CRAN release 4.2.0

• The term 'boot' is now preferred for what used to be called 'bootstrap', mainly to avoid confusion with statistical bootstrap. To taf.boot() is similar to booting a computer, readying the components required for subsequent computations. Help pages now refer to 'boot', but all TAF functions fully support existing analyses that have a legacy 'bootstrap' folder.

• The filename method.R is now an alternative to the default filename model.R script, for analyses where the term 'model' would be misleading or ambiguous.

• Added function clean.boot() to clean the boot directory.

• Added argument 'imports' to taf.session().

• Added argument 'model.script' to taf.skeleton().

• Improved draft.data() so it returns source = {folder} for folders.

• Improved taf.boot() so it returns a logical vector, as documented.

• Improved taf.library() to ensure it returns to the previous working directory. Code contributed by Alexandros Kokkalis.

• Fixed a taf.boot() bug introduced in 4.1.0, checking GitHub references.

• New admin tools, mainly for use inside TAF functions: boot.dir(), boot.dir.inside(), boot.exists(), model.dir(), and model.script().

CRAN release 4.1.0

• Added function taf2html() to convert a TAF table to HTML code.

• Added argument 'pkgs' to taf.skeleton().

• Improved deps() to include Rmd files.

• Improved read.taf() and write.taf() to warn when column names are missing or duplicated and also when a data frame has zero rows. Changed write.taf() so it no longer enforces Dos line endings.

• Improved taf.bootstrap() so it only connects to GitHub when necessary to look up SHA codes.

• Provided alternative spelling variations for several functions:

  • make.all() is equivalent to makeAll()
  • make.taf() is equivalent to makeTAF()
  • source.all() is equivalent to sourceAll()
  • source.dir() is equivalent to sourceDir()
  • source.taf() is equivalent to sourceTAF()
  • taf.boot() is equivalent to taf.bootstrap()

CRAN release 4.0.0

• Package renamed and focus changed to providing general support for the ICES Transparent Assessment Framework.

• Removed all non-base package dependencies.

• Changed sourceAll() and makeAll() so they start by sourcing utilities.R. Code contributed by Hjalte Parner.

CRAN release 3.6.0

• Added function draft.data.script() to create R script template for downloading data with metadata.

• Added function read.bib(), removing 'bibtex' package dependency.

• Added function taf.boot.path() to simplify access to boot folder.

• Added function taf.data.path() to provide path to bootstrap data.

• Added function taf.roxygenise() to build DATA.bib file from Roxygen documentation.

• Added function taf.sources() to extract data and software sources used in a project.

• Improved taf2long() so it works on tibbles.

• Moved all bib entry processing to process.bib().

CRAN release 3.5-0

• Added function clean.data() to selectively clean the bootstrap data folder.

• Added function detach.packages() to detach all packages.

• Added argument 'overwrite' to cp().

• Added arguments 'detach' and 'taf' to sourceTAF().

• Added argument 'taf' to taf.bootstrap().

• Added argument 'remove' to taf.libPaths().

• Added argument 'details' to taf.session().

• Changed taf.bootstrap() to skip download of files if they already exist, and skip bootstrap script if the destination folder already contains files.

• Changed taf.png() to use 'res' rather than 'pointsize', improving consistency between base, lattice, and ggplot2 plots. Code contributed by Iago Mosqueira.

CRAN release 3.4-0

• Added function is.r.package() to check if tar.gz file is an R package.

• Added functions long2xtab() and xtab2long() to convert between table formats.

• Added function taf.libPaths() to add TAF library to search path.

• Added function taf.session() to show session information.

• Added argument 'force' to clean(), clean.library(), and clean.software().

• Added argument 'ignore' to cp().

• Improved clean.software() to remove software folder, not just software files.

• Improved download.github() to store GitHub metadata in the DESCRIPTION file, if the GitHub resource is an R package. Warn if the tar.gz file looks like an R package nested inside a repository.

• Improved taf.bootstrap() to support GitHub references in DATA.bib. Runs taf.install() only when software from GitHub contains a DESCRIPTION file. Added source = {folder} as a special value, similar to source = {file}. Warn if source = {owner/repo@ref} entry is missing the '@ref' part.

• Renamed internal function process.bib() to process.bibfile() and process.inner() to process.entry().

CRAN release 3.3-3

• Moved documentation of metadata (DATA.bib and SOFTWARE.bib) entries from process.bib() help page to https://github.com/ices-taf/doc/wiki/Bib-entries.

CRAN release 3.3-2

• Improved process.bib() so it allows 'access' to be undefined.

CRAN release 3.3-1

• Improved handling of SOFTWARE.bib GitHub entries that have owner/repo/subdir. Code contributed by Ibrahim Umar.

• Improved process.bib() so it verifies that 'access' values match the allowed values.

CRAN release 3.3-0

• Added function get.remote.sha() to look up a SHA reference code on GitHub. Fixed a bug introduced in 3.2-0.

• Improved clean.library() and clean.software() to remove bootstrap/library and bootstrap/software when SOFTWARE.bib file does not exist. Improved clean.software() to remove software file when version does not match SOFTWARE.bib.

• Improved download.github() to handle packages that are nested inside a repository. Set default to quiet=FALSE.

• Changed write.taf() so it no longer converts line endings.

• Removed 'remotes' package dependency.