NEWS.md

In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

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
• include NOAA disclaimer in README

ss3sim 1.0.2

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

ss3sim 1.0.1

• fixed 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

• Improved the documentation of many functions
• Updated, added, or removed examples increasing the number of functions with helpful examples
• Update profile_fmsy to allow for relative or absolute paths to directories and provide a better message if verbose = TRUE warning users when they may have not run their model long enough to reach equilibrium
• Remove reliance on tidyverse packages
• Change to 'iteration' instead of 'replicate'
• Update the license to 2019
• Change readme from Rmd to md file
• Deleted the vignette on making functions and updated remaining vignettes
• Remove bias adjustment capability and sampling of conditional age-at-length data; both will eventually be added back to the package with better code
• Remove 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
• Create change_o for the operating model so users can input INIT values for parameters in their operating model rather than having to use a dev vector and the change_tv function
• Implement 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 operating model 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.
• Fix get_results working directory issue
• Deprecate change_year, change_fltname, change_maturity, and pastef
• Reduce restrictions placed on the operating and estimation models used by individual users to allow for multiple fleets, two-sexed models, and other trivial changes such as different fleet names. Feel free to email the developers if there is a feature that you want or one that isn't working as expected because more work in planned in this area.
• Implement the use of more r4ss functions such as SS_readstarter and SS_writestarter to decrease the amount of original code in ss3sim
• Increase the number of functions with examples and update examples to not change the users working directory when possible.
• Change to providing a single model inside the package rather than maintaining models both in the package and in ss3sim/ss3models
• Kelli Faye Johnson is now the maintainer of the package
• updated authors to reflect current contributors
• reduced the complexity of sampling functions by initiating the same protocol for ages and lengths, where each function calls a simple function
• Update functions to work with latest version of r4ss, which is compatible with SS 3.3.0, and change to using the newer executable of SS without the option to specify safe or optimized

ss3sim 0.9.5

• Adds citation to Description field

ss3sim 0.9.4

• Fix compatibility with dplyr 0.6.0
• Fix issue with SS3 binary in development version #239

ss3sim 0.9.3

• Fix LICENSE for CRAN
• Update author list
• Incorporate @cstawitz's additions to the making-models vignette
• Fixes to executable locating for Windows

ss3sim 0.9.2

• Revise package description

ss3sim 0.9.1

• Fix compatibility with dplyr 0.4.3.9001.

ss3sim 0.9.0

• Fix compatibility of vignette with ggplot2 2.0.0.

• Add new data types: conditional age at length, mean length at age, and empirical weight at age.

• sample_agecomp and sample_lcomp now take new effective sample size (ESS) argument as inputs, so the user can weight the composition data as desired.

• 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())

• 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.

• 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 run time, a list of parameters that were on bounds, and recruitment deviations.

• Switch vignette to R Markdown and HTML output (#194)

• Add re-binning within the estimation model of 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)

• Added 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).

• Copy wtatage.ss_new from OM to EM (#163).

• Add Travis CI testing of the package https://travis-ci.org/ss3sim/ss3sim

• Added 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).

• Re-write case file parsing to be more robust and allow for scientific notations (#157).

• Add the option to use the optimized SS executables (#138 and #147) and ability to have spaces in the path name to the executable.

• Add Cole Monnahan's ss3sim plotting functions (#134).

• change_lcomp, change_agecomp, and change_index are now sample_lcomp, sample_agecomp, and sample_index. The old functions point to the new functions with warnings that they are depreciated. Existing code should continue to work (#145).

• ss3sim now requires the SS3 binary to be named according to the version (#138 and #147).

• Bump required version of r4ss to 1.22.1 since 1.22.0 did not export functions that ss3sim needs.

• ss3sim now requires R 3.1.0 since we cannot easily test on earlier versions.

ss3sim 0.8.2

New features

• Added ability to pass seed value to get_recdevs() (#125).

• Added dimension check of user_recdevs to ensure recruitment deviations are supplied for all iterations (#130).

• Vignette now uses a custom Solarized colour theme.

Bug fixes

• Moved vignette data files to the data folder so they are user-accessible after installing the package (#126).

• Updated out-dated paper citations. All papers are now accepted.

• Removed multi-core code in vignette for CRAN checks.

ss3sim documentation built on Nov. 9, 2019, 1:06 a.m.