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Fix proportion female #654

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What is the feature?

  • Reverts proportion_female to a single constant of 0.5

How have you implemented the solution?

  • Using a constant scalar.

Does the PR impact any other area of the project, maybe another repo?

  • The case studies need to be changed to not set proportion_female.

ChristineStawitz-NOAA and others added 5 commits July 25, 2024 08:32
add tests to ParameterVector

add tests for constructors

passing unit tests for ParameterVector

add more test cases for ParameterVector

add documentation
issue #170: refactor distributions_base

issue #581: add lognormal_lpdf

issue #573: add normal_lpdf

issue #585 add multinomial_lpmf

rename SIMULATE_F to FIMS_SIMULATE_F

rename REPORT_F to FIMS_REPORT_F

Co-authored-by: Matthew-Supernaw-NOAA <matthew.supernaw@noaa.gov>
Co-authored-by: Christine Stawitz - NOAA <ChristineStawitz-NOAA@users.noreply.github.com>
issue #388

convert tests to testthat format in:
   test-unit-rcpp-interface-variable-vector.R

update name of ParameterVector id to id_m

fix parameter order warning

update Rcpp class documentation

refactor operators

-collapses methods using S4 Group Generic Functions

-define methods for Ops, Math, and Summary

-update roxygen methods documentation

add fill_min and fill_max to ParameterVector

update parameter min/max default values
* issue #586

* link new densities to fleet

* modify interface

* fix bugs

* modify tests

* modify nll call in recruitment

* fix recruit eval nll

* add conditional is_na and comment out report

* move tmb pointer here

* fix warnings

* bug fix

* fix segfault issue

* fix nll summing bug

* add macros

* fix interface

* fix tests

* fix tmb distributions test - now passing

* delete tmb_distributions

* Add more normal tests cases -- failing still

* fix observed_values loop

* fix tests and add lognormal test and dimension check

* comment out dimension mismatch error check

---------

Co-authored-by: Matthew-Supernaw-NOAA <matthew.supernaw@noaa.gov>
Co-authored-by: Christine Stawitz - NOAA <ChristineStawitz-NOAA@users.noreply.github.com>
Co-authored-by: Cole-Monnahan-NOAA <cole.monnahan@noaa.gov>
Co-authored-by: Chris Legault <chris.legault@noaa.gov>
Co-authored-by: KyleShertzer-NOAA <KyleShertzer-NOAA@users.noreply.github.com>
* issue #630

* update documentation style
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codecov bot commented Jul 25, 2024

Codecov Report

Attention: Patch coverage is 8.57143% with 64 lines in your changes missing coverage. Please review.

Project coverage is 66.06%. Comparing base (39d0743) to head (577a68b).
Report is 3 commits behind head on main.

Files with missing lines Patch % Lines
inst/include/population_dynamics/fleet/fleet.hpp 0.00% 31 Missing ⚠️
...nst/include/distributions/functors/normal_lpdf.hpp 0.00% 18 Missing ⚠️
...nclude/distributions/functors/multinomial_lpmf.hpp 0.00% 13 Missing ⚠️
...distributions/functors/density_components_base.hpp 0.00% 2 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (39d0743) and HEAD (577a68b). Click for more details.

HEAD has 1 upload less than BASE
Flag BASE (39d0743) HEAD (577a68b)
2 1
Additional details and impacted files
@@             Coverage Diff             @@
##             main     #654       +/-   ##
===========================================
- Coverage   78.88%   66.06%   -12.82%     
===========================================
  Files          36       19       -17     
  Lines        1975      725     -1250     
  Branches      141      196       +55     
===========================================
- Hits         1558      479     -1079     
+ Misses        374      165      -209     
- Partials       43       81       +38     

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@kellijohnson-NOAA kellijohnson-NOAA force-pushed the fix-proportion_female branch 2 times, most recently from 0a82bcb to 8995cd6 Compare July 25, 2024 22:25
Users thought that they could set proportion_female but it was hard-
coded to 0.5 on the back end. Now, it is back to just being a single
value that is hard coded to 0.5. Tests have also changed back to 0.5.
This partially reverts PR #543. And, was talked about in
NOAA-FIMS/seaside-chats#7 and partially addresses #638.
@kellijohnson-NOAA
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Now in cleanup_dev branch to be brought into dev.

@kellijohnson-NOAA kellijohnson-NOAA deleted the fix-proportion_female branch September 1, 2024 00:37
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4 participants