Hi r4ss users,
Recent changes merged into the main branch of r4ss on github include
some things that could break your code if you run likelihood profiles,
retrospectives, or jitters. The release notes are pasted below.
Sorry for rolling this out on a Friday afternoon. If you have
problems with the revisions please get in touch via this forum, email,
or GitHub issue. To work around any unexpected issues, you can either
install the CRAN version of r4ss (version 1.44.0) which was released
in May, or install a github version from a couple weeks ago before the
major changes started getting integrated via remotes::install_github("r4ss/r4ss@c7ecd71b").
-Ian
Release notes for r4ss version 1.46.1 copied from https://github.com/r4ss/r4ss/releases:
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
#722
- Functions that run the executable have been renamed:
#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) #718
- Introduces new "simple_small" example model but removes
older
examples, reducing total package size #700
- Uses new columns names in BIOLOGY output #711
- Numerous bug fixes
- Adds dependency on 'tidyr'
- Removes never-completed function
SSbootstrap()
