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NEWS -

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# ss3sim 1.20.2
# News

* Fixed bug in Introduction vignette regarding self-test estimation method
to allow for changing multiple parameters
## ss3sim 1.20.2

# ss3sim 1.20.1
* Fixed bug in Introduction vignette regarding self-test estimation method to
allow for changing multiple parameters

# ss3sim 1.20.0
## ss3sim 1.20.1

## ss3sim 1.20.0

* Updates {ss3sim} to use Stock Synthesis v3.30.20.
* Removes `shQuote()` from `get_bin()` where file paths with spaces are no
longer quoted.

# ss3sim 1.19.3
## ss3sim 1.19.3

* Updates {ss3sim} to use {r4ss} version 1.46.1
* `tune_comps()`
* `run()`, which requires removal of `hess_always` call and instead uses
`extras` call to `run()` to turn the hessian off.

# ss3sim 1.19.2
## ss3sim 1.19.2

* Depends on {stringi}.
* Removes deprecated arguments in `change_e()`.
* Adds `sds_out` to `sample_index()` thanks to the request and review by
Leire Citores. Now, bias in the estimation method regarding the uncertainty
of the index can be tested.
* Adds `sds_out` to `sample_index()` thanks to the request and review by Leire
Citores. Now, bias in the estimation method regarding the uncertainty of the
index can be tested.

# ss3sim 1.19.1
## ss3sim 1.19.1

* Updates `change_q()` to more modern code and removes bugs.
Errors are no longer generated when the fleet does not exist.
* `find_position()` simplifies the code to find the position of
a fleet name in a vector. As well as, the code was moved to an
exported function for others to use outside of `change_q()`.
* Updates `change_q()` to more modern code and removes bugs. Errors are no
longer generated when the fleet does not exist.
* `find_position()` simplifies the code to find the position of a fleet name in
a vector. As well as, the code was moved to an exported function for others
to use outside of `change_q()`.

# ss3sim 1.19.0
## ss3sim 1.19.0

* Bump version to match current version of SS3,
where version numbers of {ss3sim} includes three parts separated by full stops.
The first number represents the major version of {ss3sim}.
The second number is the minor version, i.e.,
third set of digits, of the SS3 executable used in {ss3sim}.
* Bump version to match current version of SS3, where version numbers of
{ss3sim} includes three parts separated by full stops. The first number
represents the major version of {ss3sim}. The second number is the minor
version, i.e., third set of digits, of the SS3 executable used in {ss3sim}.
The third number is the minor version of {ss3sim}.
* Remove dependency on {bbmle} to externally estimate growth.
* Deprecate functions that were not being used in the code base, i.e.,
`cleanup_ss3()`, `get_bin_info()`, `change_rec_devs_par()`, ...
* Does not turn on empirical weight-at-age in EM if sampling weight-at-age data.
Instead, users must specify to use empirical weight-at-age data in their
control file for the estimation method allowing users to sample the data but
not use it if they do not want to.
* Allows for no estimation method via `em_dir = NA`,
creating a way to simulate data quickly.

# ss3sim 1.1.8

* Fix bug related to tidyverse in `sample_comp()` where the composition
data were appended to the data frame as a matrix rather than integrated
as additional columns.

# ss3sim 1.1.7

* Deprecate the use of the log file in `ss3sim_base()`.
The argument `ss3sim_base(print_logfile = FALSE)` has a new default and
will warn users if they have the value set to `TRUE`.
Fully deprecated in {ss3sim} version 1.19.3.
* Create data objects for the OM and EM control and data files.
These files are often used in examples.

# ss3sim 1.1.6

* Deprecate `change_f_par()` which was not being used by any downstream code because
{ss3sim} uses the control file instead of the par file.
* Move Anderson et al. (2014) to a dedicated repository ss3sim/ss3sim_andersonetal.
* Does not turn on empirical weight-at-age in EM if sampling weight-at-age
data. Instead, users must specify to use empirical weight-at-age data in
their control file for the estimation method allowing users to sample the
data but not use it if they do not want to.
* Allows for no estimation method via `em_dir = NA`, creating a way to simulate
data quickly.

## ss3sim 1.1.8

* Fix bug related to tidyverse in `sample_comp()` where the composition data
were appended to the data frame as a matrix rather than integrated as
additional columns.

## ss3sim 1.1.7

* Deprecate the use of the log file in `ss3sim_base()`. The argument
`ss3sim_base(print_logfile = FALSE)` has a new default and will warn users if
they have the value set to `TRUE`. Fully deprecated in {ss3sim} version
1.19.3.
* Create data objects for the OM and EM control and data files. These files are
often used in examples.

## ss3sim 1.1.6

* Deprecate `change_f_par()` which was not being used by any downstream code
because {ss3sim} uses the control file instead of the par file.
* Move Anderson et al. (2014) to a dedicated repository
ss3sim/ss3sim_andersonetal.
* Allow for seas and partition in sampling.

# ss3sim 1.1.5
## ss3sim 1.1.5

# ss3sim 1.1.4
## ss3sim 1.1.4

# ss3sim 1.1.3
## ss3sim 1.1.3

* Drop fleets from sampling regimes using `NA` in the scenario data frame.
* Upgrade to Stock Synthesis 3.30.16.
Expand All @@ -89,22 +91,22 @@
* Allow for no SPR in results file.
* Fix bad param argument in `weight_comps()` with DM.

# ss3sim 1.1.2
## ss3sim 1.1.2

* Control height and width of jittering in `plot_points()`
with `jitter.height` and `jitter.width`.
* Control height and width of jittering in `plot_points()` with `jitter.height`
and `jitter.width`.

# ss3sim 1.1.1
## ss3sim 1.1.1

* Allow for custom name of results files.

# ss3sim 1.1.0
## ss3sim 1.1.0

* Upgrades to Stock Synthesis 3.30.15.03.
* Deprecates case files in favor of `run_ss3sim(simdf =)`.
* Uses more templates for parameter arguments, e.g., `par_int`.
* Simplifies scenarios, iterations, OM/EM to `dir` to increase the usability
of functions outside of {ss3sim}.
* Simplifies scenarios, iterations, OM/EM to `dir` to increase the usability of
functions outside of {ss3sim}.
* Adds `type.convert(as.is = TRUE)` because of R 4.0.
* Uses maxfn 0 to increase speed of tests and run more tests on CRAN check.
* Figures
Expand All @@ -116,13 +118,15 @@
* Adds cumulative mean figure; and
* Allows for fill in boxplots;.
* Results:
* Creates long-data format for results to allow functions to be used by {SSMSE};
* Creates long-data format for results to allow functions to be used by
{SSMSE};
* Removes columns that are not needed;
* Removes row names in summary files;
* Renames rec_dev to increase clarity;
* Creates better grep of management quantities;
* Removes parallel capacity;
* Only reads comp file if present by changing CompFile to `r4ss::SS_output()`;
* Only reads comp file if present by changing CompFile to
`r4ss::SS_output()`;
* Allows for relative directories for {SSMSE}.
* Allows for multiple fisheries in `change_f()` and change fisheries to fleets.
* Increases robustness of `get_success()`.
Expand All @@ -131,35 +135,36 @@
* Starts EM in first year with non-zero catches.
* Reinstate bias adjustment, but once for every iteration.

# ss3sim 1.0.4
## ss3sim 1.0.4

* Add `create_logo()` to generate GitHub logo.
* change [travis configuration](https://towardsdatascience.com/travis-ci-for-r-advanced-guide-719cb2d9e0e5)
* change [travis
configuration](https://towardsdatascience.com/travis-ci-for-r-advanced-guide-719cb2d9e0e5)
to use Xenial.

# ss3sim 1.0.3
## ss3sim 1.0.3

* Realized broken links are because of case not full path and changed
all links back to shorter path with lower-case first letter.
* Realized broken links are because of case not full path and changed all links
back to shorter path with lower-case first letter.
* Includes NOAA disclaimer in README.

# ss3sim 1.0.2
## ss3sim 1.0.2

* Changes link in inst/doc/making-models.html to a more explicit link
using ../doc/introduction.html.
* Changes link in inst/doc/making-models.html to a more explicit link using
../doc/introduction.html.

# ss3sim 1.0.1
## ss3sim 1.0.1

* Fixes broken links in README.md and inst/doc/introduction.html.
* Confirmed that the links in inst/doc/making-models.html are working.

# ss3sim 1.0.0
## ss3sim 1.0.0

* Improves documentation.
* Updates, adds, or removes examples.
* Updates `profile_fmsy()` to allow for relative or absolute paths to directories
and provide a better message if `verbose = TRUE` when users may have
not run their model long enough to reach equilibrium.
* Updates `profile_fmsy()` to allow for relative or absolute paths to
directories and provide a better message if `verbose = TRUE` when users may
have not run their model long enough to reach equilibrium.
* Removes reliance on {tidyverse}.
* Changes to 'iteration' instead of 'replicate'.
* Updates the license to 2019.
Expand All @@ -168,64 +173,63 @@
* Removes bias adjustment capability and sampling of conditional age-at-length
data; both will eventually be added back to the package with better code
* Removes `write_file` argument from many functions and rely on other input
arguments to determine if a file should be written to the disk, such as
if the name of the file is `NULL` then nothing is written.
* Creates `change_o()` for the OM so users can input INIT values
for parameters in their OM rather than having to use a dev
vector and `change_tv()`.
* Implements check of q parameter such that a given q is created from a template
for each survey-like data set included after sampling.
* Manipulate control file rather than par file and delete the par
file from the OM folder.
* Use `merge()` rather than `cbind()` for those instances that the names of the
arguments to determine if a file should be written to the disk, such as if
the name of the file is `NULL` then nothing is written.
* Creates `change_o()` for the OM so users can input INIT values for parameters
in their OM rather than having to use a dev vector and `change_tv()`.
* Implements check of q parameter such that a given q is created from a
template for each survey-like data set included after sampling.
* Manipulate control file rather than par file and delete the par file from the
OM folder.
* Use `merge()` rather than `cbind()` for those instances that the names of the
columns in the results file from the OM do not exactly match the EM.
* Fixes `get_results()` working directory issue.
* Deprecates
* `change_year()`,
* `change_fltname()`,
* `change_maturity()`, and
* `pastef()`.
* Reduces restrictions placed on the OMs and EMs used
by individual users to allow for multiple fleets, two-sexed models, and other
trivial changes such as different fleet names.
* Reduces restrictions placed on the OMs and EMs used by individual users to
allow for multiple fleets, two-sexed models, and other trivial changes such
as different fleet names.
* Implements the use of more {r4ss} functions.
* Increases the number of functions with examples and update examples
to not change the users working directory when possible.
* Provides a single model inside the package rather than
maintaining models both in the package and in ss3sim/ss3models.
* Increases the number of functions with examples and update examples to not
change the users working directory when possible.
* Provides a single model inside the package rather than maintaining models
both in the package and in ss3sim/ss3models.
* Kelli F. Johnson is now the maintainer of the package.
* Updates authors to reflect current contributors.
* Reduces the complexity of sampling functions by initiating the same
protocol for ages and lengths, where each function calls a simple function.
* Reduces the complexity of sampling functions by initiating the same protocol
for ages and lengths, where each function calls a simple function.
* Updates functions to work with latest version of {r4ss}, which is compatible
with Stock Synthesis 3.3.0
* Removes option to specify safe or optimized version of SS3.

# ss3sim 0.9.5
## ss3sim 0.9.5

* Adds citation to Description.

# ss3sim 0.9.4
## ss3sim 0.9.4

* Fixes compatibility with {dplyr} 0.6.0.
* Fixes issue with SS3 binary in development version #239.

# ss3sim 0.9.3
## ss3sim 0.9.3

* Fixes LICENSE for CRAN.
* Updates author list.
* Incorporate @cstawitz's additions to the `making-models` vignette.
* Fixes to executable locating for Windows.

# ss3sim 0.9.2
## ss3sim 0.9.2

* Updates DESCRIPTION.

# ss3sim 0.9.1
## ss3sim 0.9.1

* Fixes compatibility with {dplyr} 0.4.3.9001.

# ss3sim 0.9.0
## ss3sim 0.9.0

* Fixes compatibility of vignette with {ggplot2} 2.0.0.
* Adds new data types:
Expand All @@ -238,49 +242,49 @@
* Add functions to estimate von Bertalanffy growth. These are used internally
by `change_e()`.
* Add `change_maturity()` to alter the SS3 maturity option.
* Check that fleet name in the data frame matches the newest SS3 version
(see `change_fltname()`).
* Check that fleet name in the data frame matches the newest SS3 version (see
`change_fltname()`).
* Add `change_data()`, which prepares the OM .dat files to have the correct
data used for sampling that scenario. It also can manipulate length
bin widths, the SS3 robustification constant, and the SS3 tail
compression value. It takes care of calling the new
`change_tail_compression()` and `change_lcomp_constant()` functions.
data used for sampling that scenario. It also can manipulate length bin
widths, the SS3 robustification constant, and the SS3 tail compression value.
It takes care of calling the new `change_tail_compression()` and
`change_lcomp_constant()` functions.
* Add `calculate_re()` to calculate relative errors on the result data frames.
* Add internal checking of the validity of SS3 .dat files (#203).
* The `get_results()` function now returns the following:
* run time,
* a list of parameters that were on bounds, and
* recruitment deviations.
* Switches vignette to R Markdown and HTML output (#194).
* Adds re-binning within the EM for length and conditional
age-at-length data (#201, #205).
* Adds re-binning within the EM for length and conditional age-at-length data
(#201, #205).
* Add Kelli's `profile_fmsy()` function (#173).
* Merrill added parallel processing option to the get results functions (#171).
* Adds parallel iterations processing option (#168).
* Function argument descriptions now indicate which ones need to be specified
in case files with an asterisk (#161).
* Merrill updated the get-results functions to work without bias runs, to
check for folders that look like ss3sim runs, and to issue a warning if
there are problems reading the files (#155).
* Merrill updated the get-results functions to work without bias runs, to check
for folders that look like ss3sim runs, and to issue a warning if there are
problems reading the files (#155).
* Copy wtatage.ss_new from OM to EM (#163).
* Adds Travis CI testing of the package https://travis-ci.org/ss3sim/ss3sim.
* Adds Travis CI testing of the package <https://travis-ci.org/ss3sim/ss3sim>.
* Adds much more extensive testing of the package in the root `tests` folder.
This is for internal testing only and not bundled with the package (#156).
* Allow for missing arguments in case files. This allows us to add new
arguments to existing functions without breaking old code. A missing
argument gets passed as `NULL` via the `add_nulls()` function (within #148).
arguments to existing functions without breaking old code. A missing argument
gets passed as `NULL` via the `add_nulls()` function (within #148).
* Re-write case file parsing to be more robust and allow for scientific
notations (#157).
* Adds the option to use the optimized Stock Synthesis executables (#138 and #147) and
ability to have spaces in the path name to the executable.
* Adds the option to use the optimized Stock Synthesis executables (#138 and
#147) and ability to have spaces in the path name to the executable.
* Adds Cole Monnahan's plotting functions (#134).
* `change_lcomp()`, `change_agecomp()`, and `change_index()` are now
`sample_lcomp()`, `sample_agecomp()`, and `sample_index()` (#145).
* Requires the SS3 binary to be named according to the version (#138 and #147).
* Bump required version of {r4ss} to 1.22.1.
* Requires R 3.1.0.

# ss3sim 0.8.2
## ss3sim 0.8.2

## New features

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