Maturity not 0 if multiple birthseas, but only seasson 1 is really us…

…ed in SRR

R/build330.R

@@ -61,7 +61,8 @@ buildFLSss330 <- function(out, morphs=out$morph_indexing$Index, name=out$Control
   wt <- ss3wt30(endgrowth, dmns, birthseas=1)
 
   # MAT
-  mat <- ss3mat30(endgrowth, dmns, spawnseas=out$Spawn_seas,
+  # NOTE birthseas from morph_indexing
+  mat <- ss3mat30(endgrowth, dmns, spawnseas=out$morph_indexing$BirthSeas,
     option=out$Maturity_option)
 
   # CORRECT Mat*Fecund to by unit body weight

R/check.R

@@ -82,6 +82,7 @@ extractFbar <- function(out) {
 
   # 
   } else {
+    fbar <- fbar$Value
     warning(paste("Returned F is relative to", out$F_report_basis))
   }
   return(FLQuant(fbar, dimnames=list(age="all",

R/load.R

@@ -48,7 +48,7 @@ loadOMS <- function(dir=".", subdirs=list.dirs(path=dir, recursive=FALSE),
 
 	# LOOP over subdirs
   out <- foreach(i=seq(length(subdirs)),
-    .final = function(x) setNames(x, seq(length(subdirs))),
+    .final = function(x) setNames(x, nm=seq(length(subdirs))),
     .inorder=TRUE, .errorhandling="remove") %dopar% {
 
     if(progress)

R/read.R

@@ -66,17 +66,17 @@ readFLomss3 <- function(dir, birthseas=out$birthseas, fleets,
 
 # readOutputss3 {{{
 readOutputss3 <- function(dir, repfile = "Report.sso",
-  compfile = "CompReport.sso", compress="gz") {
+  compfile = "CompReport.sso", covarfile = "covar.sso", compress="gz") {
 
   # Possibly compressed files
-  cfiles <- c(repfile = repfile, compfile = compfile)
+  cfiles <- c(repfile = repfile, compfile = compfile, covarfile = covarfile)
 
   # CHECK compressed files
   idx <- file.exists(file.path(dir, paste(cfiles, compress, sep = ".")))
   cfiles[idx] <- paste(cfiles, compress, sep = ".")
 
   out <- SS_output(dir, verbose=FALSE, hidewarn=TRUE, warn=FALSE,
-    printstats=FALSE, covar=FALSE, forecast=FALSE,
+    printstats=FALSE, covarfile=cfiles["covarfile"], forecast=FALSE,
     repfile=cfiles["repfile"], compfile=cfiles["compfile"])
 
   return(out) 
@@ -312,7 +312,7 @@ readFLomeOMss3 <- function(dir, birthseas=out$birthseas, fleets,
 } # }}}
 
 # readOMSss3 {{{
-readOMSss3 <- function(dir, birthseas=out$birthseas, fleets,
+readOMSss3 <- function(dir, fleets,
   repfile="Report.sso", compfile="CompReport.sso", ...) {
 
   # LOAD SS_output list
@@ -321,14 +321,14 @@ readOMSss3 <- function(dir, birthseas=out$birthseas, fleets,
   if(out$SS_versionNumeric == 3.24) {
 
     # FLStock
-    stk <- buildFLSss3(out, birthseas=birthseas, ...)
+    stk <- buildFLSss3(out, birthseas=out$birthseas, ...)
     # FLIndexBiomass
     idx <- buildFLIBss3(out, fleets=fleets)
     # refpts
     rps <- buildFLRPss3(out)
     # results
     res <- buildRESss3(out)
-  } else{ 
+  } else { 
 
     # FLStock
     stk <- buildFLSss330(out, ...)

exec/packss3run

@@ -1,8 +1,9 @@
+
 #!/bin/bash
 
 GZFILES=("Report.sso" "covar.sso" "wtatage.ss_new" "CompReport.sso")
-KEEPFILES=("warning.sso" "Forecast-report.sso" "starter.ss" "forecast.ss", "ss3.par", "admodel.hes")
-INPUTFILES=`find . \( -name "*.dat" -or -name "*.ctl" \) -exec basename {} ';'`
+KEEPFILES=("warning.sso" "Forecast-report.sso" "starter.ss" "forecast.ss" "ss3.par" "admodel.hes" "ss.par" "ss.cor" "watatage.ss")
+INPUTFILES=("control.ss" "data.ss" `find . \( -name "*.dat" -or -name "*.ctl" \) -exec basename {} ';'`)
 GZEDFILES=("Report.sso.gz" "covar.sso.gz" "wtatage.ss_new.gz" "CompReport.sso.gz")
 EXCEPT=("${INPUTFILES[@]}" "${KEEPFILES[@]}" "${GZEDFILES[@]}")