ypr: Yield-Per-Recruit Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/ypr.R

Description

Yield-per-recruit (YPR) analysis is conducted following the modified Thompson-Bell algorithm. Reference points Fmax and F0.1 are calculated.

Usage

1
2
ypr(age = NULL, wgt = NULL, partial = NULL, M = NULL,
 plus = FALSE, oldest = NULL, maxF = 2, incrF = 0.001, graph = TRUE)

Arguments

age

the vector of cohort ages, e.g. c(1,2,3,4,5). If the last age is a plus group, do not add a "+" to the age.

wgt

the vector of catch weights for each age, e.g. c(0.2,0.4,0.7,1.0,1.2). Length of vector must correspond to the length of the age vector.

partial

the partial recruitment vector applied to fishing mortality (F) to obtain partial F-at-age. Length of the partial recruitment vector must correspond to the length of the age vector.

M

vector containing a single natural mortality (M) rate if M is assumed constant over all ages, or a vector of Ms, one for each age. If the latter, the vector length must correspond to the length of the age vector.

plus

a logical value indicating whether the last age is a plus-group. Default is FALSE.

oldest

if plus=TRUE, a numeric value indicating the oldest age in the plus group.

maxF

the maximum value of F range over which YPR will be calculated. YPR is calculated for F = 0 to maxF.

incrF

F increment for YPR calculation.

graph

logical indicating whether YPR versus F should be plotted. Default=TRUE.

Details

Yield-per-recruit analysis is conducted following the modified Thompson-Bell algorithm. Reference points Fmax and F0.1 are calculated. If the last age is a plus-group, the cohort is expanded to the oldest age and the wgt, partial, and M values for the plus age are applied to the expanded cohort ages.

Value

Reference_Points

F and yield-per-recruit values for Fmax and F0.1

F_vs_YPR

Yield-per-recruit values for each F increment

Author(s)

Gary A. Nelson, Massachusetts Division of Marine Fisheries [email protected]

References

Gabriel, W. L., M. P. Sissenwine, and W. J. Overholtz. 1989. Analysis of spawning stock biomass per recruit: an example for Georges Bank haddock. North American Journal of Fisheries Management 9: 383-391.

See Also

sbpr

Examples

1
2
3
data(haddock)
ypr(age=haddock$age,wgt=haddock$ssbwgt,partial=haddock$partial,M=0.4,
plus=TRUE,oldest=100,maxF=2,incrF=0.01)

Example output

Loading required package: MASS
Loading required package: boot
Loading required package: bootstrap
Loading required package: lme4
Loading required package: Matrix
Loading required package: numDeriv
$Reference_Points
              F Yield_Per_Recruit
F0.10 0.3419092         0.3262356
Fmax  0.6800000         0.3555560

$F_vs_YPR
       F        YPR
1   0.00 0.00000000
2   0.01 0.02461255
3   0.02 0.04739566
4   0.03 0.06850703
5   0.04 0.08808835
6   0.05 0.10626713
7   0.06 0.12315840
8   0.07 0.13886607
9   0.08 0.15348425
10  0.09 0.16709825
11  0.10 0.17978556
12  0.11 0.19161671
13  0.12 0.20265593
14  0.13 0.21296186
15  0.14 0.22258807
16  0.15 0.23158359
17  0.16 0.23999335
18  0.17 0.24785856
19  0.18 0.25521708
20  0.19 0.26210373
21  0.20 0.26855057
22  0.21 0.27458714
23  0.22 0.28024072
24  0.23 0.28553649
25  0.24 0.29049774
26  0.25 0.29514601
27  0.26 0.29950127
28  0.27 0.30358204
29  0.28 0.30740550
30  0.29 0.31098760
31  0.30 0.31434318
32  0.31 0.31748605
33  0.32 0.32042904
34  0.33 0.32318414
35  0.34 0.32576252
36  0.35 0.32817459
37  0.36 0.33043009
38  0.37 0.33253811
39  0.38 0.33450715
40  0.39 0.33634518
41  0.40 0.33805963
42  0.41 0.33965750
43  0.42 0.34114532
44  0.43 0.34252923
45  0.44 0.34381500
46  0.45 0.34500803
47  0.46 0.34611340
48  0.47 0.34713589
49  0.48 0.34808000
50  0.49 0.34894995
51  0.50 0.34974972
52  0.51 0.35048307
53  0.52 0.35115352
54  0.53 0.35176442
55  0.54 0.35231889
56  0.55 0.35281992
57  0.56 0.35327028
58  0.57 0.35367264
59  0.58 0.35402948
60  0.59 0.35434316
61  0.60 0.35461593
62  0.61 0.35484988
63  0.62 0.35504702
64  0.63 0.35520924
65  0.64 0.35533833
66  0.65 0.35543598
67  0.66 0.35550380
68  0.67 0.35554332
69  0.68 0.35555597
70  0.69 0.35554314
71  0.70 0.35550611
72  0.71 0.35544612
73  0.72 0.35536434
74  0.73 0.35526188
75  0.74 0.35513981
76  0.75 0.35499911
77  0.76 0.35484075
78  0.77 0.35466563
79  0.78 0.35447461
80  0.79 0.35426851
81  0.80 0.35404811
82  0.81 0.35381415
83  0.82 0.35356734
84  0.83 0.35330834
85  0.84 0.35303781
86  0.85 0.35275634
87  0.86 0.35246452
88  0.87 0.35216289
89  0.88 0.35185199
90  0.89 0.35153231
91  0.90 0.35120434
92  0.91 0.35086853
93  0.92 0.35052531
94  0.93 0.35017510
95  0.94 0.34981829
96  0.95 0.34945527
97  0.96 0.34908638
98  0.97 0.34871197
99  0.98 0.34833237
100 0.99 0.34794789
101 1.00 0.34755883
102 1.01 0.34716548
103 1.02 0.34676810
104 1.03 0.34636695
105 1.04 0.34596229
106 1.05 0.34555434
107 1.06 0.34514334
108 1.07 0.34472949
109 1.08 0.34431302
110 1.09 0.34389410
111 1.10 0.34347293
112 1.11 0.34304969
113 1.12 0.34262455
114 1.13 0.34219768
115 1.14 0.34176922
116 1.15 0.34133933
117 1.16 0.34090816
118 1.17 0.34047583
119 1.18 0.34004248
120 1.19 0.33960823
121 1.20 0.33917320
122 1.21 0.33873751
123 1.22 0.33830126
124 1.23 0.33786456
125 1.24 0.33742750
126 1.25 0.33699018
127 1.26 0.33655269
128 1.27 0.33611512
129 1.28 0.33567754
130 1.29 0.33524004
131 1.30 0.33480269
132 1.31 0.33436556
133 1.32 0.33392873
134 1.33 0.33349224
135 1.34 0.33305618
136 1.35 0.33262059
137 1.36 0.33218553
138 1.37 0.33175106
139 1.38 0.33131723
140 1.39 0.33088408
141 1.40 0.33045167
142 1.41 0.33002003
143 1.42 0.32958922
144 1.43 0.32915926
145 1.44 0.32873020
146 1.45 0.32830207
147 1.46 0.32787491
148 1.47 0.32744875
149 1.48 0.32702362
150 1.49 0.32659955
151 1.50 0.32617657
152 1.51 0.32575471
153 1.52 0.32533399
154 1.53 0.32491443
155 1.54 0.32449605
156 1.55 0.32407889
157 1.56 0.32366295
158 1.57 0.32324826
159 1.58 0.32283484
160 1.59 0.32242270
161 1.60 0.32201185
162 1.61 0.32160231
163 1.62 0.32119411
164 1.63 0.32078724
165 1.64 0.32038172
166 1.65 0.31997756
167 1.66 0.31957478
168 1.67 0.31917338
169 1.68 0.31877338
170 1.69 0.31837477
171 1.70 0.31797757
172 1.71 0.31758179
173 1.72 0.31718743
174 1.73 0.31679450
175 1.74 0.31640300
176 1.75 0.31601294
177 1.76 0.31562432
178 1.77 0.31523715
179 1.78 0.31485143
180 1.79 0.31446717
181 1.80 0.31408436
182 1.81 0.31370300
183 1.82 0.31332311
184 1.83 0.31294467
185 1.84 0.31256770
186 1.85 0.31219219
187 1.86 0.31181815
188 1.87 0.31144556
189 1.88 0.31107444
190 1.89 0.31070478
191 1.90 0.31033658
192 1.91 0.30996984
193 1.92 0.30960456
194 1.93 0.30924074
195 1.94 0.30887837
196 1.95 0.30851745
197 1.96 0.30815798
198 1.97 0.30779996
199 1.98 0.30744339
200 1.99 0.30708825
201 2.00 0.30673456

fishmethods documentation built on Nov. 17, 2017, 7:43 a.m.

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