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Open Sustainable Technology

A curated list of open technology projects to sustain a stable climate, energy supply, biodiversity and natural resources.

Recent Releases of r4ss

r4ss - version 1.51.0

This release contains minor bug fixes, compatibility with the current SS3 release (3.30.23.1), and a few minor improvements.

Thanks to @haighr and @efletcherPIFSC for the inspiration to add this release which should have been more closely timed to the SS3 version 3.30.23 release in October.

The development of r4ss hasn't focused on specific releases and users are encouraged to install the latest version rather than a named release. However, for package dependencies, it's nice to be able to reference a tag or release.

What's Changed

Full Changelog: https://github.com/r4ss/r4ss/compare/v1.50.0...v1.51.0

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA 4 months ago

r4ss - version 1.50.0

As suggested by @k-doering-NOAA in #951, there's value in having releases or tags for dependent packages when a big change breaks things.

The previous release https://github.com/r4ss/r4ss/releases/tag/v1.49.3 has a long automatically generated list of changes since the release before that which was version 1.46.1 in 2022.

The primary change made here is a long-overdue clean up columns in SS_read* functions thanks to @e-perl-NOAA in https://github.com/r4ss/r4ss/pull/945. Most of the changes are as follows:

old new
"Yr" "year"
"Seas" "month" (except where it's actually season and then it's "seas")
"FltSvy" "fleet"
"Gender" "sex"
"Part" "part"
"Ageerr" "ageerr"

Full Changelog: https://github.com/r4ss/r4ss/compare/v1.49.3...v1.50.0

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA 9 months ago

r4ss - v1.49.3

This release is from a few commits ago, just prior to changes in the read/write functions that will be included in a v1.50.0 release that reflects the current state of the code.

What's Changed (automatically generated by github)

New Contributors

Full Changelog: https://github.com/r4ss/r4ss/compare/v1.46.1...v1.49.3

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA 9 months ago

r4ss - version 1.46.1

This release includes a few significant changes that should make the {r4ss} package easier to use and maintain.
However, it includes some breaking changes with renamed functions names and renamed or deprecated input arguments.

The main changes (also described in NEWS.md) are as follows, where details and discussion of the changes are available via the numbered pull requests and issues linked below:

  • Major revamp of all functions that run the Stock Synthesis executable
    https://github.com/r4ss/r4ss/pull/722
    • Functions that run the executable have been renamed:
      https://github.com/r4ss/r4ss/issues/723:
      • run_SS_models() -> run() (now has defaults which allow you to
        simply call run() in the current working directory as well as
        and better support for having the Stock Synthesis executable in
        your path)
      • SS_profile() -> profile()
      • SS_doRetro() -> retro()
      • SS_RunJitter() -> jitter()
      • SS_tune_comps() -> tune_comps()
    • Functions have more consistent inputs (e.g., always dir instead of
      mydir, File, or masterdir, and now defaulting to the current
      working directory)
    • Input show_in_console = FALSE can be used with all these functions
      and will pipe output to a text file keeping R console cleaner while
      models run
  • Deprecates functions that relate to 3.24 models, like
    SS_readdat_3.24() (although SS_output() is still compatible back
    to version 3.24) https://github.com/r4ss/r4ss/pull/718
  • Introduces new "simple_small" example model but removes older
    examples, reducing total package size https://github.com/r4ss/r4ss/pull/700
  • Uses new columns names in BIOLOGY output https://github.com/r4ss/r4ss/pull/711
  • Numerous bug fixes
  • Adds dependency on 'tidyr'
  • Removes never-completed function SSbootstrap()

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA over 2 years ago

r4ss - version 1.44.0

This {r4ss} release matches a version just added to CRAN today (at https://cran.r-project.org/web/packages/r4ss/index.html). It works with Stock Synthesis version 3.30.19.01 (released 15 April 2022) and should be compatible back through the 3.24 versions of SS3. The associated SS3 release is available at https://github.com/nmfs-stock-synthesis/stock-synthesis/releases.

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA almost 3 years ago

r4ss - version 1.43.0

This r4ss release works with Stock Synthesis version 3.30.17.00 (released 11 June 2021) and should be compatible back through the 3.24 versions of SS. The associated SS release is available on VLab and at https://github.com/nmfs-stock-synthesis/stock-synthesis/releases/tag/v3.30.17.

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA almost 4 years ago

r4ss - version 1.38.0

This release works with Stock Synthesis version 3.30.15.00 and should be compatible back through the 3.24 versions of SS.

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA about 5 years ago

r4ss - version 1.36.1

This release corresponds to version 1.36.1 available CRAN published 18 October 2019.
Works (as far as we know) with SS versions 3.24 through 3.30.14.07.

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA over 5 years ago

r4ss - version 1.35.0 works with SS version 3.30.13

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA about 6 years ago

r4ss - r4ss version used for the 2019 Pacific Hake stock assessment

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA about 6 years ago

r4ss - r4ss version 1.27.0 includes many changes to work with 3.30

Designating current state of r4ss code with a GitHub release number "v1.27.0" which will allow anyone working on west coast groundfish assessments which are due soon to reference this version of r4ss and install the package associated with this current state using the command devtools::install_github("r4ss/r4ss", ref="v1.27.0"). Future changes within this cycle for west coast groundfish will surely occur in which case I will try to remember to assign new version numbers and releases, but they can also be restored using the SHA code associated with each commit, as in devtools::install_github("r4ss/r4ss", ref="1cdef4e").

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA almost 8 years ago

r4ss - assorted minor changes since last release

At this point, not everything has been updated for upcoming SS version 3.30 but it's been a while since the last numbered release so it's good to get something out there while things are mostly working.

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA over 8 years ago

r4ss - version 1.24.0 on CRAN

First version released to CRAN since 1.22.1. See NEWS.md for changes.
No known bugs.

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA over 9 years ago

r4ss - 1.23.1, no known bugs, March 24, 2015,

Providing a release number closer to the version that may be used for 2015 Darkblotched and Canary Rockfish stock assessments.

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA about 10 years ago

r4ss - variety of improvements, works with SSv3.24U

Largest changes since v1.22.1 are in composition plots. Some aggregate plots are currently not yet implemented in new code.

Biosphere - Marine Life and Fishery - R
Published by iantaylor-NOAA over 10 years ago