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Fix proportion female #654

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wants to merge 6 commits into from
Closed

Fix proportion female #654

wants to merge 6 commits into from

Commits on Jul 25, 2024

  1. add ParameterVector class and expose in Rcpp 

    add tests to ParameterVector

add tests for constructors

passing unit tests for ParameterVector

add more test cases for ParameterVector

add documentation
    @ChristineStawitz-NOAA @Andrea-Havron-NOAA
    ChristineStawitz-NOAA authored and Andrea-Havron-NOAA committed Jul 25, 2024
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  2. refactor distributions 

    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 <[email protected]>
Co-authored-by: Christine Stawitz - NOAA <[email protected]>
    @Andrea-Havron-NOAA @msupernaw @ChristineStawitz-NOAA
    3 people committed Jul 25, 2024
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  3. quality control edits to ParameterVector 

    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
    @msupernaw @Andrea-Havron-NOAA
    msupernaw authored and Andrea-Havron-NOAA committed Jul 25, 2024
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  4. edit connections between fleet and distributions 

    * 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 <[email protected]>
Co-authored-by: Christine Stawitz - NOAA <[email protected]>
Co-authored-by: Cole-Monnahan-NOAA <[email protected]>
Co-authored-by: Chris Legault <[email protected]>
Co-authored-by: KyleShertzer-NOAA <[email protected]>
    @Andrea-Havron-NOAA @msupernaw
    @ChristineStawitz-NOAA @Cole-Monnahan-NOAA @cmlegault @KyleShertzer-NOAA
    6 people committed Jul 25, 2024
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  5. document densities functions 

    * issue #630

* update documentation style
    @Andrea-Havron-NOAA
    Andrea-Havron-NOAA committed Jul 25, 2024
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  6. fix(proportion_female): Remove user interface 

    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
    kellijohnson-NOAA committed Jul 25, 2024
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