SRR bevholt can have different labels

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ss3om
 Title: Tools for Conditioning Fisheries Operating Models Using Stock Synthesis 3
-Version: 0.5.2.9005
+Version: 0.5.2.9008
 Authors@R: person("Iago", "Mosqueira", email = "[email protected]",
   role = c("aut", "cre"))
 Description: Tools for loading Stock Synthesis (SS3) models into FLR. Used in

R/build.R

@@ -187,8 +187,9 @@ buildFLSRss3 <- function(out, ...) {
 
   # BH
   if(out$SRRtype %in% c(3, 6)) {
+  mname <- grep("steep",rownames(out$parameters), value=TRUE)
     params <- FLPar(
-      s=rawp[Label == "SR_BH_steep", Value],
+      s=rawp[Label == mname, Value],
       R0=exp(rawp[Label == "SR_LN(R0)", Value]),
       v=dquants[Label == "SSB_Virgin", Value],
       sratio=1 / out$nsexes,

R/build330.R

@@ -572,12 +572,14 @@ buildFLBFss330 <- function(out, morphs=out$morph_indexing$Index, name=out$Contro
   # SRR
   recdist <- out$recruitment_dist$recruit_dist
 
+  mname <- grep("steep",rownames(out$parameters), value=TRUE)
+
   spawnseas <- recdist[, "Settle#"]
   nspsea <- length(spawnseas)
 
   if(nspsea == 1) {
 
-    pars <- FLPar(s=out$parameters["SR_BH_steep", "Value"],
+    pars <- FLPar(s=out$parameters[mname, "Value"],
       R0=out$derived_quants["Recr_Virgin", "Value"],
       v=out$derived_quants["SSB_Virgin", "Value"])
 
@@ -590,7 +592,7 @@ buildFLBFss330 <- function(out, morphs=out$morph_indexing$Index, name=out$Contro
       unit=spawnseas, season=recdist[, "Seas"], iter=1))
 
     for(i in spawnseas) {
-      pars[, i, i] <- c(out$parameters["SR_BH_steep", "Value"],
+      pars[, i, i] <- c(out$parameters[mname, "Value"],
         out$derived_quants["Recr_Virgin", "Value"],
         out$derived_quants["SSB_Virgin", "Value"],
         recdist[i, "Frac/sex"])

tests/testthat/3.30/simple_with_discard/SIS_table.sso

@@ -0,0 +1 @@
+Note: SIS_table.sso is deprecated, please use the r4ss function get_SIS_info() instead

tests/testthat/3.30/simple_with_discard/derived_posteriors.sso

@@ -0,0 +1,4 @@
+Iter Objective_function SSB_Virgin SSB_Initial SSB_1971 SSB_1972 SSB_1973 SSB_1974 SSB_1975 SSB_1976 SSB_1977 SSB_1978 SSB_1979 SSB_1980 SSB_1981 SSB_1982 SSB_1983 SSB_1984 SSB_1985 SSB_1986 SSB_1987 SSB_1988 SSB_1989 SSB_1990 SSB_1991 SSB_1992 SSB_1993 SSB_1994 SSB_1995 SSB_1996 SSB_1997 SSB_1998 SSB_1999 SSB_2000 SSB_2001 SSB_2002 SSB_2003 SSB_2004 SSB_2005 SSB_2006 SSB_2007 SSB_2008 SSB_2009 SSB_2010 SSB_2011 Recr_Virgin Recr_Initial Recr_1971 Recr_1972 Recr_1973 Recr_1974 Recr_1975 Recr_1976 Recr_1977 Recr_1978 Recr_1979 Recr_1980 Recr_1981 Recr_1982 Recr_1983 Recr_1984 Recr_1985 Recr_1986 Recr_1987 Recr_1988 Recr_1989 Recr_1990 Recr_1991 Recr_1992 Recr_1993 Recr_1994 Recr_1995 Recr_1996 Recr_1997 Recr_1998 Recr_1999 Recr_2000 Recr_2001 Recr_2002 Recr_2003 Recr_2004 Recr_2005 Recr_2006 Recr_2007 Recr_2008 Recr_2009 Recr_2010 Recr_2011 SPRratio_1972 SPRratio_1973 SPRratio_1974 SPRratio_1975 SPRratio_1976 SPRratio_1977 SPRratio_1978 SPRratio_1979 SPRratio_1980 SPRratio_1981 SPRratio_1982 SPRratio_1983 SPRratio_1984 SPRratio_1985 SPRratio_1986 SPRratio_1987 SPRratio_1988 SPRratio_1989 SPRratio_1990 SPRratio_1991 SPRratio_1992 SPRratio_1993 SPRratio_1994 SPRratio_1995 SPRratio_1996 SPRratio_1997 SPRratio_1998 SPRratio_1999 SPRratio_2000 SPRratio_2001 SPRratio_2002 SPRratio_2003 SPRratio_2004 SPRratio_2005 SPRratio_2006 SPRratio_2007 SPRratio_2008 SPRratio_2009 SPRratio_2010 SPRratio_2011 F_1972 F_1973 F_1974 F_1975 F_1976 F_1977 F_1978 F_1979 F_1980 F_1981 F_1982 F_1983 F_1984 F_1985 F_1986 F_1987 F_1988 F_1989 F_1990 F_1991 F_1992 F_1993 F_1994 F_1995 F_1996 F_1997 F_1998 F_1999 F_2000 F_2001 F_2002 F_2003 F_2004 F_2005 F_2006 F_2007 F_2008 F_2009 F_2010 F_2011 Bratio_1973 Bratio_1974 Bratio_1975 Bratio_1976 Bratio_1977 Bratio_1978 Bratio_1979 Bratio_1980 Bratio_1981 Bratio_1982 Bratio_1983 Bratio_1984 Bratio_1985 Bratio_1986 Bratio_1987 Bratio_1988 Bratio_1989 Bratio_1990 Bratio_1991 Bratio_1992 Bratio_1993 Bratio_1994 Bratio_1995 Bratio_1996 Bratio_1997 Bratio_1998 Bratio_1999 Bratio_2000 Bratio_2001 Bratio_2002 Bratio_2003 Bratio_2004 Bratio_2005 Bratio_2006 Bratio_2007 Bratio_2008 Bratio_2009 Bratio_2010 Bratio_2011 SSB_unfished Totbio_unfished SmryBio_unfished Recr_unfished SSB_Btgt SPR_Btgt annF_Btgt Dead_Catch_Btgt SSB_SPR annF_SPR Dead_Catch_SPR SSB_MSY SPR_MSY annF_MSY Dead_Catch_MSY Ret_Catch_MSY B_MSY/SSB_unfished ForeCatch_2002 ForeCatch_2003 ForeCatch_2004 ForeCatch_2005 ForeCatch_2006 ForeCatch_2007 ForeCatch_2008 ForeCatch_2009 ForeCatch_2010 ForeCatch_2011 OFLCatch_2002 OFLCatch_2003 OFLCatch_2004 OFLCatch_2005 OFLCatch_2006 OFLCatch_2007 OFLCatch_2008 OFLCatch_2009 OFLCatch_2010 OFLCatch_2011 ForeCatchret_2002 ForeCatchret_2003 ForeCatchret_2004 ForeCatchret_2005 ForeCatchret_2006 ForeCatchret_2007 ForeCatchret_2008 ForeCatchret_2009 ForeCatchret_2010 ForeCatchret_2011 LenSelex_std_1_Fem_L_18 LenSelex_std_1_Fem_L_38 LenSelex_std_1_Fem_L_58 LenSelex_std_1_Fem_L_78 LenSelex_std_1_Fem_L_94 LenSelex_std_1_Mal_L_18 LenSelex_std_1_Mal_L_38 LenSelex_std_1_Mal_L_58 LenSelex_std_1_Mal_L_78 LenSelex_std_1_Mal_L_94 Grow_std_GP:_1_Fem_A_1 Grow_std_GP:_1_Fem_A_2 Grow_std_GP:_1_Fem_A_14 Grow_std_GP:_1_Fem_A_26 Grow_std_GP:_1_Fem_A_40 Grow_std_GP:_1_Mal_A_1 Grow_std_GP:_1_Mal_A_2 Grow_std_GP:_1_Mal_A_14 Grow_std_GP:_1_Mal_A_26 Grow_std_GP:_1_Mal_A_40 NatAge_std_1_Fem_A_1 NatAge_std_1_Fem_A_2 NatAge_std_1_Fem_A_14 NatAge_std_1_Fem_A_26 NatAge_std_1_Fem_A_40 NatAge_std_1_Mal_A_1 NatAge_std_1_Mal_A_2 NatAge_std_1_Mal_A_14 NatAge_std_1_Mal_A_26 NatAge_std_1_Mal_A_40 ln(SPB)_1971 ln(SPB)_1986 ln(SPB)_2001 
+0 1590.79 52643.9 52643.9 52643.9 52643.8 52554.8 52111.3 51665.7 50750.5 49353.5 47485.1 45205.8 42639.6 39449.7 35649.8 32067.7 28665.2 25408.1 22229.2 19047.3 15847.5 13147.6 11096.2 9723.65 8896.89 8811.62 8666.44 8408.03 7983.96 7373.3 7013.66 6629.6 6325.93 6203.71 6251.4 7314.06 8263 9042.66 9666.65 10186.4 10658.4 11122.1 11596.1 12082.9 7126.4 7126.4 6929.97 5414.77 6644.88 4973.67 6199.79 12038.8 5816.02 5880.39 7589.97 6784.45 6466.38 4415.35 3400.56 3905.33 7654.76 8768.81 5942.27 5132.39 2677.9 6610.41 1852 2666.74 1262.27 4892.35 2053.37 4836.56 9484.21 1734.82 1493.74 3304.93 2045.9 3347.1 3667.78 3921.62 4110.68 4250.88 4360.85 4455.79 4544.84 4631.78 4717.12 0.0386329 0.179564 0.180962 0.334181 0.468643 0.590205 0.70238 0.806892 0.968303 1.10586 1.14861 1.19205 1.23648 1.28264 1.33155 1.38339 1.40453 1.4182 1.42001 1.40674 1.29572 1.30193 1.31174 1.32745 1.35014 1.2751 1.29274 1.30739 1.3144 1.31436 0.289104 0.45876 0.55417 0.610687 0.646591 0.671821 0.691815 0.70923 0.72511 0.739719 0.0182834 0.0918771 0.0926674 0.187836 0.288325 0.397392 0.518528 0.65518 0.932441 1.27123 1.40665 1.56488 1.75383 1.98805 2.29329 2.70923 2.91692 3.06652 3.08737 2.94026 2.06304 2.10028 2.16127 2.26494 2.42953 1.94669 2.04564 2.13395 2.17831 2.17807 0.157945 0.280285 0.36294 0.417871 0.455451 0.483236 0.506121 0.526713 0.546054 0.564342 2.49577 2.47471 2.45355 2.41008 2.34374 2.25502 2.14677 2.02491 1.87343 1.69297 1.52286 1.36128 1.20661 1.05564 0.904534 0.752581 0.624364 0.526948 0.461766 0.422504 0.418454 0.41156 0.399288 0.37915 0.35015 0.333071 0.314833 0.300412 0.294607 0.296872 0.347337 0.392401 0.429426 0.459059 0.48374 0.506154 0.528178 0.550684 0.573806 52643.9 131869 131318 7126.4 18004.2 0.442117 0.0789493 3482.45 15389.1 0.0921198 3492.88 16311.6 0.414857 0.0872166 3497.87 3291.26 0.309848 252.767 505.561 717.52 886.632 1023.08 1140.38 1249.96 1358.69 1469.25 1581.52 1553.52 1757.32 1930.64 2075.31 2199.59 2312.96 2422.61 2532.41 2643.49 2755.24 234.506 471.603 671.788 831.764 960.517 1070.78 1173.53 1275.47 1379.24 1484.82 0.00440515 0.0916801 0.697197 0.981317 0.998442 0.00440515 0.0916801 0.697197 0.981317 0.998442 32.0109 37.6329 66.8153 71.7165 72.5963 32.2837 37.9686 65.8238 69.8685 70.4914 922.588 1336.22 122.649 5.67115 3.73699 922.53 1335.6 123.943 6.15046 4.23103 10.8713 10.0092 8.7329 
+Iter Objective_function SSB_Virgin SSB_Initial SSB_1971 SSB_1972 SSB_1973 SSB_1974 SSB_1975 SSB_1976 SSB_1977 SSB_1978 SSB_1979 SSB_1980 SSB_1981 SSB_1982 SSB_1983 SSB_1984 SSB_1985 SSB_1986 SSB_1987 SSB_1988 SSB_1989 SSB_1990 SSB_1991 SSB_1992 SSB_1993 SSB_1994 SSB_1995 SSB_1996 SSB_1997 SSB_1998 SSB_1999 SSB_2000 SSB_2001 SSB_2002 SSB_2003 SSB_2004 SSB_2005 SSB_2006 SSB_2007 SSB_2008 SSB_2009 SSB_2010 SSB_2011 Recr_Virgin Recr_Initial Recr_1971 Recr_1972 Recr_1973 Recr_1974 Recr_1975 Recr_1976 Recr_1977 Recr_1978 Recr_1979 Recr_1980 Recr_1981 Recr_1982 Recr_1983 Recr_1984 Recr_1985 Recr_1986 Recr_1987 Recr_1988 Recr_1989 Recr_1990 Recr_1991 Recr_1992 Recr_1993 Recr_1994 Recr_1995 Recr_1996 Recr_1997 Recr_1998 Recr_1999 Recr_2000 Recr_2001 Recr_2002 Recr_2003 Recr_2004 Recr_2005 Recr_2006 Recr_2007 Recr_2008 Recr_2009 Recr_2010 Recr_2011 SPRratio_1972 SPRratio_1973 SPRratio_1974 SPRratio_1975 SPRratio_1976 SPRratio_1977 SPRratio_1978 SPRratio_1979 SPRratio_1980 SPRratio_1981 SPRratio_1982 SPRratio_1983 SPRratio_1984 SPRratio_1985 SPRratio_1986 SPRratio_1987 SPRratio_1988 SPRratio_1989 SPRratio_1990 SPRratio_1991 SPRratio_1992 SPRratio_1993 SPRratio_1994 SPRratio_1995 SPRratio_1996 SPRratio_1997 SPRratio_1998 SPRratio_1999 SPRratio_2000 SPRratio_2001 SPRratio_2002 SPRratio_2003 SPRratio_2004 SPRratio_2005 SPRratio_2006 SPRratio_2007 SPRratio_2008 SPRratio_2009 SPRratio_2010 SPRratio_2011 F_1972 F_1973 F_1974 F_1975 F_1976 F_1977 F_1978 F_1979 F_1980 F_1981 F_1982 F_1983 F_1984 F_1985 F_1986 F_1987 F_1988 F_1989 F_1990 F_1991 F_1992 F_1993 F_1994 F_1995 F_1996 F_1997 F_1998 F_1999 F_2000 F_2001 F_2002 F_2003 F_2004 F_2005 F_2006 F_2007 F_2008 F_2009 F_2010 F_2011 Bratio_1973 Bratio_1974 Bratio_1975 Bratio_1976 Bratio_1977 Bratio_1978 Bratio_1979 Bratio_1980 Bratio_1981 Bratio_1982 Bratio_1983 Bratio_1984 Bratio_1985 Bratio_1986 Bratio_1987 Bratio_1988 Bratio_1989 Bratio_1990 Bratio_1991 Bratio_1992 Bratio_1993 Bratio_1994 Bratio_1995 Bratio_1996 Bratio_1997 Bratio_1998 Bratio_1999 Bratio_2000 Bratio_2001 Bratio_2002 Bratio_2003 Bratio_2004 Bratio_2005 Bratio_2006 Bratio_2007 Bratio_2008 Bratio_2009 Bratio_2010 Bratio_2011 SSB_unfished Totbio_unfished SmryBio_unfished Recr_unfished SSB_Btgt SPR_Btgt annF_Btgt Dead_Catch_Btgt SSB_SPR annF_SPR Dead_Catch_SPR SSB_MSY SPR_MSY annF_MSY Dead_Catch_MSY Ret_Catch_MSY B_MSY/SSB_unfished ForeCatch_2002 ForeCatch_2003 ForeCatch_2004 ForeCatch_2005 ForeCatch_2006 ForeCatch_2007 ForeCatch_2008 ForeCatch_2009 ForeCatch_2010 ForeCatch_2011 OFLCatch_2002 OFLCatch_2003 OFLCatch_2004 OFLCatch_2005 OFLCatch_2006 OFLCatch_2007 OFLCatch_2008 OFLCatch_2009 OFLCatch_2010 OFLCatch_2011 ForeCatchret_2002 ForeCatchret_2003 ForeCatchret_2004 ForeCatchret_2005 ForeCatchret_2006 ForeCatchret_2007 ForeCatchret_2008 ForeCatchret_2009 ForeCatchret_2010 ForeCatchret_2011 LenSelex_std_1_Fem_L_18 LenSelex_std_1_Fem_L_38 LenSelex_std_1_Fem_L_58 LenSelex_std_1_Fem_L_78 LenSelex_std_1_Fem_L_94 LenSelex_std_1_Mal_L_18 LenSelex_std_1_Mal_L_38 LenSelex_std_1_Mal_L_58 LenSelex_std_1_Mal_L_78 LenSelex_std_1_Mal_L_94 Grow_std_GP:_1_Fem_A_1 Grow_std_GP:_1_Fem_A_2 Grow_std_GP:_1_Fem_A_14 Grow_std_GP:_1_Fem_A_26 Grow_std_GP:_1_Fem_A_40 Grow_std_GP:_1_Mal_A_1 Grow_std_GP:_1_Mal_A_2 Grow_std_GP:_1_Mal_A_14 Grow_std_GP:_1_Mal_A_26 Grow_std_GP:_1_Mal_A_40 NatAge_std_1_Fem_A_1 NatAge_std_1_Fem_A_2 NatAge_std_1_Fem_A_14 NatAge_std_1_Fem_A_26 NatAge_std_1_Fem_A_40 NatAge_std_1_Mal_A_1 NatAge_std_1_Mal_A_2 NatAge_std_1_Mal_A_14 NatAge_std_1_Mal_A_26 NatAge_std_1_Mal_A_40 ln(SPB)_1971 ln(SPB)_1986 ln(SPB)_2001 
+0 1590.79 52643.9 52643.9 52643.9 52643.8 52554.8 52111.3 51665.7 50750.5 49353.5 47485.1 45205.8 42639.6 39449.7 35649.8 32067.7 28665.2 25408.1 22229.2 19047.3 15847.5 13147.6 11096.2 9723.65 8896.89 8811.62 8666.44 8408.03 7983.96 7373.3 7013.66 6629.6 6325.93 6203.71 6251.4 7314.06 8263 9042.66 9666.65 10186.4 10658.4 11122.1 11596.1 12082.9 7126.4 7126.4 6929.97 5414.77 6644.88 4973.67 6199.79 12038.8 5816.02 5880.39 7589.97 6784.45 6466.38 4415.35 3400.56 3905.33 7654.76 8768.81 5942.27 5132.39 2677.9 6610.41 1852 2666.74 1262.27 4892.35 2053.37 4836.56 9484.21 1734.82 1493.74 3304.93 2045.9 3347.1 3667.78 3921.62 4110.68 4250.88 4360.85 4455.79 4544.84 4631.78 4717.12 0.0386329 0.179564 0.180962 0.334181 0.468643 0.590205 0.70238 0.806892 0.968303 1.10586 1.14861 1.19205 1.23648 1.28264 1.33155 1.38339 1.40453 1.4182 1.42001 1.40674 1.29572 1.30193 1.31174 1.32745 1.35014 1.2751 1.29274 1.30739 1.3144 1.31436 0.289104 0.45876 0.55417 0.610687 0.646591 0.671821 0.691815 0.70923 0.72511 0.739719 0.00168426 0.0084637 0.00853651 0.0173034 0.0265605 0.0366077 0.0477667 0.060355 0.0858962 0.117105 0.12958 0.144157 0.161563 0.183139 0.211257 0.249574 0.268706 0.282487 0.284408 0.270856 0.190047 0.193477 0.199096 0.208646 0.223808 0.179329 0.188444 0.196579 0.200665 0.200643 0.0145498 0.0258198 0.033434 0.0384942 0.0419561 0.0445156 0.0466237 0.0485207 0.0503024 0.0519871 2.49577 2.47471 2.45355 2.41008 2.34374 2.25502 2.14677 2.02491 1.87343 1.69297 1.52286 1.36128 1.20661 1.05564 0.904534 0.752581 0.624364 0.526948 0.461766 0.422504 0.418454 0.41156 0.399288 0.37915 0.35015 0.333071 0.314833 0.300412 0.294607 0.296872 0.347337 0.392401 0.429426 0.459059 0.48374 0.506154 0.528178 0.550684 0.573806 52643.9 131869 131318 7126.4 18004.2 0.442117 0.0789493 3482.45 15389.1 0.0921198 3492.88 16311.6 0.414857 0.0872166 3497.87 3291.26 0.309848 252.767 505.561 717.52 886.632 1023.08 1140.38 1249.96 1358.69 1469.25 1581.52 1553.52 1757.32 1930.64 2075.31 2199.59 2312.96 2422.61 2532.41 2643.49 2755.24 234.506 471.603 671.788 831.764 960.517 1070.78 1173.53 1275.47 1379.24 1484.82 0.00440515 0.0916801 0.697197 0.981317 0.998442 0.00440515 0.0916801 0.697197 0.981317 0.998442 32.0109 37.6329 66.8153 71.7165 72.5963 32.2837 37.9686 65.8238 69.8685 70.4914 922.588 1336.22 122.649 5.67115 3.73699 922.53 1335.6 123.943 6.15046 4.23103 10.8713 10.0092 8.7329