diff --git a/CIEM/T3.3.6.1.csv b/CIEM/T3.3.6.1.csv index 077ae1d..2d8a258 100644 --- a/CIEM/T3.3.6.1.csv +++ b/CIEM/T3.3.6.1.csv @@ -10,27 +10,27 @@ "1992",3.39,17.11,8.01,NA "1993",2.87,19.47,4.84,NA "1994",5.58,25.09,1.31,NA -"1995",3.19,34.28,2.1,9.83 -"1996",2.7,5.51,2.71,21.7 -"1997",4.44,38.49,2.34,5.75 -"1998",2.43,21.43,2.37,4.91 -"1999",10.71,93.1,2.28,11.17 -"2000",6.92,9.81,4.13,9.63 -"2001",NA,23,0.4,4.98 -"2002",2.25,10.79,0.68,22.26 -"2003",4.46,28.33,1.69,11.05 -"2004",5.02,14.32,1.44,6.27 +"1995",3.19,34.28,2.1,10.2 +"1996",2.7,5.51,2.71,21.8 +"1997",4.44,38.49,2.34,5.66 +"1998",2.43,21.43,2.37,4.8 +"1999",10.71,93.1,2.28,11.63 +"2000",6.92,9.81,4.13,9.35 +"2001",NA,23,0.4,4.84 +"2002",2.25,10.79,0.68,22.5 +"2003",4.46,28.33,1.69,11.06 +"2004",5.02,14.32,1.44,6.3 "2005",2.49,24.17,0.98,8.32 -"2006",3.09,15.03,3.28,7.04 -"2007",3.45,12.58,2.42,4.95 -"2008",1.99,7.54,3.74,3.01 -"2009",15.03,16.16,2.09,6.51 -"2010",6.05,18.08,1.61,4.45 +"2006",3.09,15.03,3.28,7.03 +"2007",3.45,12.58,2.42,4.93 +"2008",1.99,7.54,3.74,3 +"2009",15.03,16.16,2.09,6.49 +"2010",6.05,18.08,1.61,4.43 "2011",3.25,14.81,2.84,4.97 -"2012",3.1,23.16,0.72,8.51 -"2013",9.66,21.11,1.63,8.99 -"2014",5.58,9.58,1.12,5.8 -"2015",3.17,13.77,1.32,9.42 -"2016",6.61,12.66,NA,9.08 +"2012",3.1,23.16,0.72,8.53 +"2013",9.66,21.11,1.63,9.06 +"2014",5.58,9.58,1.12,5.77 +"2015",3.17,13.77,1.32,9.32 +"2016",6.61,12.66,NA,9.17 "2017",NA,NA,NA,NA "2018",NA,NA,NA,NA diff --git a/CIEM/Table7_Scorff_2018.csv b/CIEM/Table7_Scorff_2018.csv index 295d563..0228034 100644 --- a/CIEM/Table7_Scorff_2018.csv +++ b/CIEM/Table7_Scorff_2018.csv @@ -1,26 +1,26 @@ "Year","1SW (%)","MSW (%)" -1994,7.9,25.3 -1995,9.9,12.4 -1996,13.2,12.9 -1997,7.7,11.3 -1998,12.1,18.5 -1999,9.8,7.2 -2000,13.5,23.3 -2001,9.7,15.4 -2002,4.1,4.5 -2003,0,12.3 +1994,8.1,27 +1995,9.9,11.8 +1996,12.7,13.4 +1997,7.6,11.3 +1998,12.2,18.5 +1999,10,7.2 +2000,13,21.7 +2001,9.9,15 +2002,4.2,4.5 +2003,0,12.1 2004,7.7,15.6 2005,6,20 -2006,7.9,28.6 -2007,10.3,12.8 +2006,7.9,28.3 +2007,10.4,12.8 2008,4.2,16.1 -2009,1.9,11.1 +2009,1.9,11.3 2010,7.6,4.6 2011,7.3,5.6 -2012,8.9,17.7 +2012,8.9,17.9 2013,4.8,6.7 2014,8.2,8.8 -2015,8.7,17.1 +2015,8.7,17 2016,5.3,11.5 -2017,3.8,9 -2018,4.9,11.8 +2017,3.8,9.2 +2018,4.6,10.3 diff --git a/CIEM/Table8_Scorff_2018.csv b/CIEM/Table8_Scorff_2018.csv index 7ac3865..ef3a7df 100644 --- a/CIEM/Table8_Scorff_2018.csv +++ b/CIEM/Table8_Scorff_2018.csv @@ -9,28 +9,28 @@ 1991,NA,NA,NA,NA 1992,NA,NA,NA,NA 1993,NA,NA,NA,NA -1994,472,53,0.99,1.65 -1995,643,38,1.18,1.96 -1996,584,61,1.19,1.98 -1997,411,31,0.79,1.31 -1998,508,21,0.89,1.48 -1999,229,66,0.66,1.09 -2000,261,5,0.44,0.73 -2001,286,31,0.59,0.98 -2002,559,20,0.97,1.61 -2003,223,38,0.52,0.83 -2004,1020,53,1.84,2.91 -2005,418,99,1.1,1.74 -2006,815,73,1.61,2.55 -2007,433,80,1.04,1.65 -2008,272,71,0.75,1.19 -2009,256,102,0.86,1.36 -2010,696,61,1.37,2.17 -2011,354,194,1.42,2.25 -2012,344,115,1.06,1.49 -2013,570,96,1.33,1.93 -2014,624,123,1.53,2.23 -2015,525,139,1.45,2.11 -2016,499,69,1.1,1.59 -2017,786,125,1.79,2.61 -2018,267,102,0.88,1.28 +1994,460,47,0.95,1.58 +1995,640,40,1.19,1.97 +1996,609,57,1.21,2.01 +1997,413,29,0.78,1.3 +1998,500,21,0.88,1.47 +1999,224,65,0.65,1.07 +2000,273,5,0.46,0.77 +2001,277,31,0.58,0.96 +2002,541,20,0.94,1.56 +2003,226,39,0.53,0.84 +2004,1022,53,1.84,2.92 +2005,418,98,1.1,1.74 +2006,815,75,1.62,2.56 +2007,431,80,1.04,1.64 +2008,272,72,0.75,1.19 +2009,256,100,0.86,1.36 +2010,698,60,1.37,2.17 +2011,353,190,1.4,2.23 +2012,345,113,1.05,1.48 +2013,572,95,1.33,1.93 +2014,629,123,1.54,2.24 +2015,523,140,1.45,2.11 +2016,493,68,1.08,1.57 +2017,775,124,1.77,2.58 +2018,283,121,0.99,1.43 diff --git a/CIEM/Table9_Scorff_2018.csv b/CIEM/Table9_Scorff_2018.csv index 5050a35..9bc802d 100644 --- a/CIEM/Table9_Scorff_2018.csv +++ b/CIEM/Table9_Scorff_2018.csv @@ -8,29 +8,29 @@ 1990,NA,NA,NA 1991,NA,NA,NA 1992,NA,NA,NA -1993,NA,510,NA -1994,NA,704,NA -1995,6257,615,9.83 -1996,1991,432,21.7 -1997,9984,574,5.75 -1998,4767,234,4.91 -1999,2613,292,11.17 -2000,3177,306,9.63 -2001,11980,597,4.98 -2002,1240,276,22.26 -2003,10130,1119,11.05 -2004,7829,491,6.27 +1993,NA,500,NA +1994,NA,697,NA +1995,6257,638,10.2 +1996,1991,434,21.8 +1997,9984,565,5.66 +1998,4767,229,4.8 +1999,2613,304,11.63 +2000,3177,297,9.35 +2001,11980,580,4.84 +2002,1240,279,22.5 +2003,10130,1120,11.06 +2004,7829,493,6.3 2005,10760,895,8.32 -2006,7156,504,7.04 -2007,7550,374,4.95 -2008,10540,317,3.01 -2009,13680,890,6.51 -2010,10530,469,4.45 +2006,7156,503,7.03 +2007,7550,372,4.93 +2008,10540,316,3 +2009,13680,888,6.49 +2010,10530,466,4.43 2011,8854,440,4.97 -2012,8144,693,8.51 -2013,8491,763,8.99 -2014,10240,594,5.8 -2015,6621,624,9.42 -2016,9775,888,9.08 +2012,8144,695,8.53 +2013,8491,769,9.06 +2014,10240,591,5.77 +2015,6621,617,9.32 +2016,9775,896,9.17 2017,6268,NA,NA 2018,4888,NA,NA diff --git a/CIEM/ratio_eggs_CL.png b/CIEM/ratio_eggs_CL.png index 6a8b6ae..7e7c971 100644 Binary files a/CIEM/ratio_eggs_CL.png and b/CIEM/ratio_eggs_CL.png differ diff --git a/CIEM/return_rates.png b/CIEM/return_rates.png index 293b933..86e3357 100644 Binary files a/CIEM/return_rates.png and b/CIEM/return_rates.png differ diff --git a/Scorff/Bilan_Scorff_2018.csv b/Scorff/Bilan_Scorff_2018.csv new file mode 100644 index 0000000..4b3f8bf --- /dev/null +++ b/Scorff/Bilan_Scorff_2018.csv @@ -0,0 +1,27 @@ +"Year","Parr 0+","Smolts","1SW (tot returns)","MSW (tot returns)","1SW (escapment)","MSW (escapment)" +1993,10580,NA,NA,NA,NA,NA +1994,19790,NA,508,75,464,49 +1995,9995,6257,769,92,651,40 +1996,13880,1991,724,85,609,60 +1997,9347,9984,455,70,408,29 +1998,6448,4767,565,27,493,21 +1999,10760,2613,257,93,230,62 +2000,20430,3177,317,45,275,5 +2001,3205,11980,315,40,280,31 +2002,18300,1240,566,22,541,20 +2003,14000,10130,229,58,227,39 +2004,24780,7829,1117,65,1022,53 +2005,14570,10760,452,130,417,99 +2006,15850,7156,887,107,814,75 +2007,25910,7550,483,94,431,80 +2008,21950,10540,286,88,272,73 +2009,17820,13680,262,116,256,101 +2010,22050,10530,765,65,698,60 +2011,34300,8854,385,213,351,191 +2012,32270,8144,381,145,345,113 +2013,25790,8491,603,104,571,95 +2014,26490,10240,686,136,628,122 +2015,45145,6621,599,177,525,141 +2016,20870,9775,620,87,495,69 +2017,24790,6268,950,143,776,124 +2018,16750,4888,301,146,283,121 diff --git a/Scorff/adult/analyse_adult.R b/Scorff/adult/analyse_adult.R index 66054ff..8ff6381 100755 --- a/Scorff/adult/analyse_adult.R +++ b/Scorff/adult/analyse_adult.R @@ -62,7 +62,7 @@ nChains = 2 #length(inits) # Number of chains to run. adaptSteps = 1000 # Number of steps to "tune" the samplers. nburnin=5000 # Number of steps to "burn-in" the samplers. nstore=10000 # Total number of steps in chains to save. -nthin=10 # Number of steps to "thin" (1=keep every step). +nthin=20 # Number of steps to "thin" (1=keep every step). #nPerChain = ceiling( ( numSavedSteps * thinSteps ) / nChains ) # Steps per chain. ### Start of the run ### diff --git a/Scorff/adult/results/Diagnostics_adult_2018.txt b/Scorff/adult/results/Diagnostics_adult_2018.txt index 93371f6..d4efbe4 100644 --- a/Scorff/adult/results/Diagnostics_adult_2018.txt +++ b/Scorff/adult/results/Diagnostics_adult_2018.txt @@ -7,22 +7,22 @@ Convergence: gelman-Rubin R test Potential scale reduction factors: Point est. Upper C.I. -sigmapi_MP 1.01 1.03 -sigmapi_R 1.02 1.07 +sigmapi_MP 1.03 1.13 +sigmapi_R 1.03 1.14 mupi_oF 1.00 1.00 sigmapi_oF 1.00 1.00 -diffF_1SW 1.23 1.76 -diffF_MSW 1.03 1.11 +diffF_1SW 1.27 1.87 +diffF_MSW 1.03 1.08 diff1SW 1.00 1.00 diffMSW 1.00 1.00 -pi_oD 1.01 1.04 +pi_oD 1.08 1.31 shape_lambda 1.00 1.00 rate_lambda 1.00 1.00 -lambda_tot0 1.00 1.02 +lambda_tot0 1.01 1.03 Multivariate psrf -1.16 +1.22 Approximate convergence is diagnosed when the upper limit is close to 1 and <1.1 --------------------------- @@ -36,65 +36,65 @@ heidel.diag also implements a convergence diagnostic, and removes up to half the Stationarity start p-value test iteration -sigmapi_MP passed 1 0.613 -sigmapi_R passed 3001 0.302 -mupi_oF passed 1 0.550 -sigmapi_oF passed 1 0.795 -diffF_1SW passed 1 0.302 -diffF_MSW passed 1 0.483 -diff1SW passed 1 0.639 -diffMSW passed 1 0.260 -pi_oD passed 1 0.210 -shape_lambda passed 1 0.207 -rate_lambda passed 1 0.231 -lambda_tot0 passed 1 0.963 +sigmapi_MP passed 1 0.129 +sigmapi_R passed 1 0.761 +mupi_oF passed 1 0.588 +sigmapi_oF passed 1 0.933 +diffF_1SW passed 1 0.538 +diffF_MSW passed 1 0.547 +diff1SW passed 1 0.570 +diffMSW passed 1 0.848 +pi_oD passed 1 0.134 +shape_lambda passed 1 0.181 +rate_lambda passed 1 0.214 +lambda_tot0 passed 1 0.244 Halfwidth Mean Halfwidth test -sigmapi_MP passed 0.32972 3.31e-03 -sigmapi_R passed 0.26802 1.91e-03 -mupi_oF passed 0.64272 1.18e-03 -sigmapi_oF passed 0.71411 5.30e-03 -diffF_1SW passed -0.35007 3.90e-03 -diffF_MSW passed -0.72883 9.36e-03 -diff1SW passed 0.43340 2.08e-02 -diffMSW passed 0.77589 2.10e-02 -pi_oD passed 0.22921 6.30e-03 -shape_lambda passed 5.89504 5.58e-02 -rate_lambda passed 0.00928 9.18e-05 -lambda_tot0 passed 588.16694 6.48e+00 +sigmapi_MP passed 0.35157 2.56e-03 +sigmapi_R passed 0.26009 1.30e-03 +mupi_oF passed 0.64384 1.18e-03 +sigmapi_oF passed 0.71671 5.12e-03 +diffF_1SW passed -0.30016 3.91e-03 +diffF_MSW passed -0.70074 7.23e-03 +diff1SW passed 0.43770 1.45e-02 +diffMSW passed 0.77570 1.65e-02 +pi_oD passed 0.22068 5.07e-03 +shape_lambda passed 5.95880 4.22e-02 +rate_lambda passed 0.00936 6.95e-05 +lambda_tot0 passed 576.68300 4.81e+00 [[2]] Stationarity start p-value test iteration -sigmapi_MP passed 1 0.726 -sigmapi_R passed 1 0.406 -mupi_oF passed 1 0.997 -sigmapi_oF passed 1 0.445 -diffF_1SW passed 1 0.384 -diffF_MSW passed 1 0.774 -diff1SW passed 1 0.258 -diffMSW passed 1 0.594 -pi_oD passed 1 0.841 -shape_lambda passed 1 0.746 -rate_lambda passed 1 0.542 -lambda_tot0 passed 1 0.758 +sigmapi_MP passed 1 0.8942 +sigmapi_R passed 1 0.5549 +mupi_oF passed 1 0.6806 +sigmapi_oF passed 1 0.5715 +diffF_1SW passed 1 0.1105 +diffF_MSW passed 1 0.0728 +diff1SW passed 1 0.8970 +diffMSW passed 1 0.9822 +pi_oD passed 1 0.2941 +shape_lambda passed 1 0.3601 +rate_lambda passed 1 0.5495 +lambda_tot0 passed 1 0.8959 Halfwidth Mean Halfwidth test -sigmapi_MP passed 0.32277 0.00363 -sigmapi_R passed 0.27820 0.00163 -mupi_oF passed 0.64251 0.00120 -sigmapi_oF passed 0.71849 0.00543 -diffF_1SW passed -0.44984 0.00410 -diffF_MSW passed -0.78854 0.00974 -diff1SW passed 0.42065 0.01861 -diffMSW passed 0.77539 0.02152 -pi_oD passed 0.21798 0.00550 -shape_lambda passed 5.99315 0.06277 -rate_lambda passed 0.00939 0.00010 -lambda_tot0 passed 612.46937 6.66842 +sigmapi_MP passed 0.36893 2.42e-03 +sigmapi_R passed 0.27465 1.40e-03 +mupi_oF passed 0.64303 1.19e-03 +sigmapi_oF passed 0.71680 5.09e-03 +diffF_1SW passed -0.40933 3.46e-03 +diffF_MSW passed -0.75133 7.58e-03 +diff1SW passed 0.43447 1.52e-02 +diffMSW passed 0.78157 1.91e-02 +pi_oD passed 0.20531 4.16e-03 +shape_lambda passed 6.04264 4.51e-02 +rate_lambda passed 0.00944 7.17e-05 +lambda_tot0 passed 601.54710 4.98e+00 --------------------------- @@ -112,9 +112,9 @@ Fraction in 1st window = 0.1 Fraction in 2nd window = 0.5 sigmapi_MP sigmapi_R mupi_oF sigmapi_oF diffF_1SW diffF_MSW - 1.0101 -0.1190 -0.5714 -0.5183 -0.4149 0.9140 + 2.02039 -0.10315 -0.19011 -0.15228 0.06082 1.18671 diff1SW diffMSW pi_oD shape_lambda rate_lambda lambda_tot0 - -0.2988 1.0230 0.8824 -0.5949 -0.8110 -0.7553 + -0.45806 -0.74449 -1.14196 0.13754 -0.08787 -2.21512 [[2]] @@ -123,9 +123,9 @@ Fraction in 1st window = 0.1 Fraction in 2nd window = 0.5 sigmapi_MP sigmapi_R mupi_oF sigmapi_oF diffF_1SW diffF_MSW - 1.17924 -0.09048 -0.15236 0.31722 -0.01773 -0.90937 + -0.43714 0.68732 0.03385 0.77921 1.55785 -2.48267 diff1SW diffMSW pi_oD shape_lambda rate_lambda lambda_tot0 - -1.08133 0.91322 0.03265 1.38118 1.61243 -0.86423 + -0.11278 1.03816 -0.13402 0.58903 0.46431 0.78725 @@ -139,18 +139,18 @@ Probability (s) = 0.95 Burn-in Total Lower bound Dependence (M) (N) (Nmin) factor (I) - sigmapi_MP 100 114500 3746 30.60 - sigmapi_R 40 49960 3746 13.30 - mupi_oF 20 36760 3746 9.81 - sigmapi_oF 20 37100 3746 9.90 - diffF_1SW 20 38970 3746 10.40 - diffF_MSW 30 42630 3746 11.40 - diff1SW 80 100500 3746 26.80 - diffMSW 40 48320 3746 12.90 - pi_oD 350 363000 3746 96.90 - shape_lambda 30 43740 3746 11.70 - rate_lambda 30 45580 3746 12.20 - lambda_tot0 40 48320 3746 12.90 + sigmapi_MP 160 195520 3746 52.2 + sigmapi_R 60 85580 3746 22.8 + mupi_oF 40 73600 3746 19.6 + sigmapi_oF 40 74220 3746 19.8 + diffF_1SW 40 78580 3746 21.0 + diffF_MSW 60 81600 3746 21.8 + diff1SW 60 91160 3746 24.3 + diffMSW 60 85340 3746 22.8 + pi_oD 560 628000 3746 168.0 + shape_lambda 40 79280 3746 21.2 + rate_lambda 60 80620 3746 21.5 + lambda_tot0 60 83940 3746 22.4 [[2]] @@ -161,17 +161,17 @@ Probability (s) = 0.95 Burn-in Total Lower bound Dependence (M) (N) (Nmin) factor (I) - sigmapi_MP 120 126540 3746 33.8 - sigmapi_R 40 46470 3746 12.4 - mupi_oF 20 37100 3746 9.9 - sigmapi_oF 20 40070 3746 10.7 - diffF_1SW 20 38020 3746 10.1 - diffF_MSW 60 80900 3746 21.6 - diff1SW 50 53900 3746 14.4 - diffMSW 40 46740 3746 12.5 - pi_oD 640 702560 3746 188.0 - shape_lambda 30 45020 3746 12.0 - rate_lambda 40 48110 3746 12.8 - lambda_tot0 30 43740 3746 11.7 + sigmapi_MP 160 206320 3746 55.1 + sigmapi_R 60 84280 3746 22.5 + mupi_oF 40 74460 3746 19.9 + sigmapi_oF 40 74200 3746 19.8 + diffF_1SW 40 73600 3746 19.6 + diffF_MSW 60 87480 3746 23.4 + diff1SW 60 91160 3746 24.3 + diffMSW 60 86400 3746 23.1 + pi_oD 480 609280 3746 163.0 + shape_lambda 40 76040 3746 20.3 + rate_lambda 40 76040 3746 20.3 + lambda_tot0 60 81220 3746 21.7 diff --git a/Scorff/adult/results/Results_adult_2018.csv b/Scorff/adult/results/Results_adult_2018.csv index b4a1e95..1bc56ce 100644 --- a/Scorff/adult/results/Results_adult_2018.csv +++ b/Scorff/adult/results/Results_adult_2018.csv @@ -1,689 +1,689 @@ "Parameters","mean","sd","2.5%","25%","50%","75%","97.5%","Rhat","n.eff" -"logit_int_MP[1]","0.776049275","0.0896893763758345","0.602087494936818","0.7163","0.7753","0.8357","0.954104999489117","1.01105642503199","150" -"logit_int_MP[2]","-0.2228414810235","0.125685111896273","-0.472905","-0.306825","-0.2222","-0.1386","0.0193812499999999","1.00276006598565","830" 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-"sigmapi_F[1]","0.48462618","0.0799979358114589","0.3474","0.4295","0.4773","0.5318","0.665502499816885","1.0082134066807","210" -"sigmapi_F[2]","0.5349194085","0.139897274469109","0.2822","0.4401","0.5264","0.623","0.832602499853633","1.37183225431807","8" -"rho_F[1]","0.3747986401785","0.253743941647054","-0.1806025","0.212475","0.39975","0.5627","0.7947025","1.01251508691158","130" -"rho_F[2]","0.255490184042","0.388578237198977","-0.5322025","-0.0195075","0.27595","0.555775","0.9117025","1.17942279027722","13" -"logit_int_R[1]","-2.09309465","0.0694413550880693","-2.230025","-2.139","-2.093","-2.048","-1.958","1.00169185927381","2000" -"logit_int_R[2]","-1.93543965","0.126289737163251","-2.188","-2.018","-1.934","-1.851","-1.689","1.0009484942315","20000" -"logit_effort_R[1]","0.278371967575","0.0760950098381302","0.1316","0.2273","0.2776","0.3282","0.431907499999999","1.00097764500074","20000" 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+"Plambda[24,2]","0.135411651","0.0223267461288884","0.0969589997988315","0.1197","0.1334","0.1493","0.184102499338232","1.0012525891691","4900" +"Plambda[25,1]","0.8143964","0.0907876715534951","0.605297499798632","0.7605","0.8266","0.8812","0.9538","1.00192739794366","1500" +"Plambda[25,2]","0.18560364035","0.0907876196278258","0.0462197499736278","0.1188","0.1734","0.2395","0.394702499691272","1.00165250759659","2100" +"s[1]","18.52182955","5.42947542393975","9.61374987314487","14.64","17.94","21.8","30.68","1.00147408493123","2900" +"s[2]","3.62485035","1.00942515795494","1.96497499379563","2.903","3.518","4.23624997787132","5.894","1.00094848930765","20000" +"e_tot[1]","526.86325","91.5738015891793","378","461","517","581","735","1.00905315217913","190" +"e_tot[2]","695.6011","57.6052488669639","593","655","692","732","818","1.52565647942521","6" +"e_tot[3]","672.70265","40.6275726934387","600","644","670","698","758","1.00106879632108","12000" +"e_tot[4]","441.77315","34.1835196363428","382","418","439","463","516","1.02767910325186","61" +"e_tot[5]","517.4668","28.10564167769","469","497","515","535","579","1.16942174617619","13" +"e_tot[6]","295.58685","26.3048370894065","249","277","294","312","352","1.01552420017752","100" +"e_tot[7]","287.9054","44.8249586133187","218","256","282","313","392","1.00278448438232","820" +"e_tot[8]","313.6208","21.5099684169239","275","299","312","327","360","1.04974540606176","36" +"e_tot[9]","564.5298","33.8654684812978","507","541","562","585","640","1.00131986349443","4000" +"e_tot[10]","269.34385","23.5173674229499","229","253","267","283","321","1.00228365647663","1100" +"e_tot[11]","1077.69905","42.6360114289673","1001.97498782883","1048","1075.49988377498","1105","1167","1.00288964453481","770" +"e_tot[12]","519.14925","27.0901230742112","471","500","518","536","576","1.01383569157642","120" +"e_tot[13]","894.00425","42.0936185849325","820","864","891","920","984","1.00596362386556","300" +"e_tot[14]","515.22345","35.0865169727798","455","491","513","537","592","1.00592670792242","300" +"e_tot[15]","348.67615","26.306776189818","303","330","346","365","406","1.00094931829639","20000" +"e_tot[16]","361.6241","27.8378563560904","314","342","359","378","423","1.00687741236744","250" +"e_tot[17]","761.29715","35.682409021718","698","736","759","784","837","1.00123185664071","5300" +"e_tot[18]","545.4919","30.0432232650428","491","525","544","565","609","1.01342491849536","120" +"e_tot[19]","465.1949","42.9711873251951","392","435","462","492","560","1.00192282746946","1500" +"e_tot[20]","671.11945","39.1126216400292","602","644","668","696","756","1.00143170140177","3100" +"e_tot[21]","755.28845","43.6329558744238","679","725","752","782","850","1.00676246722009","260" +"e_tot[22]","669.9585","41.5196022574709","595","641","668","696","758","1.00343459205691","610" +"e_tot[23]","564.77445","48.3838674263319","469","533","565","596","660","1.00365992681214","550" +"e_tot[24]","898.9209","54.4493845691942","784","865","901","936","999","1.01818023913259","89" +"e_tot[25]","409.78865","39.5026417358726","342","382","406","434","497","1.00165561659044","2100" +"e_1SW[1]","474.5763","87.7671158899595","335","412","464","526","675","1.00268766966785","860" +"e_1SW[2]","654.48705","55.682047886373","555","616","651","690","773","1.52289806388072","6" +"e_1SW[3]","611.5318","37.7586397332283","545","585","609","635","692","1.00698993267242","250" +"e_1SW[4]","411.223","31.0191099204831","359","389","408","430","480","1.014333753474","110" +"e_1SW[5]","495.1122","27.292655708318","449","476","493","512","555","1.18689876665753","13" +"e_1SW[6]","231.96765","21.7308723943207","196","217","230","245","281","1.09011139213661","22" +"e_1SW[7]","281.0859","44.1067295474236","212","250","275","306","383","1.0013484603197","3800" +"e_1SW[8]","281.9492","18.4187291048838","250","269","280","293","323","1.01459693261358","110" +"e_1SW[9]","543.3082","33.6502456114586","487","519","541","564","618","1.00119454316458","6100" +"e_1SW[10]","229.6636","21.376297208453","195","215","227","243","277","1.00321649346857","660" +"e_1SW[11]","1023.83655","41.6197722767643","949","995","1022","1050","1112","1.00655786862901","270" +"e_1SW[12]","418.62625","21.7349575881014","381","403","417","432","465","1.00228674215046","1100" +"e_1SW[13]","816.96835","38.8344132678761","750","789","814","841","901","1.00122808136953","5400" +"e_1SW[14]","433.89435","32.2248973664465","379","411","431","454","504","1.00498233273129","370" +"e_1SW[15]","274.554","22.5540133496438","237","259","272","288","325","1.00314997091909","680" +"e_1SW[16]","258.3646","22.2764893764468","222","242.749613268765","256","271","309","1.00415396224643","470" +"e_1SW[17]","699.83555","34.2531891981756","639","676","698","721","773.024984246919","1.00114577867537","7600" +"e_1SW[18]","353.2616","21.2711421535005","317","338","351","366","400","1.00474118097085","400" +"e_1SW[19]","349.7116","36.9415749452832","290","324","345","372","434","1.00210592527508","1300" +"e_1SW[20]","573.92535","35.7873205757738","512","549","571","596","653","1.00100287920825","20000" +"e_1SW[21]","631.40335","41.0934860106456","561","602","628","657","720.024983088376","1.00611565281826","290" +"e_1SW[22]","527.00295","34.9131005143754","465","503","525","549","602","1.00647246844363","270" +"e_1SW[23]","494.7731","45.42586919223","405","465","495","524","585","1.00470230444725","400" +"e_1SW[24]","773.5572","51.1340949166322","665","742","776","808","867","1.01164203924248","140" +"e_1SW[25]","286.07135","28.5956560469372","240","266","283","302","352","1.00215187917604","1200" +"e_MSW[1]","52.28695","24.5494407970869","15","35","49","66","111","1.03704864661873","47" +"e_MSW[2]","41.11405","12.3080630896316","21","32","40","48","69","1.00898968414102","190" +"e_MSW[3]","61.17085","14.6191328822817","37","51","60","70","94","1.06372686360115","29" +"e_MSW[4]","30.55015","13.263279409955","9","21","29","39","60","1.0206645473952","84" +"e_MSW[5]","22.3546","7.05786437334096","12","17","21","26","39","1.00106182379078","13000" +"e_MSW[6]","63.6192","15.4420178136054","37","53","62","73","98","1.02972381897278","57" +"e_MSW[7]","6.8195","6.75833585323897","0","2","5","10","24","1.03631838516824","69" +"e_MSW[8]","31.6716","10.1571803102826","12","25","31","38","54","1.0384415681914","45" +"e_MSW[9]","21.2216","5.75584484915085","12","17","20","24","35","1.00128000232659","4500" +"e_MSW[10]","39.68025","8.98433892141168","24","34","39","45","60","1.001321215308","4000" +"e_MSW[11]","53.8625","9.22984036956558","39","47","53","59","74","1.0194694674252","84" +"e_MSW[12]","100.523","15.6543388207933","74","90","99","110","136","1.02325087498083","72" +"e_MSW[13]","77.0359","16.0261802408639","51","65","75","86","114","1.06454107725996","29" +"e_MSW[14]","81.3291","13.3170627541519","59","72","80","89","111","1.00206558369403","1300" +"e_MSW[15]","74.12215","13.8429263780472","52","64","73","82","106","1.00670757610549","260" +"e_MSW[16]","103.2595","16.2963596645667","77","92","101","113","140","1.00393352700993","500" +"e_MSW[17]","61.4616","10.4101510076559","44","54","60","68","85","1.00107722108962","12000" +"e_MSW[18]","192.2303","20.4666095388391","157","178","191","205","236","1.01098581106469","150" +"e_MSW[19]","115.4833","22.0379083531135","79","100","113","128","165","1.01473027898268","110" +"e_MSW[20]","97.1941","16.1290741377683","71","86","95","106","134","1.00223990716163","1200" +"e_MSW[21]","123.8851","15.3016013848305","98","113","122","133","158","1.00151587251464","2600" +"e_MSW[22]","142.95555","21.6163627272115","107","128","141","155","191","1.00154371065057","2500" +"e_MSW[23]","70.00135","13.987820814339","46","60","69","78","102","1.00131125390485","4100" +"e_MSW[24]","125.3637","14.0216387283239","102","116","124","134","157","1.01885389147236","89" +"e_MSW[25]","123.7173","26.8377512834943","79.9748463908157","105","121","139","184","1.00096370542279","20000" diff --git a/Scorff/script_bilan.R b/Scorff/script_bilan.R index 747dc44..1a7be99 100755 --- a/Scorff/script_bilan.R +++ b/Scorff/script_bilan.R @@ -1,14 +1,18 @@ rm(list=ls()) # Clear memory -year <- 2017 +#setwd("~/Documents/RESEARCH/PROJECTS/ORE-DiaPFC/") +wdir <- "/media/hdd/mbuoro/ORE-DiaPFC/Abundance/" +setwd(wdir) + +year <- 2018 ##________________________SCORFF (starting in 1994) site <- "Scorff" -setwd(paste("~/Documents/RESEARCH/PROJECTS/ORE-DiaPFC/Abundance/",site,"/",sep="")) +#setwd(paste(wdir,site,"/",sep="")) years <- seq(1993, year, 1) -table <- array(, dim=c(length(years), 5)) -colnames(table) <- c( "Year","Parr 0+","Smolts", "1SW (escapment)", "MSW (escapment)") +table <- array(, dim=c(length(years), 7)) +colnames(table) <- c( "Year","Parr 0+","Smolts","1SW (tot returns)", "MSW (tot returns)", "1SW (escapment)", "MSW (escapment)") rownames(table) <- years smolt.years <- years table[,1] <- years @@ -16,9 +20,9 @@ table[,1] <- years ## PARR (from 1993 to now on) stade <- "tacon" -dir <- paste("~/Documents/RESEARCH/PROJECTS/ORE-DiaPFC/Abundance/",site,"/",stade,sep="") +dir <- paste(wdir,site,"/",stade,sep="") if (file.exists(dir)){ - load(paste("~/Documents/RESEARCH/PROJECTS/ORE-DiaPFC/Abundance/",site,"/",stade,"/results/Results_",stade,"_",year,".RData",sep="")) + load(paste0(site,"/",stade,"/results/Results_",stade,"_",year,".RData")) n_parr <- fit$median$ntot_Sc table[,2] <- round(n_parr,0) # 1995 to now } @@ -27,27 +31,35 @@ if (file.exists(dir)){ ## SMOLTS (from 1995 to now on) stade <- "smolt" -dir <- paste("~/Documents/RESEARCH/PROJECTS/ORE-DiaPFC/Abundance/",site,"/",stade,sep="") +dir <- paste(wdir,site,"/",stade,sep="") if (file.exists(dir)){ -load(paste("~/Documents/RESEARCH/PROJECTS/ORE-DiaPFC/Abundance/",site,"/",stade,"/results/Results_",stade,"_",year,".RData",sep="")) -n_smolt <- fit$median$Nesc # escapement from river + load(paste0(site,"/",stade,"/results/Results_",stade,"_",year,".RData")) + n_smolt <- fit$median$Nesc # escapement from river table[3:nrow(table),3] <- round(n_smolt,0) # 1995 to now } ## ADULTS (1984 to now) stade <- "adult" -dir <- paste("~/Documents/RESEARCH/PROJECTS/ORE-DiaPFC/Abundance/",site,"/",stade,sep="") +dir <- paste(wdir,site,"/",stade,sep="") if (file.exists(dir)){ -load(paste("~/Documents/RESEARCH/PROJECTS/ORE-DiaPFC/Abundance/",site,"/",stade,"/results/Results_",stade,"_",year,".RData",sep="")) -e_1SW <-fit$median$e_1SW # 1SW + load(paste0(site,"/",stade,"/results/Results_",stade,"_",year,".RData")) + + # n returns + n_1SW <- fit$median$n_1SW # 1SW + n_MSW <- fit$median$n_MSW # MSW + table[2:nrow(table),4] <- round(n_1SW,0) # 1995 to now + table[2:nrow(table),5] <- round(n_MSW,0) # 1995 to now + + # escapment +e_1SW <- fit$median$e_1SW # 1SW e_MSW <- fit$median$e_MSW # MSW -table[2:nrow(table),4] <- round(e_1SW,0) # 1995 to now -table[2:nrow(table),5] <- round(e_MSW,0) # 1995 to now +table[2:nrow(table),6] <- round(e_1SW,0) # 1995 to now +table[2:nrow(table),7] <- round(e_MSW,0) # 1995 to now } #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-DiaPFC/Abundance/',site,"/Bilan_",site,"_",year,'.csv',sep=""), open="wt") +con <- file(paste(wdir,site,"/Bilan_",site,"_",year,'.csv',sep=""), open="wt") write.csv( table, con, row.names = FALSE) close(con) diff --git a/out.txt b/out.txt new file mode 100644 index 0000000..6c9c980 --- /dev/null +++ b/out.txt @@ -0,0 +1,5 @@ +[1] "model/model_adult-Scorff.R" +Start of the run +Sample analyzed after 36.78914 minutes +null device + 1 diff --git a/report/Total_return_Nivelle.csv b/report/Total_return_Nivelle.csv index 4c485fc..a333f40 100644 --- a/report/Total_return_Nivelle.csv +++ b/report/Total_return_Nivelle.csv @@ -1,4 +1,4 @@ -"year","2.5%","50%","97.5%" +"","2.5%","50%","97.5%" "1984",176,201,241 "1985",118,137,169 "1986",328,372,441 @@ -6,7 +6,7 @@ "1988",134,156,189 "1989",277,324,394 "1990",275,312,373 -"1991",199,230,278 +"1991",199,230,278.024999999998 "1992",240,264,306 "1993",481,516,562 "1994",349,387,437 diff --git a/report/Total_return_Scorff.csv b/report/Total_return_Scorff.csv index 448397e..6f918dd 100644 --- a/report/Total_return_Scorff.csv +++ b/report/Total_return_Scorff.csv @@ -9,28 +9,28 @@ "1991",NA,NA,NA "1992",NA,NA,NA "1993",NA,NA,NA -"1994",457,599,818 -"1995",778,848,948 -"1996",726,785,866 -"1997",478,529,598 -"1998",562,607,670 -"1999",311,355,415 -"2000",287,347,446 -"2001",322,361,413 -"2002",548,607,689 -"2003",247,283,336 -"2004",1110,1181,1269 -"2005",542,585,641 -"2006",927,995,1085 -"2007",522,580,658 -"2008",332,374,430 -"2009",338,380,440 -"2010",771,830,905 -"2011",556,604,668 -"2012",463,529,625 -"2013",644,709,792 -"2014",750,821,912 -"2015",711,776,862 -"2016",648,708,787 -"2017",1041,1098,1170 -"2018",362,415,491 +"1994",445,583,795 +"1995",770,853,963 +"1996",743,809,896 +"1997",479,531,605 +"1998",556,600,663 +"1999",308,350,407 +"2000",297,363,475 +"2001",320,353,396 +"2002",535,590,665 +"2003",249,286,340 +"2004",1111,1184,1274 +"2005",541,585,642 +"2006",926,997,1088 +"2007",521,578,656 +"2008",332,375,434 +"2009",336,381,442 +"2010",772,832,910 +"2011",552,601,664 +"2012",461,528,626 +"2013",644,710,793 +"2014",752,825,921 +"2015",710,775,861.024999999998 +"2016",646,707,787 +"2017",1038,1095,1167 +"2018",389,450,538 diff --git a/report/Total_return_all.csv b/report/Total_return_all.csv index 9a02238..c173a26 100644 --- a/report/Total_return_all.csv +++ b/report/Total_return_all.csv @@ -9,28 +9,28 @@ "1991",191,54,231,NA "1992",185,58,264,NA "1993",78,132,516,NA -"1994",64,71,388,599 -"1995",120,147,239,848 -"1996",63,259,215,785 -"1997",46,72,123,529 -"1998",243,176,174,607 -"1999",82,238,180,356 -"2000",71,262,169,348 -"2001",111,195,218,361 -"2002",146,323,426,607 -"2003",51,217,95,283 -"2004",99,402,109,1181 +"1994",64,71,388,583 +"1995",120,147,239,854 +"1996",63,259,215,809 +"1997",46,72,123,531 +"1998",243,176,174,600 +"1999",82,238,180,350 +"2000",71,262,169,363 +"2001",111,195,218,353 +"2002",146,323,426,590 +"2003",51,217,95,286 +"2004",99,402,109,1184 "2005",313,168,104,586 -"2006",229,215,78,995 -"2007",94,212,84,580 +"2006",229,215,78,997 +"2007",94,212,84,579 "2008",144,120,90,375 -"2009",143,168,71,381 -"2010",187,509,174,830 -"2011",174,279,89,605 -"2012",172,259,93,529 -"2013",218,329,131,709 -"2014",185,290,126,821 -"2015",185,172,94,777 +"2009",143,168,71,382 +"2010",187,509,174,833 +"2011",174,279,89,601 +"2012",172,259,93,528 +"2013",218,329,131,711 +"2014",185,290,126,825 +"2015",185,172,94,776 "2016",210,305,84,708 -"2017",509,264,99,1098 -"2018",169,215,63,415 +"2017",509,264,99,1096 +"2018",169,215,63,451 diff --git a/report/Total_return_byage_Scorff.csv b/report/Total_return_byage_Scorff.csv index 128d48f..bee1994 100644 --- a/report/Total_return_byage_Scorff.csv +++ b/report/Total_return_byage_Scorff.csv @@ -9,28 +9,28 @@ "1991",1991,NA,NA,NA "1992",1992,NA,NA,NA "1993",1993,NA,NA,NA -"1994",1994,516,79,599 -"1995",1995,758,89,848 -"1996",1996,699,86,785 -"1997",1997,458,71,529 -"1998",1998,580,27,607 -"1999",1999,256,97,356 -"2000",2000,303,43,348 -"2001",2001,320,39,361 -"2002",2002,586,23,607 -"2003",2003,224,58,283 -"2004",2004,1116,64,1181 -"2005",2005,453,130,586 -"2006",2006,888,105,995 -"2007",2007,485,94,580 +"1994",1994,505,75,583 +"1995",1995,758,94,854 +"1996",1996,725,83,809 +"1997",1997,460,71,531 +"1998",1998,572,27,600 +"1999",1999,251,97,350 +"2000",2000,317,46,363 +"2001",2001,313,40,353 +"2002",2002,567,23,590 +"2003",2003,228,58,286 +"2004",2004,1118,64,1184 +"2005",2005,454,130,586 +"2006",2006,888,106,997 +"2007",2007,483,94,579 "2008",2008,286,87,375 -"2009",2009,262,118,381 -"2010",2010,763,65,830 -"2011",2011,387,217,605 -"2012",2012,381,147,529 -"2013",2013,601,105,709 -"2014",2014,683,138,821 -"2015",2015,599,176,777 +"2009",2009,264,116,382 +"2010",2010,766,65,833 +"2011",2011,387,214,601 +"2012",2012,382,145,528 +"2013",2013,605,104,711 +"2014",2014,687,137,825 +"2015",2015,598,176,776 "2016",2016,620,87,708 -"2017",2017,953,144,1098 -"2018",2018,286,127,415 +"2017",2017,951,143,1096 +"2018",2018,302,145,451 diff --git a/report/exploitation_Scorff.png b/report/exploitation_Scorff.png index 7d3e73a..6f8a545 100644 Binary files a/report/exploitation_Scorff.png and b/report/exploitation_Scorff.png differ diff --git a/report/prop_MSW_return.png b/report/prop_MSW_return.png index 3f03785..82e639f 100644 Binary files a/report/prop_MSW_return.png and b/report/prop_MSW_return.png differ diff --git a/report/total_return.png b/report/total_return.png index 9acbc8e..f754d92 100644 Binary files a/report/total_return.png and b/report/total_return.png differ diff --git a/report/total_smolt.png b/report/total_smolt.png index 4a0374b..8bc1a1c 100644 Binary files a/report/total_smolt.png and b/report/total_smolt.png differ diff --git a/report/total_tacon.png b/report/total_tacon.png index b9bec37..6db8615 100644 Binary files a/report/total_tacon.png and b/report/total_tacon.png differ