Corrected SRR residuals

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ss3om
 Title: Tools for Conditioning Fisheries Operating Models Using Stock Synthesis 3
-Version: 0.5.2.9011
+Version: 0.5.2.9015
 Authors@R: person("Iago", "Mosqueira", email = "[email protected]",
   role = c("aut", "cre"))
 Description: Tools for loading Stock Synthesis (SS3) models into FLR. Used in
@@ -20,7 +20,7 @@ Imports:
   FLFishery,
   mse,
   mvtnorm
-Additional_repositories: http://flr.r-universe.dev
+Additional_repositories: https://flr.r-universe.dev
 Remotes: https://r4ss.r-universe.dev
 BugReports: https://github.com/flr/ss3om/issues
 Suggests:

R/build.R

@@ -172,7 +172,7 @@ buildFLSRss3 <- function(out, ...) {
     "sigma_R_in", "sigma_R_info")]
 
   # EXTRACT elements
-  recruit <- data.table(out$recruit)[era %in% c("Fixed", "Main"),]
+  recruit <- data.table(out$recruit)[era %in% c("Early","Fixed","Main","Fore"),]
   parameters <- data.table(out$parameters)
   dquants <- data.table(out$derived_quants)
   lkhds <- out$likelihoods_used
@@ -213,16 +213,21 @@ buildFLSRss3 <- function(out, ...) {
 
   # rec
   rec <- FLQuant(recruit$pred_rec, dimnames=c(age=0, dms), units="1000")
+
   # ssb
   ssb <- FLQuant(recruit$SpawnBio, dimnames=c(age="all", dms), units="t")
+
   # fitted
   fitted <- FLQuant(recruit$bias_adjusted, dimnames=c(age=0, dms), 
     units="1000")
-  # residuals with bias-correction
-  residuals <- FLQuant(exp(recruit$dev -0.5 * out$sigma_R_in^2),
-    dimnames=c(age=0, dms), units="")
-  if(out$nsexes == 2)
+
+  # residuals with bias-correction  
+  residuals <- FLQuant(exp(recruit$dev - recruit$biasadjuster * 0.5 *
+    out$sigma_R_info[1, 8] ^ 2), dimnames=c(age=0, dms), units="")
+
+  if(out$nsexes == 2) {
     residuals <- expand(residuals, unit=c("F", "M"))
+  }
 
   # SETUP for multiple recruit seasons
   if(out$nseasons > 1) {