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_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_maturity() to alter the SS3 maturity option
Check that fleet name in the data frame matches the newest SS3 version (see
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
calculate_re() to calculate relative errors on the result data frames.
Add internal checking of the validity of SS3 .dat files (#203)
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 ouput (#194)
Add re-binning within the estimation model of length and conditional age-at-length data (#201, #205)
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_index are now
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.
Added ability to pass seed value to
Added dimension check of
user_recdevs to ensure recruitment deviations are supplied for all iterations (#130).
Vignette now uses a custom Solarized colour theme.
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.