updated with 2016 estimations

Bresle/adult/analyse_adult.R

 rm(list=ls())   # Clear memory
 
 
+
 ##------------------ R PACKAGES ------------------------------##
 library(R2OpenBUGS)
 library(rjags) # require to use "read.bugsdata" function
@@ -21,6 +22,9 @@ stade <- "adult"
 work.dir<-paste("/home/basp-meco88/Documents/RESEARCH/PROJECTS/ORE/Abundance",site,stade,sep="/")
 setwd(work.dir)
 
+# cleaning
+system("rm bugs/*")
+
 
 ##-----------------------------DATA ----------------------------------##
 source(paste('data/data_',stade,'.R',sep="")) # creation du fichier Rdata

CIEM/Script_CIEM.R

@@ -76,7 +76,7 @@ colnames(table) <- c("1SW",	"MSW",		"eggs (million)",	"eggs/CL")
 rownames(table) <- years
 
 #Conservation Limit:
-CL = 1.44
+CL = 1.44 # A REVISER?
 
 # Spawners:
 table[,"1SW"] <- fit$median$e_1SW # spawners 1SW
@@ -88,7 +88,7 @@ table[,"eggs/CL"] <- table[,"eggs (million)"] / CL
 
 #write.csv(round(table,2), file=paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table8_',site,"_",year,'.csv',sep=""))
 con <- file(paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table8_',site,"_",year,'.csv',sep=""), open="wt")
-writeLines(paste("# Table 8 - Index rivers :spawning stock, egg deposition and attainment of CLs -",site," (",year,")
+writeLines(paste("# Table 8 - Index rivers :spawning stock and egg deposition and attainment of CLs -",site," (",year,")
                              CL = 1.44 (millions)
                  ",sep=""), con)
 write.csv( round(table,2), con)
@@ -135,8 +135,8 @@ table[,"eggs/CL"] <- c(rep(NA,10),ratio_CL)
 
 #write.csv(round(table,2), file=paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table8_',site,"_",year,'.csv',sep=""))
 con <- file(paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table8_',site,"_",year,'.csv',sep=""), open="wt")
-writeLines(paste("# Table 8 - Index rivers :spawning stock, egg deposition and attainment of CLs -",site," (",year,") 
-                 CL = 3 eggs/m²
+writeLines(paste("# Table 8 - Index rivers :spawning stock and egg deposition and attainment of CLs -",site," (",year,") 
+                 CL = ",round(mean(CL_eggs/1e6),2)," (with 3 eggs/m²) /!\ revised from data
                  ",sep=""), con)
 write.csv( round(table,2), con)
 close(con)
@@ -147,7 +147,7 @@ site <- "Oir"
 stade <- "adult"
 nyear <- length(seq(1984,year,1))
 
-load("~/Documents/RESEARCH/PROJECTS/ORE/Abundance/",site,"/",stade,"/data/data_",stade,"_",year,".RData",sep="")) # DATA
+#load("~/Documents/RESEARCH/PROJECTS/ORE/Abundance/",site,"/",stade,"/data/data_",stade,"_",year,".RData",sep="")) # DATA
 load(paste("~/Documents/RESEARCH/PROJECTS/ORE/Abundance/",site,"/",stade,"/results/Results_",stade,"_",year,".RData",sep=""))
 
 
@@ -169,16 +169,21 @@ mcmc <- fit$sims.matrix
 e_1SW.mcmc <- mcmc[,paste("Nesc_1SW[",1:nyear,"]",sep="")] # female only
 e_MSW.mcmc <- mcmc[,paste("Nesc_MSW[",1:nyear,"]",sep="")] # female only
 
-fec_1SW = 4635 # fecondité 1SW # Prevost 1996
-fec_MSW = 7965 # fecondite MSW # prevost 1996
-eggs_tot.mcmc = e_1SW.mcmc * fec_1SW + e_MSW.mcmc * fec_MSW
+prop.female <- read.csv(paste("~/Documents/RESEARCH/PROJECTS/ORE/Abundance/",site,"/",stade,"/data/prop-female.csv",sep=""))
+fec_1SW = prop.female[,2] * 4635 # fecondité 1SW # Prevost 1996
+fec_MSW = prop.female[,3] * 7965 # fecondite MSW # prevost 1996
+
+eggs_tot.mcmc <- array(,dim=dim(e_1SW.mcmc))
+for (i in 1:dim(mcmc)[1]){
+eggs_tot.mcmc[i,] = e_1SW.mcmc[i,] * fec_1SW + e_MSW.mcmc[i,] * fec_MSW
+}
 eggs_tot <- apply(eggs_tot.mcmc,2,quantile, probs=0.5) #median
 
 # calculs basés sur la conservation limit des tableaux CIEM!! A REFAIRE à partir des données MAIS
-#/!\ chercher les données de surface d eproduction dans les données de juvéniles
+#/!\ chercher les données de surface de production dans les données de juvéniles
 #Conservation Limit de taux de depose oeufs
 CL = 3 # eggs/m²
-S_prod <- rep(26714,length(years)) # surface de production juveniles accessible aux spawners / ajout de 31 pour tenir compte des affluents non proscptés
+S_prod <- rep(26714,length(years)) # surface de production juveniles accessible aux spawners / pas de variation depuis le debut du suivi
 CL_eggs <- S_prod * CL # /!\ data$S_Sc starts in 1993 instead of 1994
 
 
@@ -191,8 +196,8 @@ table[,"eggs/CL"] <- ratio_CL
 
 #write.csv(round(table,2), file=paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table8_',site,"_",year,'.csv',sep=""))
 con <- file(paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table8_',site,"_",year,'.csv',sep=""), open="wt")
-writeLines(paste("# Table 8 - Index rivers :spawning stock, egg deposition and attainment of CLs -",site," (",year,") 
-                                  CL = 3 eggs/m²
+writeLines(paste("# Table 8 - Index rivers :spawning stock and egg deposition and attainment of CLs -",site," (",year,") 
+                                  CL =",round(mean(CL_eggs/1e6),2)," (with 3 eggs/m²) /!\ revised from data
                  ",sep=""), con)
 write.csv( round(table,2), con)
 close(con)
@@ -246,7 +251,9 @@ table[,"eggs/CL"] <- ratio_CL
 
 #write.csv(round(table,2), file=paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table8_',site,"_",year,'.csv',sep=""))
 con <- file(paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table8_',site,"_",year,'.csv',sep=""), open="wt")
-writeLines(paste("# Table 8 - Index rivers :spawning stock, egg deposition and attainment of CLs -",site," (",year,")",sep=""), con)
+writeLines(paste("# Table 8 - Index rivers :spawning stock and egg deposition and attainment of CLs -",site," (",year,") 
+                                  CL =",round(mean(CL_eggs/1e6),2)," (with 3 eggs/m²) /!\ NOT revised from data
+                 ",sep=""), con)
 write.csv( round(table,2), con)
 close(con)
 
@@ -265,10 +272,10 @@ site <- "Nivelle"
 
 years <- seq(1984, year, 1)
 table <- array(, dim=c(length(years), 4))
-colnames(table) <- c( "smolt year","0+ parr", 	"adults",	"survival rate (%)")
+colnames(table) <- c( "PARR 0+ year","0+ parr", 	"adults",	"survival rate (%)")
 rownames(table) <- years
-smolt.years <- years+1
-table[,1] <- smolt.years
+#smolt.years <- years+1
+table[,1] <- years #smolt.years
   
 ## JUVENILES
 stade <- "tacon"
@@ -292,12 +299,12 @@ table[,4] <- (table[,3] / table[,2])*100
 #write.csv(round(table,2), file=paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table9_',site,"_",year,'.csv',sep=""))
 con <- file(paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table9_',site,"_",year,'.csv',sep=""), open="wt")
 writeLines(paste("# Table 9 - juvenile and adult salmon  numbers (estim.) in-river return rate in the monitored rivers - ",site," (",year,")
-                  Nota : juvenile fish are smolts except in r. Nivelle (parrs O+; cohort parr 0+ = smolt.years -1). 
+                  Nota : juvenile fish are smolts except in r. Nivelle which are parrs O+ (cohort parr 0+ = smolt.years -1). 
                   Adult numbers refer to the smolt year N: runs of N+1 and N+2
                   These are estimated trap-return numbers of wild fish except in 94-95 years in Nivelle when some stocked fish returned. 
                  Stocking is considered to adjust numbers"
                   ,sep=""), con)
-write.csv( round(table,2), con)
+write.csv( round(table,2), con, row.names = FALSE)
 close(con)
 
 
@@ -332,12 +339,12 @@ table[,4] <- (table[,3] / table[,2])*100
 #write.csv(round(table,2), file=paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table9_',site,"_",year,'.csv',sep=""))
 con <- file(paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table9_',site,"_",year,'.csv',sep=""), open="wt")
 writeLines(paste("# Table 9 - juvenile and adult salmon  numbers (estim.) in-river return rate in the monitored rivers - ",site," (",year,")
-                  Nota : juvenile fish are smolts except in r. Nivelle (parrs O+; cohort parr 0+ = smolt.years -1). 
+                  Nota : juvenile fish are smolts except in r. Nivelle which are parrs O+ (cohort parr 0+ = smolt.years -1). 
                   Adult numbers refer to the smolt year N: runs of N+1 and N+2
                   These are estimated trap-return numbers of wild fish except in 94-95 years in Nivelle when some stocked fish returned. 
                  Stocking is considered to adjust numbers"
                  ,sep=""), con)
-write.csv( round(table,2), con)
+write.csv( round(table,2), con, row.names = FALSE)
 close(con)
 
 ##________________________BRESLE (starting in 1984)
@@ -375,12 +382,12 @@ table[,4] <- (table[,3] / table[,2])*100
 #write.csv(round(table,2), file=paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table9_',site,"_",year,'.csv',sep=""))
 con <- file(paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table9_',site,"_",year,'.csv',sep=""), open="wt")
 writeLines(paste("# Table 9 - juvenile and adult salmon  numbers (estim.) in-river return rate in the monitored rivers - ",site," (",year,")
-                  Nota : juvenile fish are smolts except in r. Nivelle (parrs O+; cohort parr 0+ = smolt.years -1). 
+                  Nota : juvenile fish are smolts except in r. Nivelle which are parrs O+ (cohort parr 0+ = smolt.years -1). 
                   Adult numbers refer to the smolt year N: runs of N+1 and N+2
                   These are estimated trap-return numbers of wild fish except in 94-95 years in Nivelle when some stocked fish returned. 
                  Stocking is considered to adjust numbers"
                  ,sep=""), con)
-write.csv( round(table,2), con)
+write.csv( round(table,2), con, row.names = FALSE)
 close(con)
 
 
@@ -418,10 +425,10 @@ table[,4] <- (table[,3] / table[,2])*100
 #write.csv(round(table,2), file=paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table9_',site,"_",year,'.csv',sep=""))
 con <- file(paste('~/Documents/RESEARCH/PROJECTS/ORE/Abundance/CIEM/Table9_',site,"_",year,'.csv',sep=""), open="wt")
 writeLines(paste("# Table 9 - juvenile and adult salmon  numbers (estim.) in-river return rate in the monitored rivers - ",site," (",year,")
-                  Nota : juvenile fish are smolts except in r. Nivelle (parrs O+; cohort parr 0+ = smolt.years -1). 
+                  Nota : juvenile fish are smolts except in r. Nivelle which are parrs O+ (cohort parr 0+ = smolt.years -1). 
                   Adult numbers refer to the smolt year N: runs of N+1 and N+2
                   These are estimated trap-return numbers of wild fish except in 94-95 years in Nivelle when some stocked fish returned. 
                  Stocking is considered to adjust numbers"
                  ,sep=""), con)
-write.csv( round(table,2), con)
-close(con)
\ No newline at end of file
+write.csv( round(table,2), con, row.names = FALSE)
+close(con)

CIEM/Table7_Scorff_2016.csv

-# Table 7 - Exploitation rate in the rivers Scorff - 1994-2016)
+# Table 7 - Exploitation rate in the river Scorff - 1994-2016)
 "","1SW (%)","MSW (%)"
 "1994",7.6,24.1
 "1995",9.6,11.5

CIEM/Table8_Bresle_2016.csv

+# Table 8 - Index rivers :spawning stock and egg deposition and attainment of CLs -Bresle (2016) 
+                                  CL =0 (with 3 eggs/m²) /! NOT revised from data
+                 
 "","1SW","MSW","eggs (million)","eggs/CL"
-"1984",61,47,0.31,0.86
-"1985",101,40,0.34,0.95
-"1986",172.5,41,0.46,1.28
-"1987",129,45,0.41,1.14
+"1984",62,43,0.29,0.82
+"1985",100,41,0.34,0.95
+"1986",168,40,0.45,1.25
+"1987",131,39,0.39,1.08
 "1988",97,37,0.33,0.91
-"1989",183,50,0.53,1.48
-"1990",67,58,0.37,1.02
-"1991",158,32,0.4,1.1
-"1992",134,47,0.42,1.18
-"1993",45,28,0.2,0.56
-"1994",43,19,0.16,0.44
-"1995",110,8,0.21,0.59
-"1996",34,27,0.18,0.49
-"1997",32,15,0.12,0.33
-"1998",221,15,0.41,1.15
-"1999",27,52,0.28,0.78
-"2000",57,14,0.17,0.46
-"2001",89,20,0.25,0.69
-"2002",107,36,0.34,0.93
-"2003",27,25,0.16,0.44
-"2004",81,16,0.2,0.56
-"2005",257,52,0.64,1.77
-"2006",106,122,0.72,1.99
-"2007",71,23,0.22,0.61
-"2008",128,12,0.26,0.72
-"2009",85,59,0.4,1.11
-"2010",138,49,0.44,1.21
-"2011",136,39,0.39,1.09
-"2012",132,41,0.4,1.1
-"2013",138,81,0.59,1.64
-"2014",125,66,0.5,1.38
-"2015",122,68,0.5,1.38
-"2016",177,35,0.44,1.22
+"1989",171,53,0.52,1.43
+"1990",68,59,0.38,1.04
+"1991",157,32,0.4,1.1
+"1992",133,44,0.41,1.14
+"1993",47,26,0.2,0.55
+"1994",45,19,0.16,0.45
+"1995",111,8,0.22,0.6
+"1996",34,28,0.18,0.5
+"1997",30,15,0.12,0.33
+"1998",221,14,0.41,1.14
+"1999",28,51,0.28,0.78
+"2000",56,13,0.16,0.44
+"2001",82,18,0.22,0.62
+"2002",108,33,0.32,0.89
+"2003",27,25,0.16,0.45
+"2004",82,16,0.2,0.56
+"2005",257,51,0.64,1.77
+"2006",107,122,0.71,1.98
+"2007",70,22,0.21,0.59
+"2008",132,11,0.26,0.73
+"2009",85,58,0.4,1.1
+"2010",135,47,0.42,1.18
+"2011",134,39,0.39,1.08
+"2012",128,37,0.37,1.04
+"2013",132,71,0.53,1.49
+"2014",117,61,0.46,1.28
+"2015",119,65,0.48,1.33
+"2016",173,32,0.42,1.17

CIEM/Table8_Nivelle_2016.csv

-# Table 8 - Index rivers :spawning stock, egg deposition and attainment of CLs -Nivelle(2016)
+# Table 8 - Index rivers :spawning stock and egg deposition and attainment of CLs -Nivelle (2016)
+                             CL = 1.44 (millions)
+                 
 "","1SW","MSW","eggs (million)","eggs/CL"
 "1984",64,16,0.25,0.17
 "1985",37,27,0.23,0.16

CIEM/Table8_Oir_2016.csv

+# Table 8 - Index rivers :spawning stock and egg deposition and attainment of CLs -Oir (2016) 
+                                  CL =0.08 (with 3 eggs/m²) /! revised from data
+                 
 "","1SW","MSW","eggs (million)","eggs/CL"
-"1984",229,32,0.94,7.83
-"1985",228,70,1.05,8.74
-"1986",84,84,0.78,6.52
-"1987",167,13,0.65,5.42
-"1988",156,84,0.85,7.12
-"1989",198,41,0.77,6.38
-"1990",80,22,0.37,3.12
-"1991",46,5,0.19,1.61
-"1992",43,12,0.18,1.53
-"1993",119,13,0.43,3.54
-"1994",52,15,0.23,1.89
-"1995",141,4,0.49,4.1
-"1996",246,7,0.91,7.54
-"1997",62,6,0.18,1.46
-"1998",159,16,0.64,5.31
-"1999",202,33,0.88,7.31
-"2000",231,33,1,8.33
-"2001",176,15,0.7,5.84
-"2002",281,37,1.19,9.91
-"2003",183,32,0.81,6.75
-"2004",325,73,1.55,12.88
-"2005",139,24,0.63,5.22
-"2006",176,37,0.82,6.87
-"2007",182,28,0.8,6.64
-"2008",95,20,0.45,3.76
-"2009",139,25,0.63,5.29
-"2010",495,23,1.84,15.36
-"2011",202,70,1.1,9.15
-"2012",206,53,1.04,8.66
-"2013",256,64,1.26,10.47
-"2014",228.5,54,1.12,9.34
-"2015",123,44,0.69,5.72
-"2016",270,30,1.12,9.31
+"1984",223,28,0.47,5.93
+"1985",201,59,0.66,8.25
+"1986",66,48,0.37,4.6
+"1987",161,13,0.16,1.96
+"1988",126,73,0.62,7.79
+"1989",177,26,0.38,4.79
+"1990",77,16,0.21,2.66
+"1991",46,5,0.09,1.09
+"1992",37,9,0.14,1.8
+"1993",102,10,0.15,1.89
+"1994",40,13,0.23,2.86
+"1995",134,3,0.29,3.63
+"1996",245,7,0.53,6.58
+"1997",39,6,0.12,1.47
+"1998",155,15,0.34,4.28
+"1999",200,30,0.47,5.89
+"2000",228,31,0.71,8.88
+"2001",175,15,0.34,4.26
+"2002",284,37,0.74,9.18
+"2003",181,32,0.56,6.95
+"2004",324,75,1.2,15.03
+"2005",138,24,0.32,4.02
+"2006",175,38,0.63,7.86
+"2007",182,28,0.48,6.01
+"2008",94,20,0.38,4.76
+"2009",136,26,0.36,4.47
+"2010",476,22,1.05,13.11
+"2011",201,72,0.91,11.41
+"2012",199,52,0.45,5.62
+"2013",257,64,0.7,8.73
+"2014",227,56,0.78,9.79
+"2015",121,45,0.55,6.83
+"2016",271,30,0.63,7.84

CIEM/Table8_Scorff_2016.csv

+# Table 8 - Index rivers :spawning stock and egg deposition and attainment of CLs -Scorff (2016) 
+                 CL = 0.63 (with 3 eggs/m²) /! revised from data
+                 
 "","1SW","MSW","eggs (million)","eggs/CL"
 "1984",NA,NA,NA,NA
 "1985",NA,NA,NA,NA
@@ -9,26 +12,26 @@
 "1991",NA,NA,NA,NA
 "1992",NA,NA,NA,NA
 "1993",NA,NA,NA,NA
-"1994",430,60,0.96,1.59
-"1995",657,36,1.2,2
-"1996",608,62,1.24,2.05
-"1997",411,33,0.8,1.33
-"1998",499,21,0.88,1.46
-"1999",228,60,0.63,1.04
-"2000",250,4,0.42,0.69
-"2001",286,32,0.59,0.99
-"2002",549,20,0.96,1.59
-"2003",233,40,0.55,0.87
-"2004",1027,53,1.85,2.93
-"2005",414,98,1.09,1.72
-"2006",816,67,1.58,2.5
-"2007",435,81,1.05,1.66
-"2008",274,71,0.75,1.19
-"2009",257,101,0.86,1.36
-"2010",692,61,1.36,2.16
-"2011",354,195,1.43,2.27
-"2012",338,109,1.02,1.43
-"2013",561,95,1.31,1.9
-"2014",628,120,1.53,2.22
-"2015",525,138,1.44,2.1
-"2016",483,62,1.04,1.52
+"1994",500,57,1.06,1.76
+"1995",667,42,1.24,2.06
+"1996",580,55,1.16,1.93
+"1997",400,32,0.78,1.29
+"1998",500,21,0.88,1.47
+"1999",225,61,0.63,1.04
+"2000",252,3,0.42,0.69
+"2001",280,34,0.59,0.99
+"2002",539,20,0.94,1.56
+"2003",229,40,0.54,0.86
+"2004",1024,55,1.86,2.94
+"2005",416,100.5,1.1,1.75
+"2006",815,72,1.6,2.54
+"2007",435,83,1.06,1.68
+"2008",272,71,0.75,1.19
+"2009",254,101,0.85,1.35
+"2010",695,62,1.37,2.17
+"2011",355,199,1.45,2.3
+"2012",334,113,1.03,1.45
+"2013",567,94,1.31,1.91
+"2014",627,123,1.53,2.23
+"2015",531,142,1.47,2.14
+"2016",503,66,1.09,1.58

CIEM/Table9_Bresle_2016.csv

+# Table 9 - juvenile and adult salmon  numbers (estim.) in-river return rate in the monitored rivers - Bresle (2016)
+                  Nota : juvenile fish are smolts except in r. Nivelle which are parrs O+ (cohort parr 0+ = smolt.years -1). 
+                  Adult numbers refer to the smolt year N: runs of N+1 and N+2
+                  These are estimated trap-return numbers of wild fish except in 94-95 years in Nivelle when some stocked fish returned. 
+                 Stocking is considered to adjust numbers
 "smolt year","smolt","adults","survival rate (%)"
-1982,1373,NA,NA
-1983,2030,103,5.07
-1984,2101,139,6.62
-1985,3646.5,216,5.92
-1986,1889,162,8.58
-1987,593.5,140,23.59
-1988,NA,235,NA
+1982,4140,NA,NA
+1983,3971,103,2.59
+1984,2109.5,140,6.64
+1985,5250,207,3.94
+1986,1997,168,8.41
+1987,2419,150,6.2
+1988,NA,230,NA
 1989,NA,100,NA
-1990,NA,210,NA
-1991,NA,158,NA
-1992,898,70,7.8
-1993,1653,53,3.21
-1994,2403,154,6.41
-1995,628.5,51,8.11
-1996,1398,43,3.08
-1997,6281.5,280,4.46
-1998,1578,54,3.42
-1999,545.5,108,19.8
-2000,1594,167,10.48
-2001,NA,140,NA
-2002,1771.5,50,2.82
-2003,2863.5,135,4.71
-2004,7413.5,374,5.04
-2005,5348,128,2.39
-2006,2703,92,3.4
-2007,5202,199,3.83
-2008,6541,131,2
-2009,1191,169,14.19
-2010,2666,171,6.41
-2011,6269.5,207,3.3
-2012,6397.5,208,3.25
-2013,2005.5,193,9.62
-2014,2287.5,158,6.91
-2015,7631,NA,NA
-2016,7587,NA,NA
+1990,NA,201,NA
+1991,NA,159,NA
+1992,2562,66,2.58
+1993,1740,53,3.05
+1994,2444,139,5.69
+1995,2036,49,2.41
+1996,1659,44,2.65
+1997,6255,272,4.35
+1998,1662,41,2.47
+1999,643,74,11.51
+2000,1773,115,6.49
+2001,NA,133,NA
+2002,2458,43,1.75
+2003,2969,133,4.48
+2004,7567,379,5.01
+2005,5163,129,2.5
+2006,2704,81,3
+2007,5410,190,3.51
+2008,6617,132,1.99
+2009,1162.5,174,14.97
+2010,2865,171,5.97
+2011,6464,199,3.08
+2012,6485.5,193,2.98
+2013,1856,182,9.81
+2014,2722,151,5.55
+2015,7466,NA,NA
+2016,7778,NA,NA

CIEM/Table9_Nivelle_2016.csv

 # Table 9 - juvenile and adult salmon  numbers (estim.) in-river return rate in the monitored rivers - Nivelle (2016)
-                  # Nota : juvenile fish are smolts except in r. Nivelle (parrs O+). Adult numbers refer to the smolt year N: runs of N+1 and N+2
-                  # These are estimated trap-return numbers of wild fish except in 94-95 years in Nivelle when some stocked fish returned. Stocking is considered to adjust numbers
-"","smolt year","0+ parr","adults","survival rate (%)"
-"1984",1985,NA,380,NA
-"1985",1986,1319,226,17.13
-"1986",1987,8022,187,2.33
-"1987",1988,11761,291,2.47
-"1988",1989,11033,334,3.03
-"1989",1990,10664,221,2.07
-"1990",1991,5809.5,254,4.37
-"1991",1992,6932,516,7.44
-"1992",1993,4901,390,7.96
-"1993",1994,4733,231,4.88
-"1994",1995,13750,183,1.33
-"1995",1996,5889,127,2.16
-"1996",1997,7143,196,2.74
-"1997",1998,7459.5,179,2.4
-"1998",1999,6854,171,2.49
-"1999",2000,9873,226,2.29
-"2000",2001,10891,455,4.18
-"2001",2002,12322.5,50,0.41
-"2002",2003,15266,103,0.67
-"2003",2004,7083,118,1.67
-"2004",2005,4431,64,1.44
-"2005",2006,9395,93,0.99
-"2006",2007,2488,83,3.34
-"2007",2008,3155,76,2.41
-"2008",2009,5181,192,3.71
-"2009",2010,2784,60,2.16
-"2010",2011,7247,104,1.44
-"2011",2012,4775,130,2.72
-"2012",2013,15332,101,0.66
-"2013",2014,4750,67,1.41
-"2014",2015,6895,NA,NA
-"2015",2016,8255,NA,NA
-"2016",2017,10125,NA,NA
+                  Nota : juvenile fish are smolts except in r. Nivelle which are parrs O+ (cohort parr 0+ = smolt.years -1). 
+                  Adult numbers refer to the smolt year N: runs of N+1 and N+2
+                  These are estimated trap-return numbers of wild fish except in 94-95 years in Nivelle when some stocked fish returned. 
+                 Stocking is considered to adjust numbers
+"PARR 0+ year","0+ parr","adults","survival rate (%)"
+1984,NA,380,NA
+1985,1301,226,17.37
+1986,7835.5,187,2.39
+1987,11664,291,2.49
+1988,10952,334,3.05
+1989,10377,221,2.13
+1990,5625.5,254,4.52
+1991,6902.5,516,7.48
+1992,4668.5,390,8.35
+1993,4613,231,5.01
+1994,13567,183,1.35
+1995,5668.5,127,2.24
+1996,6925,196,2.83
+1997,7481,179,2.39
+1998,6615.5,171,2.58
+1999,9499,226,2.38
+2000,10662.5,455,4.27
+2001,12190.5,50,0.41
+2002,14865.5,103,0.69
+2003,6947,118,1.7
+2004,4378,64,1.46
+2005,9264,93,1
+2006,2390,83,3.47
+2007,3092,76,2.46
+2008,5112,192,3.76
+2009,2730.5,60,2.2
+2010,6885,104,1.51
+2011,4669,130,2.78
+2012,15019.5,101,0.67
+2013,4501,67,1.49
+2014,6749,NA,NA
+2015,7744,NA,NA
+2016,9459,NA,NA

CIEM/Table9_Oir_2016.csv

+# Table 9 - juvenile and adult salmon  numbers (estim.) in-river return rate in the monitored rivers - Oir (2016)
+                  Nota : juvenile fish are smolts except in r. Nivelle which are parrs O+ (cohort parr 0+ = smolt.years -1). 
+                  Adult numbers refer to the smolt year N: runs of N+1 and N+2
+                  These are estimated trap-return numbers of wild fish except in 94-95 years in Nivelle when some stocked fish returned. 
+                 Stocking is considered to adjust numbers
 "smolt year","smolt","adults","survival rate (%)"
-1984,NA,297,NA
-1985,NA,82,NA
-1986,737.5,226,30.64
-1987,355,150,42.25
-1988,415,191,46.02
-1989,816,78,9.56
-1990,799,55,6.88
-1991,199,45,22.61
-1992,667,110,16.49
-1993,225,45,20
-1994,530.5,138,26.01
-1995,751,241.5,32.16
-1996,988,54,5.47
-1997,449,185,41.2
-1998,1049,232,22.12
-1999,267,255.5,95.69
-2000,2159.5,208,9.63
-2001,1377,310,22.51
-2002,2381,252,10.58
-2003,1240,344,27.74
-2004,1228,178,14.5
-2005,845,204,24.14
-2006,1365,202,14.8
-2007,960,123,12.81
-2008,2161,163,7.54
-2009,3428.5,578,16.86
-2010,1397,255.5,18.29
-2011,1811.5,256,14.13
-2012,1367,295,21.58
-2013,1303,276,21.18
-2014,1543,139,9.01
-2015,2315,NA,NA
-2016,1856,NA,NA
+1984,NA,249,NA
+1985,NA,79,NA
+1986,743,234,31.49
+1987,355,152,42.82
+1988,414,193,46.62
+1989,820,82,10
+1990,807,55,6.82
+1991,200,47,23.5
+1992,673,115,17.09
+1993,227,43,18.94
+1994,567,141,24.87
+1995,743,251,33.78
+1996,1000,54,5.4
+1997,466,185,39.7
+1998,1074.5,231,21.5
+1999,261,243,93.1
+2000,2165,212,9.79
+2001,1355,316,23.32
+2002,2365,256,10.82
+2003,1230,348,28.29
+2004,1230,176,14.31
+2005,846,203,24
+2006,1355,202,14.91
+2007,955,120,12.57
+2008,2151,158,7.35
+2009,3383,548,16.2
+2010,1405,253,18.01
+2011,1798,263,14.63
+2012,1358,313,23.05
+2013,1286,272,21.15
+2014,1569,151,9.62
+2015,2301,NA,NA
+2016,1961,NA,NA