Commit baffec1a authored by Poulet Camille's avatar Poulet Camille
Browse files

Merge branch 'SpawnerRunAnalysis' of gitlab-ssh.irstea.fr:SimAquaLife/GR3D into SpawnerRunAnalysis

parents 398b3be9 3c34625e
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -333,6 +333,16 @@
<exportSeason>SPRING</exportSeason>
<fileNameOutput>biomassFluxes</fileNameOutput>
</species.WriteBiomassFluxes>
<species.IdentifyPopulation>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<consoleDisplay>false</consoleDisplay>
<years>
<long>1813</long>
</years>
<fluxesSeason>SPRING</fluxesSeason>
<fileNameOutput>effectiveFluxes</fileNameOutput>
</species.IdentifyPopulation>
</processesAtEnd>
</processes>
<useCemetery>false</useCemetery>
......
inshore_basin_id,inshore_basin_name,wintering_offshore_basin_id,wintering_offshore_basin_name,summering_offshore_basin_id,summering_offshore_basin_name
93,Pearl,1,Off Florida,4,Bay of Fundy
94,Escambia,1,Off Florida,4,Bay of Fundy
95,Choctawhatchee,1,Off Florida,4,Bay of Fundy
99,Ochlockonee,1,Off Florida,4,Bay of Fundy
98,Aucilla,1,Off Florida,4,Bay of Fundy
97,Ecofina River,1,Off Florida,4,Bay of Fundy
85,Waccasassa,1,Off Florida,4,Bay of Fundy
86,Withlacoochee,1,Off Florida,4,Bay of Fundy
91,Manatee,1,Off Florida,4,Bay of Fundy
90,Little Manatee,1,Off Florida,4,Bay of Fundy
88,Hillsborough,1,Off Florida,4,Bay of Fundy
89,Alafia,1,Off Florida,4,Bay of Fundy
87,Myakka,1,Off Florida,4,Bay of Fundy
96,Peace,1,Off Florida,4,Bay of Fundy
55,St. Marys,1,Off Florida,4,Bay of Fundy
56,Nassau,1,Off Florida,4,Bay of Fundy
38,Satilla,1,Off Florida,4,Bay of Fundy
1,St. Johns,1,Off Florida,4,Bay of Fundy
3,Altamaha,1,Off Florida,4,Bay of Fundy
2,Ogeechee,1,Off Florida,4,Bay of Fundy
10,Savannah,1,Off Florida,4,Bay of Fundy
59,Coosawatchie,1,Off Florida,4,Bay of Fundy
39,White Oak,2,Mid-Atlantic Bight,4,Bay of Fundy
20,Paskamanset,2,Mid-Atlantic Bight,4,Bay of Fundy
81,Mersey,3,Scotian Shelf,4,Bay of Fundy
37,Alligator,2,Mid-Atlantic Bight,4,Bay of Fundy
6,Penobscot,3,Scotian Shelf,4,Bay of Fundy
13,Susquehanna,2,Mid-Atlantic Bight,4,Bay of Fundy
108,Exploits,3,Scotian Shelf,5,Off Newfoundland and Labrador
60,Salkehatchie,1,Off Florida,4,Bay of Fundy
50,Edisto,1,Off Florida,4,Bay of Fundy
92,Loxahatchee,1,Off Florida,4,Bay of Fundy
54,Patuxent,2,Mid-Atlantic Bight,4,Bay of Fundy
65,Petitcodiac,3,Scotian Shelf,4,Bay of Fundy
103,St. Marguerite,3,Scotian Shelf,6,St. Lawrence Estuary
55,St. Marys,1,Off Florida,4,Bay of Fundy
61,Cooper,1,Off Florida,4,Bay of Fundy
11,Santee,1,Off Florida,4,Bay of Fundy
49,Pee Dee,1,Off Florida,4,Bay of Fundy
8,Cape Fear,1,Off Florida,4,Bay of Fundy
42,New,1,Off Florida,4,Bay of Fundy
39,White Oak,1,Off Florida,4,Bay of Fundy
5,Potomac,2,Mid-Atlantic Bight,4,Bay of Fundy
7,Neuse,1,Off Florida,4,Bay of Fundy
48,Pamlico-Tar,1,Off Florida,4,Bay of Fundy
45,Rappahannock,2,Mid-Atlantic Bight,4,Bay of Fundy
12,James,2,Mid-Atlantic Bight,4,Bay of Fundy
46,York,2,Mid-Atlantic Bight,4,Bay of Fundy
9,Roanoke,2,Mid-Atlantic Bight,4,Bay of Fundy
47,Chowan,2,Mid-Atlantic Bight,4,Bay of Fundy
54,Patuxent,2,Mid-Atlantic Bight,4,Bay of Fundy
40,Perquimmans,2,Mid-Atlantic Bight,4,Bay of Fundy
41,Pasquotank,2,Mid-Atlantic Bight,4,Bay of Fundy
53,Chester-Sassafras,2,Mid-Atlantic Bight,4,Bay of Fundy
13,Susquehanna,2,Mid-Atlantic Bight,4,Bay of Fundy
37,Alligator,2,Mid-Atlantic Bight,4,Bay of Fundy
34,Transquaking,2,Mid-Atlantic Bight,4,Bay of Fundy
35,Blackwater,2,Mid-Atlantic Bight,4,Bay of Fundy
26,Manasquan,2,Mid-Atlantic Bight,4,Bay of Fundy
92,Loxahatchee,1,Off Florida,4,Bay of Fundy
82,Cornwallis,3,Scotian Shelf,4,Bay of Fundy
52,Choptank,2,Mid-Atlantic Bight,4,Bay of Fundy
51,Nanticoke,2,Mid-Atlantic Bight,4,Bay of Fundy
33,Wicomico,2,Mid-Atlantic Bight,4,Bay of Fundy
58,Pokomoke-Western Lower Delmarva,2,Mid-Atlantic Bight,4,Bay of Fundy
14,Delaware,2,Mid-Atlantic Bight,4,Bay of Fundy
28,Mullica,2,Mid-Atlantic Bight,4,Bay of Fundy
62,Raritan,2,Mid-Atlantic Bight,4,Bay of Fundy
36,Pawcatuck,2,Mid-Atlantic Bight,4,Bay of Fundy
56,Nassau,1,Off Florida,4,Bay of Fundy
27,Metedeconk,2,Mid-Atlantic Bight,4,Bay of Fundy
26,Manasquan,2,Mid-Atlantic Bight,4,Bay of Fundy
25,Shark,2,Mid-Atlantic Bight,4,Bay of Fundy
62,Raritan,2,Mid-Atlantic Bight,4,Bay of Fundy
78,Maccan-Hebert-LaPlanche,3,Scotian Shelf,4,Bay of Fundy
19,Blackstone-Providence,2,Mid-Atlantic Bight,4,Bay of Fundy
101,Philip,3,Scotian Shelf,6,St. Lawrence Estuary
79,Kennetcook,3,Scotian Shelf,4,Bay of Fundy
5,Potomac,2,Mid-Atlantic Bight,4,Bay of Fundy
35,Blackwater,2,Mid-Atlantic Bight,4,Bay of Fundy
110,Romaine,3,Scotian Shelf,6,St. Lawrence Estuary
75,Medway,3,Scotian Shelf,4,Bay of Fundy
71,Shubenacadie,3,Scotian Shelf,4,Bay of Fundy
4,Merrimack,3,Mid-Atlantic Bight,4,Bay of Fundy
7,Neuse,2,Mid-Atlantic Bight,4,Bay of Fundy
18,Sakonnet,2,Mid-Atlantic Bight,4,Bay of Fundy
44,Hudson,2,Mid-Atlantic Bight,4,Bay of Fundy
102,Gander,3,Scotian Shelf,5,Off Newfoundland and Labrador
112,Eagle,3,Scotian Shelf,5,Off Newfoundland and Labrador
15,Connecticut,2,Mid-Atlantic Bight,4,Bay of Fundy
68,Restigouche,3,Scotian Shelf,6,St. Lawrence Estuary
40,Perquimmans,2,Mid-Atlantic Bight,4,Bay of Fundy
106,Manicouagan,3,Scotian Shelf,6,St. Lawrence Estuary
66,St. John,3,Scotian Shelf,4,Bay of Fundy
67,St. Croix,3,Scotian Shelf,4,Bay of Fundy
14,Delaware,2,Mid-Atlantic Bight,4,Bay of Fundy
104,Natashquan,3,Scotian Shelf,6,St. Lawrence Estuary
105,Churchill,3,Scotian Shelf,5,Off Newfoundland and Labrador
28,Mullica,2,Mid-Atlantic Bight,4,Bay of Fundy
24,Nissequogue,2,Mid-Atlantic Bight,4,Bay of Fundy
77,Avon,3,Scotian Shelf,4,Bay of Fundy
47,Chowan,2,Mid-Atlantic Bight,4,Bay of Fundy
72,John,3,Scotian Shelf,6,St. Lawrence Estuary
59,Coosawatchie,1,Off Florida,4,Bay of Fundy
31,Palmer,2,Mid-Atlantic Bight,4,Bay of Fundy
109,Humber,3,Scotian Shelf,6,St. Lawrence Estuary
49,Pee Dee,1,Off Florida,4,Bay of Fundy
3,Altamaha,1,Off Florida,4,Bay of Fundy
100,Richibucto,3,Scotian Shelf,6,St. Lawrence Estuary
32,Taunton,2,Mid-Atlantic Bight,4,Bay of Fundy
8,Cape Fear,1,Off Florida,4,Bay of Fundy
1,St. Johns,1,Off Florida,4,Bay of Fundy
51,Nanticoke,2,Mid-Atlantic Bight,4,Bay of Fundy
74,Musquodoboit,3,Scotian Shelf,4,Bay of Fundy
58,Pokomoke-Western Lower Delmarva,2,Mid-Atlantic Bight,4,Bay of Fundy
2,Ogeechee,1,Off Florida,4,Bay of Fundy
70,Margaree,3,Scotian Shelf,6,St. Lawrence Estuary
84,St. Lawrence,3,Scotian Shelf,6,St. Lawrence Estuary
42,New,2,Mid-Atlantic Bight,4,Bay of Fundy
80,Tusket,3,Scotian Shelf,4,Bay of Fundy
22,Hammonasset,2,Mid-Atlantic Bight,4,Bay of Fundy
50,Edisto,1,Off Florida,4,Bay of Fundy
64,Miramichi,3,Scotian Shelf,6,St. Lawrence Estuary
63,Saco,3,Scotian Shelf,4,Bay of Fundy
33,Wicomico,2,Mid-Atlantic Bight,4,Bay of Fundy
46,York,2,Mid-Atlantic Bight,4,Bay of Fundy
69,LaHave,3,Scotian Shelf,4,Bay of Fundy
76,Annapolis,3,Scotian Shelf,4,Bay of Fundy
9,Roanoke,2,Mid-Atlantic Bight,4,Bay of Fundy
57,Housatonic,2,Mid-Atlantic Bight,4,Bay of Fundy
83,Mira,3,Scotian Shelf,6,St. Lawrence Estuary
30,Sheepscot,3,Scotian Shelf,4,Bay of Fundy
41,Pasquotank,2,Mid-Atlantic Bight,4,Bay of Fundy
53,Chester-Sassafras,2,Mid-Atlantic Bight,4,Bay of Fundy
38,Satilla,1,Off Florida,4,Bay of Fundy
48,Pamlico-Tar,2,Mid-Atlantic Bight,4,Bay of Fundy
45,Rappahannock,2,Mid-Atlantic Bight,4,Bay of Fundy
21,Farm,2,Mid-Atlantic Bight,4,Bay of Fundy
22,Hammonasset,2,Mid-Atlantic Bight,4,Bay of Fundy
23,Menunketesuck,2,Mid-Atlantic Bight,4,Bay of Fundy
15,Connecticut,2,Mid-Atlantic Bight,4,Bay of Fundy
107,George,3,Scotian Shelf,5,Off Newfoundland and Labrador
73,St. Mary's,3,Scotian Shelf,4,Bay of Fundy
10,Savannah,1,Off Florida,4,Bay of Fundy
16,Kennebec,3,Scotian Shelf,4,Bay of Fundy
43,Thames,2,Mid-Atlantic Bight,4,Bay of Fundy
36,Pawcatuck,2,Mid-Atlantic Bight,4,Bay of Fundy
19,Blackstone-Providence,2,Mid-Atlantic Bight,4,Bay of Fundy
31,Palmer,2,Mid-Atlantic Bight,4,Bay of Fundy
84,St Lawrence,3,Scotian Shelf,6,St. Lawrence Estuary
18,Sakonnet,2,Mid-Atlantic Bight,4,Bay of Fundy
32,Taunton,2,Mid-Atlantic Bight,4,Bay of Fundy
20,Paskamanset,2,Mid-Atlantic Bight,4,Bay of Fundy
4,Merrimack,3,Scotian Shelf,4,Bay of Fundy
63,Saco,3,Scotian Shelf,4,Bay of Fundy
25,Shark,2,Mid-Atlantic Bight,4,Bay of Fundy
17,Nonesuch,3,Scotian Shelf,4,Bay of Fundy
16,Kennebec,3,Scotian Shelf,4,Bay of Fundy
30,Sheepscot,3,Scotian Shelf,4,Bay of Fundy
6,Penobscot,3,Scotian Shelf,4,Bay of Fundy
106,Manicouagan,3,Scotian Shelf,6,St. Lawrence Estuary
29,Pleasant,3,Scotian Shelf,4,Bay of Fundy
67,St. Croix,3,Scotian Shelf,4,Bay of Fundy
68,Restigouche,3,Scotian Shelf,6,St. Lawrence Estuary
103,St Marguerite,3,Scotian Shelf,6,St. Lawrence Estuary
66,St John,3,Scotian Shelf,4,Bay of Fundy
80,Tusket,3,Scotian Shelf,4,Bay of Fundy
107,George,3,Scotian Shelf,5,Off Newfoundland and Labrador
64,Miramichi,3,Scotian Shelf,6,St. Lawrence Estuary
76,Annapolis,3,Scotian Shelf,4,Bay of Fundy
100,Richibucto,3,Scotian Shelf,6,St. Lawrence Estuary
81,Mersey,3,Scotian Shelf,4,Bay of Fundy
65,Petitcodiac,3,Scotian Shelf,4,Bay of Fundy
75,Medway,3,Scotian Shelf,4,Bay of Fundy
82,Cornwallis,3,Scotian Shelf,4,Bay of Fundy
69,LaHave,3,Scotian Shelf,4,Bay of Fundy
78,Maccan-Hebert-LaPlanche,3,Scotian Shelf,4,Bay of Fundy
77,Avon,3,Scotian Shelf,4,Bay of Fundy
79,Kennetcook,3,Scotian Shelf,4,Bay of Fundy
110,Romaine,3,Scotian Shelf,6,St. Lawrence Estuary
101,Philip,3,Scotian Shelf,6,St. Lawrence Estuary
71,Shubenacadie,3,Scotian Shelf,4,Bay of Fundy
74,Musquodoboit,3,Scotian Shelf,4,Bay of Fundy
72,John,3,Scotian Shelf,6,St. Lawrence Estuary
73,St Mary's,3,Scotian Shelf,4,Bay of Fundy
104,Natashquan,3,Scotian Shelf,6,St. Lawrence Estuary
70,Margaree,3,Scotian Shelf,6,St. Lawrence Estuary
111,Kanairiktok,3,Scotian Shelf,5,Off Newfoundland and Labrador
105,Churchill,3,Scotian Shelf,5,Off Newfoundland and Labrador
83,Mira,3,Scotian Shelf,6,St. Lawrence Estuary
109,Humber,3,Scotian Shelf,6,St. Lawrence Estuary
112,Eagle,3,Scotian Shelf,5,Off Newfoundland and Labrador
108,Exploits,3,Scotian Shelf,5,Off Newfoundland and Labrador
102,Gander,3,Scotian Shelf,5,Off Newfoundland and Labrador
34,Transquaking,2,Mid-Atlantic Bight,4,Bay of Fundy
gid,name,obs_1751_1850
basin_id,basin_name,obs_1900_1950
1,St. Johns,1
2,Ogeechee,1
3,Altamaha,1
......@@ -64,14 +64,14 @@ gid,name,obs_1751_1850
63,Saco,1
64,Miramichi,1
65,Petitcodiac,1
66,St John,1
66,St. John,1
67,St. Croix,1
68,Restigouche,1
69,LaHave,1
70,Margaree,1
71,Shubenacadie,1
72,John,1
73,St Mary's,1
73,St. Mary's,1
74,Musquodoboit,1
75,Medway,1
76,Annapolis,1
......@@ -82,26 +82,12 @@ gid,name,obs_1751_1850
81,Mersey,1
82,Cornwallis,1
83,Mira,1
84,St Lawrence,1
85,Waccasassa,0
86,Withlacoochee,0
87,Myakka,0
88,Hillsborough,0
89,Alafia,0
90,Little Manatee,0
91,Manatee,0
84,St. Lawrence,1
92,Loxahatchee,0
93,Pearl,0
94,Escambia,0
95,Choctawhatchee,0
96,Peace,0
97,Ecofina River,0
98,Aucilla,0
99,Ochlockonee,0
100,Richibucto,1
101,Philip,1
102,Gander,0
103,St Marguerite,0
103,St. Marguerite,0
104,Natashquan,0
105,Churchill,0
106,Manicouagan,0
......
basin_id,basin_name,long_outlet,lat_outlet,areasqkm,ordre,pdam
93,Pearl,-89.5264828744249,30.1840957507959,22502.86,1,1
94,Escambia,-87.1869986588541,30.5474851606918,10994.59,2,1
95,Choctawhatchee,-86.1368211590464,30.4272062037018,12062.44,3,1
99,Ochlockonee,-84.4387396068327,29.9794602714836,6443.8,4,1
98,Aucilla,-83.996137230487,30.0850832468076,2469.93,5,1
97,Ecofina River,-83.9253330403762,30.0376943527939,604.87,6,1
85,Waccasassa,-82.8164398707204,29.1572434723382,2333.96,7,1
86,Withlacoochee,-82.7547782589596,29.0019245944418,5392.69,8,1
91,Manatee,-82.654463857619,27.5281168603338,943.64,9,1
90,Little Manatee,-82.4693774381326,27.7145207481533,586.56,10,1
88,Hillsborough,-82.4578476309911,27.9403701084067,1698.63,11,1
89,Alafia,-82.3939511667447,27.854811089483,1091.26,12,1
87,Myakka,-82.1989602873793,26.9559650977769,1557.25,13,1
96,Peace,-82.0782782531587,26.9438310652739,6063.17,14,1
55,St. Marys,-81.4502928202904,30.7094031056253,4097.78,15,1
56,Nassau,-81.4296014822575,30.5060065992272,1109.48,16,1
38,Satilla,-81.4247477431296,30.9947520835842,7220.09,17,1
1,St. Johns,-81.3973992896245,30.400134358449,24604.51,18,1
3,Altamaha,-81.2844582284656,31.3157821876964,37402.01,19,1
2,Ogeechee,-81.0237674410297,31.8438533049897,15372.53,20,1
10,Savannah,-80.8646615058929,32.0362734521014,28499.28,21,1
59,Coosawatchie,-80.6636354441333,32.2516594177392,2588.83,22,1
60,Salkehatchie,-80.4321220175571,32.4584970998355,4894.77,23,1
50,Edisto,-80.1872703688737,32.562942800606,8344.02,24,1
92,Loxahatchee,-80.0709743843059,26.9441253762972,696.12,25,1
61,Cooper,-79.8662003081486,32.753843926302,3274.44,26,1
11,Santee,-79.2478784404616,33.1120785803593,39992.56,27,1
49,Pee Dee,-79.1811873299253,33.2014102347386,38392.54,28,1
8,Cape Fear,-78.0059946892597,33.8850977125776,23890.7,29,1
42,New,-77.4076801547335,34.7095429986313,1077.25,30,1
39,White Oak,-77.126148395255,34.7545637592522,708.15,31,1
5,Potomac,-77.0785676003281,38.7004187160194,36801.61,32,1
7,Neuse,-77.0151553327195,35.0853995116449,15703.67,33,1
48,Pamlico-Tar,-76.9651369998172,35.4669031049334,11566.11,34,1
45,Rappahannock,-76.9182139854417,38.0431663276391,7025.77,35,1
12,James,-76.8978563228362,37.2281141110066,26780.72,36,1
46,York,-76.782132528935,37.5074806770657,6927.38,37,1
9,Roanoke,-76.7207971019963,35.9437258469624,24543.07,38,1
47,Chowan,-76.6891105151735,36.2723820431766,12458.86,39,1
54,Patuxent,-76.6705173847298,38.5594586875552,2401.05,40,1
40,Perquimmans,-76.4397214955593,36.1816647207066,568.44,41,1
41,Pasquotank,-76.1801527643399,36.2910089070369,890.16,42,1
53,Chester-Sassafras,-76.1495290604082,39.0973377061934,3372.41,43,1
13,Susquehanna,-76.0812895285516,39.5511740535483,71212.74,44,1
37,Alligator,-76.0366844746414,35.6624542080488,1519.11,45,1
34,Transquaking,-76.0109477977893,38.3744819461209,294.13,46,1
35,Blackwater,-76.0109047269252,38.3565966733888,500.26,47,1
52,Choptank,-75.9861691586157,38.5967438638352,2844.38,48,1
51,Nanticoke,-75.8612890694107,38.3694353397457,2142.39,49,1
33,Wicomico,-75.8598924455485,38.2400474606153,596.63,50,1
58,Pokomoke-Western Lower Delmarva,-75.6481310731537,37.9538845896276,2397.29,51,1
14,Delaware,-75.3013884900285,39.8497321514991,35239.83,52,1
28,Mullica,-74.4097961651648,39.5472613072392,1694.8,53,1
62,Raritan,-74.2760700523965,40.4962663793923,2862.94,54,1
27,Metedeconk,-74.116252100513,40.0560473098006,234.65,55,1
26,Manasquan,-74.0980801033845,40.1224644906355,211.5,56,1
25,Shark,-74.010818459579,40.1875375570468,100.77895458,57,1
44,Hudson,-73.9451025106576,41.2879327365844,34735.21,58,1
24,Nissequogue,-73.2295076776254,40.9049744110648,110.03007654,59,1
57,Housatonic,-73.1108278784223,41.1707615606671,5049.49,60,1
21,Farm,-72.8586188494766,41.2488028401749,66.20258274,61,1
22,Hammonasset,-72.5466995167004,41.2626351311135,126.39153152,62,1
23,Menunketesuck,-72.4717782695425,41.2703469875451,45.03750494,63,1
15,Connecticut,-72.3443734022539,41.2879566167935,29174.09,64,1
43,Thames,-72.0813526709553,41.3192283277741,4127.28,65,1
36,Pawcatuck,-71.8587284504506,41.3207331271847,783.91,66,1
19,Blackstone-Providence,-71.394049282611,41.8070911375075,1314.44,67,1
31,Palmer,-71.2883156071925,41.7191808844642,181.33,68,1
84,St Lawrence,-71.2514592254256,46.7586441066743,473515.463842578,69,1
18,Sakonnet,-71.2209473866008,41.4725051082407,144.71976046,70,1
32,Taunton,-71.1184654847485,41.8013390341006,1462.12,71,1
20,Paskamanset,-71.0029099839194,41.5627044769003,113.87054668,72,1
4,Merrimack,-70.8137629007522,42.8201767019634,12963.78,73,1
63,Saco,-70.3800324874386,43.4615894192541,4405.18,74,1
17,Nonesuch,-70.3276605568215,43.544895288487,66.0069,75,1
16,Kennebec,-69.8114840512903,44.0307826072371,24746.3,76,1
30,Sheepscot,-69.6235422587278,44.0320072032423,1007.38,77,1
6,Penobscot,-68.7927779180648,44.4922431066342,22313.89,78,1
106,Manicouagan,-68.282463014821,49.1830721148814,45800,79,1
29,Pleasant,-67.7537483004799,44.5653192556577,472.47,80,1
67,St. Croix,-67.1701889739528,45.1949833695871,4271.8,81,1
68,Restigouche,-66.7442455421173,48.001108582058,12820,82,1
103,St Marguerite,-66.608721549525,50.1576836666073,6862.31197613555,83,1
66,St John,-66.0618369819529,45.2639183840459,54986,84,1
80,Tusket,-66.0038114829035,43.8361334433411,2000,85,1
107,George,-65.9001017867297,58.6132431688499,41700,86,1
64,Miramichi,-65.5706564230523,46.9758537190176,14000,87,1
76,Annapolis,-65.489400676568,44.7546239520923,2279,88,1
100,Richibucto,-64.8411032115544,46.6964766974031,1088.5,89,1
81,Mersey,-64.6791044223094,44.0388110472936,3030,90,1
65,Petitcodiac,-64.6604963563116,45.9587004920393,1999,91,1
75,Medway,-64.6133850739989,44.1347172422293,2012,92,1
82,Cornwallis,-64.3676089595062,45.1015618608634,361,93,1
69,LaHave,-64.3487655764554,44.2762526133617,1700,94,1
78,Maccan-Hebert-LaPlanche,-64.2827973848823,45.7706337994887,1304,95,1
77,Avon,-64.1448250555968,45.0149967491405,1306,96,1
79,Kennetcook,-64.1212115823586,45.0496296897753,1125,97,1
110,Romaine,-63.8204387046597,50.2994155046405,14350,98,1
101,Philip,-63.728526959108,45.8558476314525,726,99,1
71,Shubenacadie,-63.4819847588174,45.3145758498337,1304,100,1
74,Musquodoboit,-63.1109579892519,44.7277935252589,1409,101,1
72,John,-63.0712258999245,45.7577777483581,1117,102,1
73,St Mary's,-61.9264135275239,45.0725963206144,1350,103,1
104,Natashquan,-61.6117622585923,50.1536928104822,16100,104,1
70,Margaree,-61.1085716425609,46.4407710875427,1375,105,1
111,Kanairiktok,-60.6270086070208,55.049748240344,17049.8467206538,106,1
105,Churchill,-60.1937771910176,53.3138179497015,79800,107,1
83,Mira,-59.9680418073987,46.0355788476948,2914,108,1
109,Humber,-57.9280456921027,48.9760951594807,7680,109,1
112,Eagle,-57.4303781263665,53.5855644229823,10300,110,1
108,Exploits,-55.3165845715951,49.0869205569691,11000,111,1
102,Gander,-54.4861256205093,49.2999487615785,6398,112,1
55,St. Marys,-81.4502928202904,30.70940310562532,4097.78,1,1
56,Nassau,-81.42960148225745,30.50600659922722,1109.48,2,1
38,Satilla,-81.42474774312959,30.994752083584217,7220.09,3,1
1,St. Johns,-81.3973992896245,30.400134358449034,24604.51,4,1
3,Altamaha,-81.28445822846561,31.315782187696428,37402.01,5,1
2,Ogeechee,-81.02376744102966,31.84385330498972,15372.53,6,1
10,Savannah,-80.86466150589291,32.03627345210138,28499.28,7,1
59,Coosawatchie,-80.66363544413333,32.251659417739226,2588.83,8,1
60,Salkehatchie,-80.43212201755712,32.45849709983554,4894.77,9,1
50,Edisto,-80.18727036887367,32.56294280060601,8344.02,10,1
92,Loxahatchee,-80.07097438430593,26.944125376297247,696.12,11,1
61,Cooper,-79.86620030814865,32.75384392630198,3274.44,12,1
11,Santee,-79.2478784404616,33.11207858035934,39992.56,13,1
49,Pee Dee,-79.18118732992525,33.20141023473864,38392.54,14,1
8,Cape Fear,-78.00599468925965,33.885097712577554,23890.7,15,1
42,New,-77.40768015473351,34.709542998631285,1077.25,16,1
39,White Oak,-77.12614839525504,34.75456375925222,708.15,17,1
5,Potomac,-77.07856760032807,38.70041871601939,36801.61,18,1
7,Neuse,-77.01515533271954,35.08539951164485,15703.67,19,1
48,Pamlico-Tar,-76.96513699981725,35.46690310493342,11566.11,20,1
45,Rappahannock,-76.91821398544171,38.043166327639106,7025.77,21,1
12,James,-76.89785632283623,37.22811411100656,26780.72,22,1
46,York,-76.78213252893497,37.50748067706571,6927.38,23,1
9,Roanoke,-76.72079710199627,35.94372584696238,24543.07,24,1
47,Chowan,-76.68911051517348,36.272382043176584,12458.86,25,1
54,Patuxent,-76.6705173847298,38.55945868755525,2401.05,26,1
40,Perquimmans,-76.43972149555928,36.18166472070665,568.44,27,1
41,Pasquotank,-76.18015276433987,36.291008907036854,890.16,28,1
53,Chester-Sassafras,-76.1495290604082,39.09733770619342,3372.41,29,1
13,Susquehanna,-76.08128952855161,39.55117405354831,71212.74,30,1
37,Alligator,-76.03668447464143,35.66245420804876,1519.11,31,1
34,Transquaking,-76.01094779778929,38.37448194612087,294.13,32,1
35,Blackwater,-76.0109047269252,38.35659667338876,500.26,33,1
52,Choptank,-75.9861691586157,38.59674386383523,2844.38,34,1
51,Nanticoke,-75.86128906941072,38.36943533974573,2142.39,35,1
33,Wicomico,-75.85989244554852,38.24004746061526,596.63,36,1
58,Pokomoke-Western Lower Delmarva,-75.64813107315373,37.95388458962756,2397.29,37,1
14,Delaware,-75.30138849002849,39.84973215149913,35239.83,38,1
28,Mullica,-74.40979616516485,39.54726130723921,1694.8,39,1
62,Raritan,-74.27607005239655,40.496266379392324,2862.94,40,1
27,Metedeconk,-74.116252100513,40.05604730980057,234.65,41,1
26,Manasquan,-74.09808010338446,40.12246449063553,211.5,42,1
25,Shark,-74.010818459579,40.187537557046845,100.77895458,43,1
44,Hudson,-73.94510251065762,41.28793273658435,34735.21,44,1
24,Nissequogue,-73.22950767762536,40.904974411064835,110.03007654,45,1
57,Housatonic,-73.11082787842233,41.17076156066706,5049.49,46,1
21,Farm,-72.85861884947664,41.248802840174875,66.20258274,47,1
22,Hammonasset,-72.54669951670043,41.2626351311135,126.39153152,48,1
23,Menunketesuck,-72.47177826954247,41.27034698754507,45.03750494,49,1
15,Connecticut,-72.34437340225394,41.287956616793494,29174.09,50,1
43,Thames,-72.08135267095527,41.319228327774105,4127.28,51,1
36,Pawcatuck,-71.85872845045061,41.32073312718465,783.91,52,1
19,Blackstone-Providence,-71.39404928261095,41.807091137507456,1314.44,53,1
31,Palmer,-71.28831560719246,41.71918088446415,181.33,54,1
84,St. Lawrence,-71.25145922542565,46.75864410667434,473515.46384257753,55,1
18,Sakonnet,-71.22094738660083,41.4725051082407,144.71976046,56,1
32,Taunton,-71.11846548474853,41.8013390341006,1462.12,57,1
20,Paskamanset,-71.00290998391938,41.56270447690034,113.87054668,58,1
4,Merrimack,-70.81376290075221,42.820176701963405,12963.78,59,1
63,Saco,-70.38003248743857,43.461589419254054,4405.18,60,1
17,Nonesuch,-70.3276605568215,43.54489528848697,66.0069,61,1
16,Kennebec,-69.81148405129025,44.03078260723705,24746.3,62,1
30,Sheepscot,-69.62354225872778,44.03200720324225,1007.38,63,1
6,Penobscot,-68.79277791806483,44.49224310663417,22313.89,64,1
106,Manicouagan,-68.28246301482105,49.183072114881426,45800,65,1
29,Pleasant,-67.75374830047987,44.56531925565769,472.47,66,1
67,St. Croix,-67.17018897395282,45.1949833695871,4271.8,67,1
68,Restigouche,-66.7442455421173,48.001108582057995,12820,68,1
103,St. Marguerite,-66.608721549525,50.15768366660728,6862.311976134703,69,1
66,St. John,-66.06183698195287,45.263918384045915,54986,70,1
80,Tusket,-66.00381148290346,43.83613344334111,2000,71,1
107,George,-65.90010178672972,58.61324316884986,41700,72,1
64,Miramichi,-65.57065642305227,46.97585371901762,14000,73,1
76,Annapolis,-65.48940067656798,44.7546239520923,2279,74,1
100,Richibucto,-64.84110321155444,46.69647669740313,1088.5,75,1
81,Mersey,-64.67910442230936,44.0388110472936,3030,76,1
65,Petitcodiac,-64.66049635631158,45.95870049203926,1999,77,1
75,Medway,-64.61338507399894,44.13471724222929,2012,78,1
82,Cornwallis,-64.3676089595062,45.10156186086337,361,79,1
69,LaHave,-64.3487655764554,44.27625261336168,1700,80,1
78,Maccan-Hebert-LaPlanche,-64.28279738488226,45.77063379948874,1304,81,1
77,Avon,-64.14482505559677,45.01499674914045,1306,82,1
79,Kennetcook,-64.12121158235864,45.04962968977533,1125,83,1
110,Romaine,-63.820438704659715,50.299415504640464,14350,84,1
101,Philip,-63.728526959108024,45.85584763145254,726,85,1
71,Shubenacadie,-63.481984758817376,45.3145758498337,1304,86,1
74,Musquodoboit,-63.110957989251865,44.72779352525894,1409,87,1
72,John,-63.07122589992446,45.75777774835809,1117,88,1
73,St. Mary's,-61.92641352752389,45.07259632061437,1350,89,1
104,Natashquan,-61.61176225859233,50.153692810482205,16100,90,1
70,Margaree,-61.1085716425609,46.44077108754266,1375,91,1
111,Kanairiktok,-60.627008607020805,55.04974824034399,17049.846720654685,92,1
105,Churchill,-60.193777191017645,53.31381794970146,79800,93,1
83,Mira,-59.96804180739866,46.035578847694794,2914,94,1
109,Humber,-57.92804569210275,48.9760951594807,7680,95,1
112,Eagle,-57.43037812636648,53.58556442298227,10300,96,1
108,Exploits,-55.31658457159512,49.08692055696912,11000,97,1
102,Gander,-54.486125620509334,49.29994876157853,6398,98,1
library(XML)
#read the XML file to upload the set of parameters included in GR3D-US
fishXML <- xmlToList(xmlParse("../../data/input/northeastamerica/fishRIOBasin_Sapidissima.xml"))
#Upload parameters linked to reproduction
reproducePar = data.frame(t(unlist(fishXML[[1]][["processes"]][["processesEachStep"]][["species.ReproduceAndSurviveAfterReproductionWithDiagnose"]]))) %>%
select(-c(synchronisationMode, reproductionSeason, proportionOfFemaleAtBirth,
sigmaRecruitment, maxNumberOfSuperIndividualPerReproduction, withDiagnose,
displayFluxesOnConsole)) %>%
rename("TminRep" = "tempMinRep",
"ToptRep" = "tempOptRep",
"TmaxRep" = "tempMaxRep",
"ratioS95_S50" = "ratioS95__S50",
"deltaT" = "delta__t") %>%
mutate_all(~as.numeric(as.character(.)))
#Upload parameters linked to survival in river
survivePar = data.frame(t(unlist(fishXML[[1]][["processes"]][["processesEachStep"]][["species.Survive"]]))) %>%
select(-synchronisationMode) %>%
rename("TminSurv" = "tempMinSurvivalSpawnerInRiv",
"ToptSurv" = "tempOptSurvivalSpawnerInRiv",
"TmaxSurv" = "tempMaxSurvivalSpawnerInRiv",
"survProbOptRiver" = "survivalProbOptSpawnerInRiv") %>%
mutate_all(~as.numeric(as.character(.)))
#Upload parameters linked to growth at sea
growPar = data.frame(t(unlist(fishXML[[1]][["processes"]][["processesEachStep"]][["species.Grow"]]))) %>%
select(-synchronisationMode ) %>%
mutate(linfVonBertForMale = fishXML[[1]][["linfVonBertForMale"]],
linfVonBertForFemale = fishXML[[1]][["linfVonBertForFemale"]],
lengthAtHatching = fishXML[[1]][["lengthAtHatching"]],
lFirstMaturityForMale = fishXML[[1]][["lFirstMaturityForMale"]],
lFirstMaturityForFemale = fishXML[[1]][["lFirstMaturityForFemale"]]) %>%
mutate_all(~as.numeric(as.character(.)))
#-------------------------------------
#Read and upload environmental data
#-------------------------------------
library(readr)
#---------Temperature ----------------
#temperature in river basins
tempInriver <- read_csv("../../data/input/northeastamerica/observed_river_temperatures.csv")
#temperature in inshore basins
tempInInshore <- read_csv("../../data/input/northeastamerica/observed_inshore_temperatures.csv")
#temperature in offshore basins
tempInOffshore <- read_csv("../../data/input/northeastamerica/observed_offshore_temperatures.csv")
#connections between inshore and offshore
#---------Characteristic----------------
#characteristics of the river basins
nea_riverBasinFeatures <- read_csv("../../data/input/northeastamerica/nea_riverbasins.csv")
#Upload presence and absence in US river basins
nea_presence <- read_csv("../../data/input/northeastamerica/nea_presence.csv")
#upload connections between inshore and offshore basins
connections <- read_csv("../../data/input/northeastamerica/inshore_offshore_connections.csv")
\ No newline at end of file
#----------------------------------------------
# Temperature effect
#----------------------------------------------
# temperature effect in GR3D
# from Rosso
temperatureEffect = function(tempWater, Tmin, Topt, Tmax){
......@@ -18,9 +20,9 @@ thermalRange = function(pct = 0.8, Tmin, Topt, Tmax){
#optimalThermalRange(Tmin = 3, Topt = 17, Tmax =27)
# ----------------------------------------------
# growth simulation
#=---------------------------------------------
#----------------------------------------------
# Growth simulation
#---------------------------------------------
# von Bertalaffy : L = f(age)
vonBertalanffyGrowth = function(age, L0, Linf, K){
t0 = log(1 - L0 / Linf) / K
......@@ -34,6 +36,7 @@ vonBertalanffyInverse = function(L, L0, Linf, K){
return(t0 - log(1 - L/Linf)/K)
}
# von Bertalanffy increment
# pas cohérent avec la temperature effet sur le coeff de croissance mais ca marche
vonBertalanffyIncrement = function(nStep, L0, Linf, K, timeStepDuration, sigma, withTempEffect=FALSE, TrefAtSea = c(9.876946, 13.489854, 15.891487, 11.554104) ){
......@@ -58,7 +61,7 @@ vonBertalanffyWithNextIncrement = function(L, L0, Linf, K, timeStepDuration, sig
}
else {
mu = log((Linf - L) * (1 - exp(-K * timeStepDuration))) - (sigma * sigma) / 2
increment = exp(rnorm(1, mu, sigma))
increment = exp(rnorm(length(mu), mu, sigma))
}
L = L + increment * tempEffect
return(L)
......@@ -88,3 +91,113 @@ strayerSurvival = function(distance, m ){
# m: extra mortality rate for strayers (L-1)
return(exp(-m * distance))
}
#-------------------------------------------------------
# Spwaner survival before reproduction
# Dome-shape curve with temperature effect
#-------------------------------------------------------
spawnerSurvivalPreReproduction <- function(Triver,Tmin, Topt, Tmax){
#River survival
survProbOptRiver = survivePar$survProbOptRiver
spRiver = survProbOptRiver * TemperatureEffect(Triver, Tmin, Topt, Tmax)
#StockAfterSurv = S * SpRiver