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

@@ -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())

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())

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.
 

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())

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())