fix selectivity for N1_model = 1 option. Fix infinte residual plot is…

…sue for Ecov
timjmiller · May 2, 2022 · 865ca3d · 865ca3d
1 parent 9ae86ab
commit 865ca3d
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diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,10 @@
 wham 1.0.6.9000
 =========================
 
+### Bug fixes
+
+* Fix age of full selection for N1_model = 1 [issue 56][https://github.com/timjmiller/wham/issues/56].
+
 
 wham 1.0.6 (2022-04-08)
 =========================

diff --git a/R/wham_plots_tables.R b/R/wham_plots_tables.R
@@ -171,7 +171,7 @@ plot.osa.residuals <- function(mod, do.tex=FALSE, do.png=FALSE, fontfam="", res=
       # set plot lims using max residual for any component (easier to compare if all the same)
       ylim.max <- max(abs(range(resids, na.rm=TRUE)))
       if(is.infinite(ylim.max)) {
-        cat("Infinite osa residuals for catch proportions at age in fleet ", f, ", so using +/-10 for range of y axis \n")
+        cat("Infinite osa residuals for catch proportions at age in fleet ", f, ", so using +/-10 for range \n")
         ylim.max = 10
       }
       ylims <- c(-ylim.max, ylim.max)
@@ -333,7 +333,7 @@ plot.osa.residuals <- function(mod, do.tex=FALSE, do.png=FALSE, fontfam="", res=
       # set plot lims using max residual for any component (easier to compare if all the same)
       ylim.max <- max(abs(range(resids, na.rm=TRUE)))
       if(is.infinite(ylim.max)) {
-        cat("Infinite osa residuals for proportions at age in  index ", f, ", so using +/-10 for range of y axis \n")
+        cat("Infinite osa residuals for proportions at age in  index ", f, ", so using +/-10 for range \n")
         ylim.max = 10
       }
       ylims <- c(-ylim.max, ylim.max)
@@ -427,6 +427,10 @@ plot.osa.residuals <- function(mod, do.tex=FALSE, do.png=FALSE, fontfam="", res=
 
       # set plot lims using max residual for any component (easier to compare if all the same)
       ylim.max <- max(abs(range(dat$residual, na.rm=TRUE)))
+      if(is.infinite(ylim.max)) {
+        cat("Infinite osa residuals for Environmental observations in series ", f, ", so using +/-10 for range of y axis \n")
+        ylim.max = 10
+      }
       ylims <- c(-ylim.max, ylim.max)
 
       # 1. trend vs. year

diff --git a/src/wham_v0.cpp b/src/wham_v0.cpp
@@ -715,8 +715,8 @@ Type objective_function<Type>::operator() ()
       if(a==0) NAA(0,0) = exp(log_N1_pars(0));
       else
       {
-        if(a == n_ages-1) NAA(0,a) = NAA(0,a-1)/(1.0 + exp(-MAA(0,a) - exp(log_N1_pars(1)) * FAA_tot(0,a)/FAA_tot(0,n_ages-1)));
-        else NAA(0,a) = NAA(0,a-1)* exp(-MAA(0,a) -  exp(log_N1_pars(1)) * FAA_tot(0,a)/FAA_tot(0,n_ages-1));
+        if(a == n_ages-1) NAA(0,a) = NAA(0,a-1)/(1.0 + exp(-MAA(0,a) - exp(log_N1_pars(1)) * FAA_tot(0,a)/FAA_tot(0,which_F_age(0)-1)));
+        else NAA(0,a) = NAA(0,a-1)* exp(-MAA(0,a) -  exp(log_N1_pars(1)) * FAA_tot(0,a)/FAA_tot(0,which_F_age(0)-1));
       }
     }
     SSB(0) += NAA(0,a) * waa(waa_pointer_ssb-1,0,a) * mature(0,a) * exp(-ZAA(0,a)*fracyr_SSB(0));