From 3e8f058d636ccc1737e17a063e7df4ec03c8106e Mon Sep 17 00:00:00 2001 From: kellijohnson-NOAA Date: Fri, 26 Jul 2024 09:49:26 -0700 Subject: [PATCH] refactor(proportion_female): Remove comments proportion_female was commented out in all of the case studies because setting it was not doing anything to the model. In M2 we will remove the ability to set this parameter vector because it was not doing anything. In the future we will add the feature back. This change does nothing to the results. Simplified a comment in the scamp case study to say that it is fixed at 0.5 instead of you have the ability to estimate it. Part of NOAA-FIMS/FIMS#638 and NOAA-FIMS/seaside-chats#7 --- content/NWFSC-petrale.qmd | 1 - content/PFISC-opakapaka.r | 1 - content/SEFSC-scamp.qmd | 5 ++--- content/SWFSC-sardine.qmd | 1 - content/sardine_fims.R | 2 -- 5 files changed, 2 insertions(+), 8 deletions(-) diff --git a/content/NWFSC-petrale.qmd b/content/NWFSC-petrale.qmd index 24ee3de..c0ac3cd 100644 --- a/content/NWFSC-petrale.qmd +++ b/content/NWFSC-petrale.qmd @@ -275,7 +275,6 @@ population$ages <- ages population$nfleets <- 2 # fleets plus surveys population$nseasons <- nseasons population$nyears <- nyears -# population$proportion_female <- rep(0.5, nages) population$SetMaturity(maturity$get_id()) population$SetGrowth(ewaa_growth$get_id()) diff --git a/content/PFISC-opakapaka.r b/content/PFISC-opakapaka.r index 01d1edf..e31fefe 100644 --- a/content/PFISC-opakapaka.r +++ b/content/PFISC-opakapaka.r @@ -237,7 +237,6 @@ population$ages <- ages population$nfleets <- 2 # fleet plus surveys population$nseasons <- 1 population$nyears <- nyears -# population$proportion_female <- rep(0.5, nages) population$SetMaturity(maturity$get_id()) population$SetGrowth(ewaa_growth$get_id()) diff --git a/content/SEFSC-scamp.qmd b/content/SEFSC-scamp.qmd index bd28b8e..3a9bddb 100644 --- a/content/SEFSC-scamp.qmd +++ b/content/SEFSC-scamp.qmd @@ -370,7 +370,6 @@ population$log_M <- population$estimate_M <- FALSE population$log_init_naa <- log(sca$N.age[1, ]) population$estimate_init_naa <- FALSE -# population$proportion_female <- rep(1.0,nages) #For scamp, assuming all females (see maturity note above) population$nages <- nages population$ages <- ages population$nfleets <- 3 # 2 fleets and 1 survey @@ -713,8 +712,8 @@ if ```FIMS::m_landings``` took fleet as an argument, similar to ```FIMS::m_ageco ## List any issues that you ran into or found -The FIMS feature to assign proportion female at age is not yet functional. FIMS accepts proportion female at age -as input, but does not use that input and instead hard-codes a 50:50 sex ratio. Many stocks +The FIMS feature to assign proportion female at age is not yet functional and +it is hard-coded using a 50:50 sex ratio. Many stocks in the southeast are protogynous hermphrodites, such that individuals start life as females and later convert to males. This life history creates a sex ratio that is tilted toward females for younger ages and males for older ages. diff --git a/content/SWFSC-sardine.qmd b/content/SWFSC-sardine.qmd index 379f833..a2a0b83 100644 --- a/content/SWFSC-sardine.qmd +++ b/content/SWFSC-sardine.qmd @@ -378,7 +378,6 @@ population$ages <- ages population$nfleets <- 2 # fleets plus surveys population$nseasons <- nseasons population$nyears <- nyears -# population$proportion_female <- rep(0.5, nages) population$SetMaturity(maturity$get_id()) population$SetGrowth(ewaa_growth$get_id()) diff --git a/content/sardine_fims.R b/content/sardine_fims.R index 9147312..5715940 100644 --- a/content/sardine_fims.R +++ b/content/sardine_fims.R @@ -566,7 +566,6 @@ population$ages <- ages population$nfleets <- 2 # fleets plus surveys population$nseasons <- nseasons population$nyears <- nyears -# population$proportion_female <- rep(0.5, nages) population$SetMaturity(maturity$get_id()) population$SetGrowth(ewaa_growth$get_id()) @@ -813,7 +812,6 @@ population$ages <- ages population$nfleets <- 2 # fleets plus surveys population$nseasons <- nseasons population$nyears <- nyears -# population$proportion_female <- rep(0.5, nages) population$SetMaturity(maturity$get_id()) population$SetGrowth(ewaa_growth$get_id())