Skip to content

Latest commit

 

History

History
92 lines (57 loc) · 3.17 KB

NEWS.md

File metadata and controls

92 lines (57 loc) · 3.17 KB
Raw

ss3sim 0.8.2.99

  • 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 can manipulate population 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)

  • Get results functions now returns run time and a list of parameters that were on bounds.

  • Add ability to work with mean-weight-at-age data (#178)

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

  • Add re-binning within the estimatin model of 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).

  • 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.