Skip to content

Commit 384c064

Browse files
saund123saund123
committed
Sarah's notes
1 parent bd57ba7 commit 384c064

File tree

3 files changed

+233
-40
lines changed

3 files changed

+233
-40
lines changed

‎AMWO harvest.csv

+99
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,99 @@
1+
Season,Pop,Frame,AF,AM,AU,IF,IM,IU,UF,UM,UU,Harvest,AF_Harvest,AM_Harvest,Imm_Harvest,AF_Banded,AM_Banded,Imm_Banded,Local_Banded,AF_Recovs,AM_Recovs,Imm_Recovs,Local_Recovs,AF_Lincoln,AM_Lincoln,Imm_Lincoln
2+
1963,C,DSS,1217,772,4,1185,1221,12,0,0,5,NA,NA,NA,NA,10,9,58,0,0,1,3,0,1027451,566645,3181711
3+
1964,C,DSS,1402,915,2,1234,1296,5,0,0,3,286058,82694.6,53969.7,149393.7,8,6,28,2,0,1,0,0,744259,188896,4332445
4+
1965,C,DSS,971,663,13,727,733,12,0,0,104,182808,57364.2,39168.3,86275.5,38,38,150,14,0,0,1,0,2237242,1527602,6513875
5+
1966,C,DSS,1296,821,33,944,1019,32,0,0,71,209457,66510.9,42133.8,100812.2,33,19,129,20,6,1,11,1,323057,421347,1092142
6+
1967,C,DSS,1273,842,61,1014,1110,64,0,0,137,244702,73439.5,48575.1,122687.4,18,14,80,15,0,1,2,1,1395369,364320,3312586
7+
1968,C,DSS,1409,855,75,1118,1163,48,0,0,127,197520,61594.9,37376.6,98548.4,70,61,426,17,9,6,63,2,437330,331058,657508
8+
1969,C,DSS,1360,885,52,1129,1127,44,0,0,61,292740,88611.7,57662.8,146465.5,40,41,326,5,7,3,40,4,454139,605469,1168159
9+
1970,C,DSS,1389,800,39,1390,1358,25,0,0,124,346125,97847.1,56355.4,191922.5,69,70,478,42,6,3,34,0,978480,1000325,2626609
10+
1971,C,DSS,1910,1086,25,1411,1361,17,0,0,78,340217,112777.4,64123.7,163315.9,78,69,526,37,0,2,8,1,8909493,1496242,9563111
11+
1972,C,DSS,1964,1210,38,1665,1719,22,0,0,45,340217,102173.8,62948.2,175095.1,76,94,853,14,3,1,18,0,1966864,2990086,7870108
12+
1973,C,DSS,2002,1231,28,2199,1934,28,0,0,67,325914,88673,54523.7,182717.3,152,112,1759,28,3,0,26,2,3391780,6161290,11910525
13+
1974,C,DSS,2086,1431,30,1877,2063,17,0,0,17,399990,112139.7,76928.1,210922.2,128,125,1416,39,4,1,15,2,2893229,4846532,18679885
14+
1975,C,DSS,2798,1830,18,2037,2274,14,0,0,13,459678,143928.4,94134.7,221614.9,54,45,530,40,3,1,28,1,1979028,2165120,4057863
15+
1976,C,DSS,2214,1562,8,1736,2081,15,0,0,20,500085,145684.6,102782,251618.4,32,33,404,7,3,0,14,0,1201905,3494621,6793723
16+
1977,C,DSS,2273,1463,10,1815,1962,17,0,0,64,528708,159810.3,102860.8,266036.9,62,63,670,5,3,2,13,0,2517027,2194384,12750815
17+
1978,C,DSS,2037,1413,32,1833,1771,22,0,0,112,571662,165345.6,114694.8,291621.6,68,101,875,20,2,2,21,1,3802971,3899656,11611881
18+
1979,C,DSS,1886,1351,17,1599,1704,16,0,0,69,437426,126170.4,90379.8,220875.8,57,71,566,45,0,0,14,0,7317940,6507417,8349142
19+
1980,C,DSS,2086,1587,53,2233,2418,30,0,0,86,641086,161365.8,122764.9,356955.3,70,80,591,22,21,8,40,1,520774,1104892,5154100
20+
1981,C,DSS,2330,1634,16,2221,2202,29,0,0,98,442820,122857.6,86158.5,233803.9,46,35,188,20,10,0,21,0,524940,3101741,2008596
21+
1982,C,DSS,2217,1444,24,1734,1911,24,0,0,85,329877,100099.5,65197.9,164579.6,23,30,159,5,9,3,23,0,240240,505290,1097203
22+
1983,C,DSS,2106,1428,29,1797,1869,24,0,0,106,394051,115356.6,78219,200475.4,25,21,72,21,1,0,4,0,1499648,1720839,2926954
23+
1984,C,DSS,1843,1303,9,1741,1810,9,0,0,75,322347,88724.5,62728.2,170894.3,25,19,99,12,2,2,5,0,768953,418194,2848254
24+
1985,C,DSS,1725,1100,20,1906,1818,18,0,0,52,267300,70496,44953.9,151850.1,9,4,47,20,0,0,0,0,704969,224774,7288852
25+
1986,C,DSS,1975,1286,27,1831,1975,28,0,0,86,335413,93783.4,61066.1,180563.5,20,7,16,12,0,0,1,0,1969471,488536,1534797
26+
1987,C,DSS,2492,1558,28,1848,2014,22,0,0,49,390656,123115.5,76971.9,190568.7,7,8,8,12,0,0,0,2,984931,692755,1715126
27+
1988,C,DSS,1258,805,16,923,962,4,0,0,22,221693,70829.8,45324.3,105538.8,12,10,36,31,0,0,0,2,920799,498577,3904972
28+
1989,C,DSS,2456,1680,75,1760,1973,24,0,0,42,270307,84828.4,58025.9,127452.7,18,18,34,26,0,0,0,1,1611758,1102510,4460879
29+
1990,C,DSS,2639,1683,27,2087,2058,24,0,0,133,226787,70700.8,45088.9,110997.3,4,10,18,19,0,0,0,0,353508,495988,2108967
30+
1991,C,DSS,3053,2346,36,2487,2673,25,0,0,47,215608,62395.5,47946.2,105266.2,11,12,37,33,1,0,2,1,374378,623313,1333384
31+
1992,C,DSS,2656,1645,28,2056,2214,9,0,0,66,208314,64693.8,40068.2,103552,23,14,40,23,0,0,2,0,1552674,601037,1415223
32+
1993,C,DSS,2834,1675,35,1971,2122,16,0,0,52,177114,58458,34550.9,84105.1,25,29,48,102,0,1,0,3,1519933,518278,4121198
33+
1994,C,DSS,2413,1519,14,1756,1778,16,0,0,39,199810,64548.9,40633.9,94627.2,44,19,59,114,2,1,2,2,968248,406348,1892563
34+
1995,C,DSS,2562,1421,20,1702,1669,19,0,0,58,229263,79848.7,44287.6,105126.7,32,19,51,91,4,0,1,1,527007,885771,2733319
35+
1996,C,DSS,2156,1334,18,1292,1401,18,0,0,39,182826,63708.9,39419.2,79697.9,48,49,81,100,3,0,3,2,780445,1971009,1633826
36+
1999,C,HIP,4136,2646,10,2216,2244,16,4,4,32,630772,231870.8,148339,250562.3,36,7,59,32,3,0,1,3,2144813,1186719,7516898
37+
2000,C,HIP,3798,2602,2,2232,2388,14,2,6,28,585978,201725.3,138201.5,246051.3,22,20,77,37,2,1,6,2,1546567,1451125,2741725
38+
2001,C,HIP,3900,2300,0,2620,2354,26,10,24,38,460595,160385.8,94586.5,205622.8,47,44,139,53,1,2,5,2,3849282,1418812,4797888
39+
2002,C,HIP,2880,1846,12,2242,2184,26,6,18,24,389087,122243.3,78354.6,188489.2,98,82,167,75,2,1,2,1,4034061,3251756,10555450
40+
2003,C,HIP,4492,2244,2,2924,2718,6,4,4,0,426908,154871.6,77366.9,194669.5,96,64,159,134,3,1,3,6,3755660,2514456,7786819
41+
2004,C,HIP,4194,2438,2,2636,2622,32,0,16,16,469532,165197.2,96030.2,208304.6,107,110,225,81,2,0,3,1,5947134,10659462,11769265
42+
2005,C,HIP,4746,2858,4,3226,3126,52,2,12,52,541908,183646,110590,247671.9,5,7,2,58,0,0,0,1,1101881,884727,743018
43+
2006,C,HIP,5014,3078,6,3848,3614,32,18,30,24,465113,149679.7,91885.5,223547.8,2,0,3,15,0,0,0,0,449041,91886,894194
44+
2007,C,HIP,5472,3180,20,3402,3516,26,10,14,26,428325,150436.2,87424.6,190464.2,3,4,7,29,0,0,0,0,601748,437127,1523721
45+
2008,C,HIP,5048,2752,6,3358,3480,24,6,12,34,348524,120037,65440.1,163046.9,9,3,7,43,0,0,0,2,1200379,261763,1304382
46+
2009,C,HIP,5206,2736,8,2768,2482,40,28,26,56,350241,137854.3,72449,139937.7,3,3,3,25,0,0,0,0,551420,289799,559754
47+
2010,C,HIP,5162,2974,28,3658,3650,52,12,36,46,546802,182446.9,105113.7,259241.4,3,1,6,32,0,0,0,0,729791,210228,1814696
48+
2011,C,HIP,5728,3162,8,3678,3606,46,22,24,46,463345,163694.1,90363.3,209287.6,28,35,47,85,0,0,0,0,4747157,3253114,10045852
49+
2012,C,HIP,5998,3526,10,3792,3912,68,34,64,58,386048,133938.9,78737.7,173371.4,41,45,55,39,0,0,0,0,5625475,3621979,9708853
50+
2013,C,HIP,5436,3088,14,3512,3766,40,12,34,42,361118,124007.4,70444.2,166666.3,6,2,9,106,0,0,0,2,868058,211335,1666672
51+
1963,E,DSS,1794,1179,10,1456,1557,15,0,0,10,NA,NA,NA,NA,116,75,248,0,6,5,14,0,636823,509277,1234006
52+
1964,E,DSS,3047,2040,7,2431,2620,8,0,0,5,166098,49916,33419.3,82762.7,66,62,319,0,4,5,28,0,668887,350912,913254
53+
1965,E,DSS,2407,1654,51,1901,1922,70,0,0,344,193391,58880.5,40460.4,94050.1,77,60,214,2,9,5,16,0,459275,411357,1189469
54+
1966,E,DSS,2135,1590,68,1985,2122,78,0,0,123,190659,51953.8,38691.6,100013.5,138,91,403,16,14,4,34,2,481447,711943,1154452
55+
1967,E,DSS,2914,2188,104,2434,2532,125,0,0,224,251363,72584.5,54500.6,124277.9,140,120,530,2,9,13,43,0,1023455,471049,1499819
56+
1968,E,DSS,3643,2578,124,3334,3545,117,0,0,319,286746,79861.9,56514.9,150369.2,206,116,638,4,29,10,67,0,551053,601123,1413037
57+
1969,E,DSS,3613,2672,88,3152,3322,134,0,0,327,296112,83570.8,61804.9,150736.3,330,236,799,0,24,23,74,0,1106490,610332,1607864
58+
1970,E,DSS,3255,2162,60,3633,3712,83,0,0,259,319678,81524.8,54149.5,184003.7,264,212,1012,2,12,11,84,0,1661871,961170,2192902
59+
1971,E,DSS,3769,2524,57,3394,3277,51,0,0,81,324266,94341.2,63177.8,166746.9,414,314,1377,3,18,17,83,0,2060631,1105628,2735459
60+
1972,E,DSS,3674,2407,86,2734,3061,94,0,0,180,324266,100215.8,65655.8,158394.4,461,302,1585,16,26,18,76,0,1714820,1047052,3262533
61+
1973,E,DSS,4396,2904,65,3851,3853,76,0,0,186,331831,97175.2,64194,170461.9,302,250,1378,4,16,10,67,0,1732022,1464812,3456886
62+
1974,E,DSS,4232,3045,48,3174,3603,51,0,0,67,354261,106629.1,76721.6,170910.3,150,130,700,2,3,13,25,0,4025285,717903,4608031
63+
1975,E,DSS,3777,2404,11,2754,3220,11,0,0,11,314639,97766.8,62227,154645.2,77,64,392,8,1,3,12,0,3812943,1011204,4675073
64+
1976,E,DSS,3457,2492,15,2738,3119,20,0,0,62,321426,94077.5,67816.3,159532.2,47,52,292,6,3,2,7,0,1128941,1198105,5842902
65+
1977,E,DSS,2982,1962,22,2188,2375,22,0,0,100,270280,84762,55768.9,129749.1,59,30,335,3,0,0,6,0,5085779,1728866,6228004
66+
1978,E,DSS,2682,1759,23,2130,2376,28,0,0,46,280276,83973.5,55074.3,141228.2,40,18,302,17,2,0,10,0,1147651,1046430,3890222
67+
1979,E,DSS,2386,1605,22,2095,2216,30,0,0,66,263862,75777.5,50973.5,137111,46,20,236,4,0,1,11,0,3561589,535231,2707961
68+
1980,E,DSS,2236,1555,35,1866,2105,20,0,0,70,228249,65891.9,45823.7,116533.4,22,19,198,11,0,1,6,1,1515536,458246,3312906
69+
1981,E,DSS,2150,1891,20,1945,2379,24,0,0,88,240513,61798.3,54353.8,124360.9,20,11,154,6,0,0,4,0,1297784,652257,3855218
70+
1982,E,DSS,1642,1049,16,1428,1599,14,0,0,56,176060,50593.1,32321.7,93145.2,22,10,109,5,0,1,0,0,1163663,177774,10246081
71+
1983,E,DSS,1786,1342,3,1436,1627,21,0,0,55,156244,44942.8,33770,77531.2,10,4,75,0,0,0,2,0,494381,168854,1964148
72+
1984,E,DSS,1553,1105,13,1194,1362,12,0,0,25,168954,50328.1,35809.7,82816.2,13,11,56,6,0,0,1,0,704606,429727,2360289
73+
1985,E,DSS,1139,797,9,1005,1075,6,0,0,33,128329,36429.2,25490.9,66408.9,28,25,111,2,0,0,1,0,1056475,662788,3718953
74+
1986,E,DSS,1151,839,6,945,1172,12,0,0,25,131685,36854.9,26864.7,67965.4,11,8,67,3,0,0,3,0,442270,241790,1155428
75+
1987,E,DSS,1371,907,9,1118,1181,13,0,0,32,162840,48735.7,32241.7,81862.6,38,26,220,22,2,1,1,0,633576,435275,9045927
76+
1988,E,DSS,671,422,7,473,569,3,0,0,21,115299,36298.9,22828.8,56171.3,32,18,255,11,0,0,3,0,1197896,433765,3595026
77+
1989,E,DSS,1443,1029,14,956,1023,12,0,0,20,122904,39838,28408.4,54657.6,21,7,77,26,0,1,1,0,876457,113637,2131684
78+
1990,E,DSS,1112,857,10,936,1047,11,0,0,49,104415,29373.1,22637.3,52404.6,24,10,136,17,1,0,1,0,367175,249020,3589783
79+
1991,E,DSS,1228,973,10,954,1168,7,0,0,42,104018,29565.5,23426.1,51026.3,18,10,121,17,1,0,1,0,280881,257697,3112664
80+
1992,E,DSS,1704,960,16,987,1117,17,0,0,44,103227,36858,20765.1,45603.9,19,7,160,21,0,0,0,0,737179,166128,7342388
81+
1993,E,DSS,806,473,6,567,521,6,0,0,15,81673,27800.4,16314.7,37557.9,37,18,126,3,1,0,2,0,528226,309997,1589992
82+
1994,E,DSS,1304,728,11,891,972,4,0,0,12,99136,33241.2,18558,47336.8,11,17,75,3,0,1,1,0,398905,167030,1798835
83+
1995,E,DSS,1431,839,7,867,928,8,0,0,18,88144,31010.5,18181.6,38951.9,16,7,92,6,0,0,0,0,527195,145460,3622619
84+
1996,E,DSS,1386,901,10,826,887,6,0,0,13,99140,34364.8,22339.6,42435.7,15,6,36,3,1,1,0,0,274925,78191,1570157
85+
1999,E,HIP,2900,1980,4,1544,1722,10,2,6,16,258840,92065.1,62858.2,103916.6,118,98,193,4,0,0,4,0,14205554,1414730,3560948
86+
2000,E,HIP,2626,1926,2,1722,1930,14,0,6,12,195834,62589.5,45905.4,87339.1,28,36,80,0,0,0,1,0,,,
87+
2001,E,HIP,2724,1720,8,1862,1870,22,6,16,24,223104,74193.2,46847.4,102063.4,30,27,81,0,0,1,1,0,,,
88+
2002,E,HIP,2880,1944,18,1934,2068,16,8,28,14,142054,46347.9,31284.8,64421.3,18,25,42,0,0,4,3,0,,,
89+
2003,E,HIP,3472,2062,4,2260,2268,20,6,6,8,178316,61427.8,36481.6,80406.6,16,3,50,0,0,0,1,0,,,
90+
2004,E,HIP,2652,1858,0,2082,2192,42,2,16,22,123076,36981.4,25909.3,60185.4,17,17,84,1,0,0,1,0,,,
91+
2005,E,HIP,3404,2322,6,2392,2482,20,8,16,26,183385,58808.3,40115.4,84461.3,52,38,83,1,0,0,1,0,,,
92+
2006,E,HIP,4378,2720,14,2818,2946,30,8,16,30,158538,53885.7,33478.5,71173.8,22,13,57,0,0,0,0,0,,,
93+
2007,E,HIP,3536,1974,10,2168,2234,32,12,8,22,151763,54009.2,30151.1,67602.7,19,11,48,5,0,1,1,0,,,
94+
2008,E,HIP,2888,1890,4,2326,2476,24,10,14,20,209402,62995.3,41226.2,105180.5,15,4,38,0,0,0,0,0,,,
95+
2009,E,HIP,3512,2264,18,2464,2632,38,14,14,50,126549,40796.6,26299.4,59453,14,12,44,1,0,0,1,0,,,
96+
2010,E,HIP,4236,2538,16,2680,2840,24,24,38,40,209839,72237.5,43281.1,94320.4,14,10,13,0,0,0,1,0,,,
97+
2011,E,HIP,3768,2372,14,2892,2846,22,12,8,36,154099,48847.5,30750.1,74501.4,14,16,30,10,0,0,1,0,,,
98+
2012,E,HIP,3770,2602,10,2560,2930,34,34,38,38,172867,54823.7,37838.6,80204.7,9,5,14,1,1,0,1,0,,,
99+
2013,E,HIP,3392,2204,10,2446,2636,36,4,20,32,125073,39631.3,25751,59690.8,2,1,10,4,0,0,0,0,,,

‎Code/AMWO_submodels/AMWO combined.R

+40-40
Original file line numberDiff line numberDiff line change
@@ -21,37 +21,37 @@ Central <- matrix(0,nrow=49,ncol=12,byrow=TRUE)
2121
Eastern <- matrix(0,nrow=49,ncol=12,byrow=TRUE)
2222

2323
for (i in 1:49){
24-
Central[i,1] <- harvest[i,1] # year
25-
Eastern[i,1] <- harvest[(i+49),1] # year
24+
Central[i,1] <- harvest[i,1] # year for C region
25+
Eastern[i,1] <- harvest[(i+49),1] # year for E region
2626
for (j in 2:12){
27-
Central[i,j] <- harvest[(i),(j+12)]
27+
Central[i,j] <- harvest[(i),(j+12)] #harvest column to local recovs column from dataset
2828
Eastern[i,j] <- harvest[(i+49),(j+12)]
2929
} # close j
3030
} # close i
3131

32-
head(Central)
32+
head(Central) #some NAs in data; 12 columns, 49 rows each
3333
tail(Eastern)
3434

3535
# specify bugs model
3636
sink("Lincoln.bug")
3737
cat("
3838
model {
3939
# priors for initial population sizes (mean first 5 years Lincoln, SD 100,000)
40-
af.N[1,1] ~ dnorm(720000,1E-10)
41-
af.N[2,1] ~ dnorm(600000,1E-10)
42-
am.N[1,1] ~ dnorm(615000,1E-10)
43-
am.N[2,1] ~ dnorm(530000,1E-10)
40+
af.N[1,1] ~ dnorm(720000,1E-10) #assuming these come from previous Lincoln analysis; adult female central (1)
41+
af.N[2,1] ~ dnorm(600000,1E-10) #adult female eastern (2)
42+
am.N[1,1] ~ dnorm(615000,1E-10) #adult male central
43+
am.N[2,1] ~ dnorm(530000,1E-10) #adult male eastern
4444
4545
# Priors and constraints for population means and variances
4646
for (i in 1:2){ # 1 Central, 2 Eastern pop
4747
f.af.x[i] ~ dunif(0.005,0.2) # uniform prior for mean Brownie recovery
48-
f.af.mu[i] <- logit(f.af.x[i])
48+
f.af.mu[i] <- logit(f.af.x[i]) #adult female mean recovery rate?
4949
f.am.x[i] ~ dunif(0.005,0.2)
50-
f.am.mu[i] <- logit(f.af.x[i])
50+
f.am.mu[i] <- logit(f.af.x[i]) #adult male mean recov rate
5151
f.juv.x[i] ~ dunif(0.005,0.2)
52-
f.juv.mu[i] <- logit(f.af.x[i])
52+
f.juv.mu[i] <- logit(f.af.x[i]) #juvenile mean recov rate
5353
s.loc.x[i] ~ dunif (0,1) # prior for S from local to HY stage
54-
s.loc.mu[i] <- logit(s.loc.x[i])
54+
s.loc.mu[i] <- logit(s.loc.x[i]) #prior for S from local to HY stage, mean
5555
5656
# priors for annual SD of annual recovery rate (logit scale)
5757
f.af.sd[i] ~ dunif(0.05,2)
@@ -64,7 +64,7 @@ cat("
6464
s.loc.tau[i] <- pow(s.loc.sd[i],-2)
6565
6666
# priors for annual growth rates and fecundities
67-
F.x[i] ~ dunif(0,4) # logical bounds on fecundity with 4 egg clutch
67+
F.x[i] ~ dunif(0,4) # logical bounds on fecundity (F) with 4 egg clutch
6868
afr.x[i] ~ dunif(-1,1) # uniform prior for mean growth rate, ad females
6969
amr.x[i] ~ dunif(-1,1) # ad males
7070
F.sd[i] ~ dunif(0.01,1)
@@ -75,54 +75,54 @@ cat("
7575
amr.tau[i] <- pow(amr.sd[i],-2)
7676
7777
# Generate annual parameter estimates
78-
for (y in 1:yrs){
78+
for (y in 1:yrs){ #yrs is 49 here
7979
# generate recovery rates
80-
logit.f.af[i,y] ~ dnorm(f.af.mu[i],f.af.tau[i])
81-
logit.f.am[i,y] ~ dnorm(f.am.mu[i],f.am.tau[i])
82-
logit.f.juv[i,y] ~ dnorm(f.juv.mu[i],f.juv.tau[i])
83-
logit.s.loc[i,y] ~ dnorm(s.loc.mu[i],s.loc.tau[i])
80+
logit.f.af[i,y] ~ dnorm(f.af.mu[i],f.af.tau[i]) #uses mean and variance from above, adult female
81+
logit.f.am[i,y] ~ dnorm(f.am.mu[i],f.am.tau[i]) #uses mean and variance from above, adult male
82+
logit.f.juv[i,y] ~ dnorm(f.juv.mu[i],f.juv.tau[i]) #uses mean and variance from above, juvenile
83+
logit.s.loc[i,y] ~ dnorm(s.loc.mu[i],s.loc.tau[i]) #uses mean and variance from above, S from local to HY stage
8484
logit(f.af[i,y]) <- logit.f.af[i,y]
8585
logit(f.am[i,y]) <- logit.f.am[i,y]
8686
logit(f.juv[i,y]) <- logit.f.juv[i,y]
8787
logit(s.loc[i,y]) <- logit.s.loc[i,y]
88-
f.loc[i,y] <- s.loc[i,y]*f.juv[i,y]
88+
f.loc[i,y] <- s.loc[i,y]*f.juv[i,y] #true recovery rates for locals a product of survival and recovery?
8989
9090
# generate process components
91-
af.r[i,y] ~ dnorm(afr.x[i],afr.tau[i]) # need F for each year, but last lambda not used
92-
am.r[i,y] ~ dnorm(amr.x[i],amr.tau[i])
91+
af.r[i,y] ~ dnorm(afr.x[i],afr.tau[i]) # need F (fecundity, not recov!) for each year, but last lambda not used, af.r is mean growth rate from above
92+
am.r[i,y] ~ dnorm(amr.x[i],amr.tau[i]) #am.r is mean growth rate for adult males pop segment
9393
F[i,y] ~ dnorm(F.x[i],F.tau[i]) # Fecundity cannot be <0 or >4
94-
af.lambda[i,y] <- exp(af.r[i,y]) # convert r to lambda by exponentiating, r = log(lambda)
94+
af.lambda[i,y] <- exp(af.r[i,y]) # convert r to lambda by exponentiating, r = log(lambda), converting from stochastic population growth rate to finite growth rate
9595
am.lambda[i,y] <- exp(am.r[i,y])
9696
9797
} # close y
9898
9999
# State process (estimate Fecundity in year 1)
100-
juv.N[i,1] <- trunc(af.N[i,1]*F[i,1])
100+
juv.N[i,1] <- trunc(af.N[i,1]*F[i,1]) #trunc truncates towards 0. juv pop size function of adult females and fecundity
101101
for (y in 2:yrs){
102-
af.N[i,y] <- trunc(af.N[i,y-1] * af.lambda[i,y-1])
103-
am.N[i,y] <- trunc(am.N[i,y-1] * am.lambda[i,y-1])
102+
af.N[i,y] <- trunc(af.N[i,y-1] * af.lambda[i,y-1]) #adult female pop size function of previous yr times lambda
103+
am.N[i,y] <- trunc(am.N[i,y-1] * am.lambda[i,y-1]) #adult male pop size function of previous yr times lambda
104104
juv.N[i,y] <- trunc(af.N[i,y] * F[i,y])
105105
} # close y
106106
} # close i
107107
108108
# observation process, recoveries and harvest data
109109
for (y in 1:yrs){
110-
C.af.R[y] ~ dbin(f.af[1,y],C.af.B[y])
111-
C.am.R[y] ~ dbin(f.am[1,y],C.am.B[y])
112-
C.juv.R[y] ~ dbin(f.juv[1,y],C.juv.B[y])
113-
C.loc.R[y] ~ dbin(f.loc[1,y],C.loc.B[y])
114-
E.af.R[y] ~ dbin(f.af[2,y],E.af.B[y])
115-
E.am.R[y] ~ dbin(f.am[2,y],E.am.B[y])
116-
E.juv.R[y] ~ dbin(f.juv[2,y],E.juv.B[y])
117-
E.loc.R[y] ~ dbin(f.loc[2,y],E.loc.B[y])
110+
C.af.R[y] ~ dbin(f.af[1,y],C.af.B[y]) #central adult female recovery data, bin distribution function of adult female recoveries and central region females banded
111+
C.am.R[y] ~ dbin(f.am[1,y],C.am.B[y]) #central adult male recovery data, function of adult male recoveries and central males banded
112+
C.juv.R[y] ~ dbin(f.juv[1,y],C.juv.B[y]) #central juvenile recovery data, function of juv recoveries and central imms banded
113+
C.loc.R[y] ~ dbin(f.loc[1,y],C.loc.B[y]) #central local recovery data, function of local recoveries and central locals banded
114+
E.af.R[y] ~ dbin(f.af[2,y],E.af.B[y]) #ditto for eastern
115+
E.am.R[y] ~ dbin(f.am[2,y],E.am.B[y]) #ditto for eastern
116+
E.juv.R[y] ~ dbin(f.juv[2,y],E.juv.B[y]) #ditto for eastern
117+
E.loc.R[y] ~ dbin(f.loc[2,y],E.loc.B[y]) #ditto for eastern
118118
}
119119
for (y in 2:yrs){
120-
C.af.H[y] ~ dbin(f.af[1,y], af.N[1,y])
121-
C.am.H[y] ~ dbin(f.am[1,y], am.N[1,y])
122-
C.juv.H[y] ~ dbin(f.juv[1,y], juv.N[1,y])
123-
E.af.H[y] ~ dbin(f.af[2,y], af.N[2,y])
124-
E.am.H[y] ~ dbin(f.am[2,y], am.N[2,y])
125-
E.juv.H[y] ~ dbin(f.juv[2,y], juv.N[2,y])
120+
C.af.H[y] ~ dbin(f.af[1,y], af.N[1,y]) #ad female harvest data dist. binom as adult female pop size (af.N) and recovery rate (f.af)
121+
C.am.H[y] ~ dbin(f.am[1,y], am.N[1,y]) #ad male harvest data dist. binom as adult male pop size (am.N) and recovery rate (f.am)
122+
C.juv.H[y] ~ dbin(f.juv[1,y], juv.N[1,y]) #juv harvest data (imm in excel sheet) dist. as juv pop size and recovery rate
123+
E.af.H[y] ~ dbin(f.af[2,y], af.N[2,y]) #ditto for eastern
124+
E.am.H[y] ~ dbin(f.am[2,y], am.N[2,y]) #ditto for eastern
125+
E.juv.H[y] ~ dbin(f.juv[2,y], juv.N[2,y]) #ditto for eastern
126126
}
127127
128128
@@ -142,7 +142,7 @@ bugs.data <- list(yrs = 49, C.af.H=trunc(Central[,2]+1), E.af.H=trunc(Eastern[,2
142142
C.am.R=Central[,10]+1, E.am.R=Eastern[,10]+1,
143143
C.juv.R=Central[,11]+1, E.juv.R=Eastern[,11]+1,
144144
C.loc.R=Central[,12]+1, E.loc.R=Eastern[,12]+1)
145-
bugs.data$C.af.H
145+
146146
# Initial values (not all priors listed)
147147
inits <- function(){list(f.af.x=c(rep(0.05,2)),f.am.x=c(rep(0.05,2)),f.juv.x=c(rep(0.05,2)))}
148148

0 commit comments

Comments
 (0)