linking the one remote package (MicrobeDS) to a separate CRAN-like
    Github repo using the "drat" package. This is to match CRAN's policy
    against no use of "Remotes".
  - Precomputing the longer running vignettes, cutting R CMD check times
    in half. The original vignettes can be found in the vignettes folder
    with a ".orig" extension for reproducibility.

                       Changes in version 0.1.14                        

  - More changes to prepare for version 0.2 (and CRAN soon), including:
  - Lots of cleaning of small warnings and notes
  - Fixing erorrs with the base plot function
  - Cleaning up some manual entries
  - Fixing the errors posted on Github (to_ilr among others)

                       Changes in version 0.1.13                        

  - tons of tiny changes to prepare for version 0.2 (and ultimately
    CRAN) featured changes include:
  - plot and coef methods for *fit objects now abide by CRAN generic
    naming scheme - may cause some problems if prior code had positional
    arguments to these functions
  - now being tested using travis integration (vignettes not tested
    there due to time constraints)
  - merged Kim's fixes to maltipoo code (will almost certainly change
    maltipoo results; there had been a bug in prior versions)
  - Internally stored mallard and mallard_family data now import as
    mallard and mallard_family rather than both importing as ps. Solved
    a R CMD CHECK warning.
  - Lots of tiny updates to documentation

                       Changes in version 0.1.12                        

  - orthus added for jointly fitting multinomial and gaussian data
    (e.g., 16S microbiome and metabolomics data)

                       Changes in version 0.1.11                        

  - Kim fixed windows installation problems (Thanks Kim!)
  - Fixed bug in predict that was effecting ppc
  - Fixed error when pars!=NULL in summary
  - lambda_to_iqlr now had default behavior when focus.cov=NULL
  - Fixed issue with Xi=NULL in pibblefit when trying to transform
  - small changes to make pibble wrapper around c++ functions faster

                       Changes in version 0.1.10                        

  - basset added for fitting non-linear regression using fido
  - numerous changes to make installation easier
  - Added a NEWS.md file to track changes to the package.