Changes in version 0.7.0 (2026-05-19)                  

  - Updated documentation for CRAN submission.

                        Changes in version 0.6.3                        

  - CRAN-readiness pass:
      - Title case in DESCRIPTION ("Item-by-Item").
      - Bumped Depends: R (>= 4.1) to reflect use of the native pipe in
        vignettes.
      - Replaced a non-canonical CRAN URL in the main vignette.
      - Added @return documentation to seqwrap_summarise(), simcounts(),
        seqwrapResults, and swcontainer.
      - Marked internal helpers (seqwrap_check, fit_fun, fit_fun_lme,
        data_helper, seqwrap_mtf) with @noRd so they no longer generate
        user-facing Rd pages.
      - Replaced seqwrap:::simcounts with seqwrap::simcounts in tests.
      - Fixed handling of cores = "max" and cores = NULL in seqwrap();
        invalid values now error early.
      - Vignettes gracefully skip evaluation when optional Suggests
        packages (including Bioconductor edgeR) are unavailable.
      - Minor typo and roxygen-tag fixes.
  - Removed the Pillon data set (moved to trainome/seqwrappaper)

                        Changes in version 0.6.2                        

  - Bugs
      - Fixed a bug in printing seqwrap_results where the variable k was
        not declared in the function environment.
      - Fixed SUGGEST dependencies for Vignette build.

                        Changes in version 0.6.1                        

  - Updated the README

                        Changes in version 0.6.0                        

  - Bugs
      - Internal fix, passing "library(broom.mixed)" to clusterEvalQ is
        not recommended. Changed to requireNamespace("seqwrap").
      - Internal fix, removed triple colon on exported functions in
        vignette.
      - Removed getwd() in saving model output on disk (seqwrap_mtf.R).
      - Updated @importFrom stats in simcounts2.R

                        Changes in version 0.5.0                        

News

  - Bugfixes

                        Changes in version 0.4.0                        

News

  - Added support for nlme::lme and nlme::gls, see the vignette for the
    use of additional_vars when working with nlme::gls
  - targetdata now supports a list of data frames. Target-specific data
    frames are made available by their column names.

                        Changes in version 0.2.0                        

This update has focused on improving the workflow of using seqwrap. A
new function (seqwrap_compose) allows for the user to collect all data
needed to iterate over targets to fit models. seqwrap can still be
specified using the same arguments, but can also use a swcontainer
created with seqwrap_compose. In seqwrap we only need to specify e.g.
the number of cores and return/save models.

Breaking changes

  - The fittin_fun argument in seqwrap has been replaced by modelfun.

New features

  - seqwrap_compose let's you collect all data elements and arguments
    needed to run iterative modelling with seqwrap without initializing
    it.

  - seqwrap:::simcounts was created as an internal function used in
    testing. It creates a simulated data set of counts based on
    variation across genes in a set of parameters.

  - A new set of classes and methods has been written using the S7 OOP
    system. This means that data is validated to prevent errors in
    setting up the models and data.

  - targetdata is now available as an argument in seqwrap and
    seqwrap_compose making it possible to supply target-wise values used
    in the arguments. E.g. setting the dispersion parameter to a fixed
    value.

  - Using a swcontainer object as the first argument in seqwrap followed
    by a named argument will lead to an update of the swcontainer object
    before any modelling.

  - seqwrap_summarise efficiently combine data frames from summary and
    evaluation functions.

  - and more...

Known limitations

  -