GMACS version 2.10.01

This new version incorporates implementations made since the GMACS version 2.01.M.09 (#21)

Changes include:

• Updates in the .tpl file:

1. Incorporate implementations made by ** AEP ** for Gmacs 2.01.M.10 - (a) corrected error with retrospective patterns and catch read-in, (d) adding units to read-in, and (c) selex and gradient output.
2. Incorporate implementations made by ** AEP ** for Gmacs 2.10 - Corrected the terminal molt
3. Incorporate implementations made by ** AEP ** for Gmacs 2.10.01 - Added immature N matrices

• Changes in the stock assessment input files
  All the input files (gmacs.dat, .ctl, .dat, .prj) have been written using the gmr package (version 1.3.7).

What's Changed

• Update README.md by @MatthVeron in #20
• Gmacs Version 2.10.01 by @MatthVeron in #21

Full Changelog: V2.01.M.09...V2.10.01

GMACS version 2.01.M.09

This new version incorporates implementations made since the GMACS version 2.01.M.02 (#9)

Changes include:

• Updates in the .TPL file:

1. Corrected a bug with labels for selectivity; Tag emphasis can be real; merged Cody changes wrt time-varying molt probability and functional maturity (GMACS version 2.01.M.03)
2. Added output for the weight units; moved where last functional call, last phase and calculate reference points occurs (GMACS version 2.01.M.04)
3. Fixed indexing for matrix-based weight-at-length; maturity-specific length-weight; formatted output for gmacsall.out; added OFLs by fleet to gmacsall.out (GMACS version 2.01.M.05)
4. Modified to output projected catches; calculated historical mortality for projections (GMACS version 2.01.M.06)
5. Updated the _in files to match the latest version of GMACS; producted inputs files with estimated parameters and expected data (GMACS version 2.01.M.07)
6. Fixed time-varying growth increment and added a trap for negative growth increments in fn calls 0 and 1 (GMACS version 2.01.M.08)
7. Added alternative format for inputting size comps data (GMACS version 2.01.M.09)
8. Renamed BOTHSEX, BOTHMATURE to UNDET_SEX, UNDET_MATURE. Added MALES(=1) macro. Need to refactor MALESANDCOMBINED functionality; removed MALESANDCOMBINED (duplicated MALES); Refactored selectivity assignments and recruitment (no need to loop over h, so cleaner not to); Reformatted some code to add parentheses, replace tabs with spaces, and correctly indent blocks; Replaced o == 1/2 with o == NEW_SHELL/OLD_SHELL, similar for m (GMACS version 2.01.M.09)
9. Reverted selectivity assignaments--needed to loop over h if slx_isex(k) was 0. Added alternative input format for fishery catch data (Update GMACS version 2.01.M.09)

• Changes in the stock assessment input files
  All the input files (gmacs.dat, .ctl, .dat, .prj) have been written using the gmr package (version 1.3.6).

What's Changed

• upgrade GMACS to version 2.01.M.02 by @MatthVeron in #18
• Upgrade GMACS to version 2.01.M.09 by @MatthVeron in #19

Full Changelog: V2.01.M.02...V2.01.M.09

GMACS version 2.01.M.02

This new version incorporates new labels and fix bugs in the Francis wights calculations

Changes include:

• Updates in the .TPL file
  1. Added labels for model output and GMACSALL.STD, mature abundance (SSBA).
  2. Fixed some bugs in the calculaton of Francis weights.

These new version of GMACS works with the gmr version 1.3.6

What's Changed

• Fix a bug in the checking section by @MatthVeron in #9

Full Changelog: V2.01.M...V2.01.M.02

GMACS version 2.01.M

This new version incorporates time varying vulnerability parameters

Changes include:

• Updates in the .TPL file
  1. Vulnerability parameters can be impacted by environmental variables
  2. Random walk deviations can also be applied to vulnerability parameters

These new version of GMACS works with the gmr version 1.3.5

What's Changed

• Upgrade GMACS to version 2.01.M by @MatthVeron in #8

Full Changelog: V2.01.L04...V2.01.M

GMACS version 2.01.L04

This new version integrates the simulation module of GMACS

Changes include:

• Updates in the .TPL file
  1. Corrected the override of the initialization of selectivity
  2. Small changes in the Format of the gmacsAll.out
• Few updates on the UpdateGMACS.R scripts
• some changes in the repo

Full Changelog: V2.01.L03...V2.01.L04

GMACS Version 2.01.L03

This new version integrates the simulation module of GMACS (#7 )

Changes include:

• Development made by Andre Punt to incorporate the simulation module in the gmacsbase.tpl file
• Few updates on the UpdateGMACS.R scripts
• some changes in the repo

What's Changed

• Simulation-estimation approach by @MatthVeron in #7

Full Changelog: V2.01.L02...V2.01.L03

GMACS V 2.01.L02

This new version integrates changes made by William Stockhausen.
Published from a branch created on devel-buck - PR (#6 )

This includes:

• Added commandline input flag "testingflag" to turn on sandbox
• Added alternative data file reader (TCSAM02 format)
• Added lots of diagnostic output when reading input files (1)
• Added ECHOSTR, WriteCtlStr, WriteProjStr macros for (1)
• Reformatted calc_relative_abundance in preparation for adding ability to handle immature data

On top of this I:

• update the DatFileReader.cpp code to make it compatible with multiple OS
• Fix a small bug on the natural mortality set up in the .TPL - We need to work on the initialization of MrelFem if nsex==1
• Added a Developer names section at the beginning of the .TPL to help identify the person implementing the TPL

What's Changed

• Minor version update by @MatthVeron in #6

Full Changelog: GMACS_Version...V2.01.L02

GMACS V 2.01.L

New GMACS Version (#1 ). This includes:

• Update catch likelihood function to use dnorm(). This has been done to unified the way of computing likelihood probabilities.
• Clean a bit the code
• Fix a small bug in the calc_predicted_project function (inverse season_type in the computation of tempZ1)

The new version has been used to run all stock assessments. When comparing with the last available assessment, small changes are observed in the OFL for all species except snow crab.

This version will be updated to set the Penalties on recruitment devs as an option during the last phase.