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seqwrap 0.7.0

• Updated documentation for CRAN submission.

seqwrap 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)

seqwrap 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.

seqwrap 0.6.1

• Updated the README

seqwrap 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

seqwrap 0.5.0

News

• Bugfixes

seqwrap 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.

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• The fittin_fun argument in seqwrap has been replaced by modelfun.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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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