1 : |
agomez |
1 |
#include "agebandmatrixratio.h" |
2 : |
|
|
#include "agebandmatrixratioptrvector.h" |
3 : |
|
|
#include "errorhandler.h" |
4 : |
|
|
#include "gadget.h" |
5 : |
|
|
#include "global.h" |
6 : |
|
|
|
7 : |
|
|
void AgeBandMatrixRatio::updateAndTagLoss(const AgeBandMatrix& Total, const DoubleVector& tagloss) {
|
8 : |
|
|
|
9 : |
|
|
int numTagExperiments = this->numTagExperiments();
|
10 : |
|
|
int minlen, maxlen, age, length, tag;
|
11 : |
|
|
if (numTagExperiments > 0) {
|
12 : |
|
|
for (age = minage; age < minage + nrow; age++) {
|
13 : |
|
|
minlen = this->minLength(age);
|
14 : |
|
|
maxlen = this->maxLength(age);
|
15 : |
|
|
for (length = minlen; length < maxlen; length++) {
|
16 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++) {
|
17 : |
|
|
(*v[age - minage])[length][tag].R *= tagloss[tag];
|
18 : |
|
|
(*(*v[age - minage])[length][tag].N) = (*v[age - minage])[length][tag].R * Total[age][length].N;
|
19 : |
|
|
}
|
20 : |
|
|
}
|
21 : |
|
|
}
|
22 : |
|
|
}
|
23 : |
|
|
}
|
24 : |
|
|
|
25 : |
|
|
void AgeBandMatrixRatio::updateNumbers(const AgeBandMatrix& Total) {
|
26 : |
|
|
|
27 : |
|
|
int numTagExperiments = this->numTagExperiments();
|
28 : |
|
|
int minlen, maxlen, age, length, tag;
|
29 : |
|
|
double number, ratio;
|
30 : |
|
|
|
31 : |
|
|
if (numTagExperiments > 0) {
|
32 : |
|
|
for (age = minage; age < minage + nrow; age++) {
|
33 : |
|
|
minlen = this->minLength(age);
|
34 : |
|
|
maxlen = this->maxLength(age);
|
35 : |
|
|
for (length = minlen; length < maxlen; length++) {
|
36 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++) {
|
37 : |
|
|
number = Total[age][length].N;
|
38 : |
|
|
ratio = (*v[age - minage])[length][tag].R;
|
39 : |
|
|
if (number < verysmall || ratio < verysmall) {
|
40 : |
|
|
(*(*v[age - minage])[length][tag].N) = 0.0;
|
41 : |
|
|
(*v[age - minage])[length][tag].R = 0.0;
|
42 : |
|
|
} else {
|
43 : |
|
|
(*(*v[age - minage])[length][tag].N) = ratio * number;
|
44 : |
|
|
}
|
45 : |
|
|
}
|
46 : |
|
|
}
|
47 : |
|
|
}
|
48 : |
|
|
}
|
49 : |
|
|
}
|
50 : |
|
|
|
51 : |
|
|
void AgeBandMatrixRatio::updateRatio(const AgeBandMatrix& Total) {
|
52 : |
|
|
|
53 : |
|
|
int numTagExperiments = this->numTagExperiments();
|
54 : |
|
|
int minlen, maxlen, age, length, tag;
|
55 : |
|
|
double tagnum, totalnum;
|
56 : |
|
|
|
57 : |
|
|
if (numTagExperiments > 0) {
|
58 : |
|
|
for (age = minage; age < minage + nrow; age++) {
|
59 : |
|
|
minlen = this->minLength(age);
|
60 : |
|
|
maxlen = this->maxLength(age);
|
61 : |
|
|
for (length = minlen; length < maxlen; length++) {
|
62 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++) {
|
63 : |
|
|
tagnum = (*(*v[age - minage])[length][tag].N);
|
64 : |
|
|
totalnum = Total[age][length].N;
|
65 : |
|
|
if (tagnum < verysmall || totalnum < verysmall) {
|
66 : |
|
|
(*(*v[age - minage])[length][tag].N) = 0.0;
|
67 : |
|
|
(*v[age - minage])[length][tag].R = 0.0;
|
68 : |
|
|
} else {
|
69 : |
|
|
(*v[age - minage])[length][tag].R = tagnum / totalnum;
|
70 : |
|
|
}
|
71 : |
|
|
}
|
72 : |
|
|
}
|
73 : |
|
|
}
|
74 : |
|
|
}
|
75 : |
|
|
}
|
76 : |
|
|
|
77 : |
|
|
void AgeBandMatrixRatio::IncrementAge(const AgeBandMatrix& Total) {
|
78 : |
|
|
|
79 : |
|
|
int numTagExperiments = this->numTagExperiments();
|
80 : |
|
|
int i, j, j1, j2, tag;
|
81 : |
|
|
|
82 : |
|
|
if (nrow <= 1)
|
83 : |
|
|
return;
|
84 : |
|
|
|
85 : |
|
|
if (numTagExperiments > 0) {
|
86 : |
|
|
i = nrow - 1;
|
87 : |
|
|
j1 = max(v[i]->minCol(), v[i - 1]->minCol());
|
88 : |
|
|
j2 = min(v[i]->maxCol(), v[i - 1]->maxCol());
|
89 : |
|
|
//For the highest age group
|
90 : |
|
|
for (j = j1; j < j2; j++)
|
91 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++)
|
92 : |
|
|
(*(*v[i])[j][tag].N) += (*(*v[i - 1])[j][tag].N);
|
93 : |
|
|
|
94 : |
|
|
for (j = v[i - 1]->minCol(); j < v[i - 1]->maxCol(); j++)
|
95 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++) {
|
96 : |
|
|
(*(*v[i - 1])[j][tag].N) = 0.0;
|
97 : |
|
|
(*v[i - 1])[j][tag].R = 0.0;
|
98 : |
|
|
}
|
99 : |
|
|
|
100 : |
|
|
//For the other age groups.
|
101 : |
|
|
//At the end of each for (i=nrow-2...) loop, the intersection of v[i-1] with
|
102 : |
|
|
//v[i] has been copied from v[i-1] to v[i] and v[i-1] has been set to 0.
|
103 : |
|
|
for (i = nrow - 2; i > 0; i--) {
|
104 : |
|
|
j1 = max(v[i]->minCol(), v[i - 1]->minCol());
|
105 : |
|
|
j2 = min(v[i]->maxCol(), v[i - 1]->maxCol());
|
106 : |
|
|
for (j = v[i - 1]->minCol(); j < j1; j++) {
|
107 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++) {
|
108 : |
|
|
(*(*v[i - 1])[j][tag].N) = 0.0;
|
109 : |
|
|
(*v[i - 1])[j][tag].R = 0.0;
|
110 : |
|
|
}
|
111 : |
|
|
}
|
112 : |
|
|
|
113 : |
|
|
for (j = j1; j < j2; j++) {
|
114 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++) {
|
115 : |
|
|
(*(*v[i])[j][tag].N) = (*(*v[i - 1])[j][tag].N);
|
116 : |
|
|
(*(*v[i - 1])[j][tag].N) = 0.0;
|
117 : |
|
|
(*v[i - 1])[j][tag].R = 0.0;
|
118 : |
|
|
}
|
119 : |
|
|
}
|
120 : |
|
|
|
121 : |
|
|
for (j = j2; j < v[i - 1]->maxCol(); j++) {
|
122 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++) {
|
123 : |
|
|
(*(*v[i - 1])[j][tag].N) = 0.0;
|
124 : |
|
|
(*v[i - 1])[j][tag].R = 0.0;
|
125 : |
|
|
}
|
126 : |
|
|
}
|
127 : |
|
|
}
|
128 : |
|
|
|
129 : |
|
|
//set number in age zero to zero.
|
130 : |
|
|
for (j = v[0]->minCol(); j < v[0]->maxCol(); j++)
|
131 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++)
|
132 : |
|
|
(*(*v[0])[j][tag].N) = 0;
|
133 : |
|
|
|
134 : |
|
|
this->updateRatio(Total);
|
135 : |
|
|
}
|
136 : |
|
|
}
|
137 : |
|
|
|
138 : |
|
|
void AgeBandMatrixRatioPtrVector::Add(const AgeBandMatrixRatioPtrVector& Addition,
|
139 : |
|
|
int area, const ConversionIndex &CI, double ratio) {
|
140 : |
|
|
|
141 : |
|
|
//JMB - note area has already been converted to internal area
|
142 : |
|
|
int minage = max(v[area]->minAge(), Addition[area].minAge());
|
143 : |
|
|
int maxage = min(v[area]->maxAge(), Addition[area].maxAge());
|
144 : |
|
|
|
145 : |
|
|
if ((maxage < minage) || isZero(ratio))
|
146 : |
|
|
return;
|
147 : |
|
|
|
148 : |
|
|
int age, minl, maxl, i, l, tagid, numtags, offset;
|
149 : |
|
|
double numfish;
|
150 : |
|
|
|
151 : |
|
|
numtags = Addition.numTagExperiments();
|
152 : |
|
|
if (numtags > tagID.Size())
|
153 : |
|
|
handle.logMessage(LOGFAIL, "Error in agebandmatrixratio - wrong number of tagging experiments");
|
154 : |
|
|
|
155 : |
|
|
if (numtags == 0)
|
156 : |
|
|
return;
|
157 : |
|
|
|
158 : |
|
|
IntVector tagconversion(numtags, -1);
|
159 : |
|
|
for (i = 0; i < numtags; i++) {
|
160 : |
|
|
tagconversion[i] = this->getTagID(Addition.getTagName(i));
|
161 : |
|
|
if (tagconversion[i] < 0)
|
162 : |
|
|
handle.logMessage(LOGFAIL, "Error in agebandmatrixratio - unrecognised tagging experiment", Addition.getTagName(i));
|
163 : |
|
|
}
|
164 : |
|
|
|
165 : |
|
|
numfish = 0.0;
|
166 : |
|
|
if (CI.isSameDl()) { //Same dl on length distributions
|
167 : |
|
|
offset = CI.getOffset();
|
168 : |
|
|
for (age = minage; age <= maxage; age++) {
|
169 : |
|
|
minl = max(v[area]->minLength(age), Addition[area].minLength(age) + offset);
|
170 : |
|
|
maxl = min(v[area]->maxLength(age), Addition[area].maxLength(age) + offset);
|
171 : |
|
|
for (l = minl; l < maxl; l++) {
|
172 : |
|
|
for (tagid = 0; tagid < numtags; tagid++) {
|
173 : |
|
|
numfish = *(Addition[area][age][l - offset][tagid].N) * ratio;
|
174 : |
|
|
*((*v[area])[age][l][tagconversion[tagid]].N) += numfish;
|
175 : |
|
|
}
|
176 : |
|
|
}
|
177 : |
|
|
}
|
178 : |
|
|
|
179 : |
|
|
} else { //Not same dl.
|
180 : |
|
|
if (CI.isFiner()) {
|
181 : |
|
|
//Stock that is added to has finer division than the stock that is added to it.
|
182 : |
|
|
for (age = minage; age <= maxage; age++) {
|
183 : |
|
|
minl = max(v[area]->minLength(age), CI.minPos(Addition[area].minLength(age)));
|
184 : |
|
|
maxl = min(v[area]->maxLength(age), CI.maxPos(Addition[area].maxLength(age) - 1) + 1);
|
185 : |
|
|
for (l = minl; l < maxl; l++) {
|
186 : |
|
|
for (tagid = 0; tagid < numtags; tagid++) {
|
187 : |
|
|
numfish = *(Addition[area][age][CI.getPos(l)][tagid].N) * ratio;
|
188 : |
|
|
numfish /= CI.getNumPos(l); //JMB CI.getNumPos() should never be zero
|
189 : |
|
|
*((*v[area])[age][l][tagconversion[tagid]].N) += numfish;
|
190 : |
|
|
}
|
191 : |
|
|
}
|
192 : |
|
|
}
|
193 : |
|
|
|
194 : |
|
|
} else {
|
195 : |
|
|
//Stock that is added to has coarser division than the stock that is added to it.
|
196 : |
|
|
for (age = minage; age <= maxage; age++) {
|
197 : |
|
|
minl = max(CI.minPos(v[area]->minLength(age)), Addition[area].minLength(age));
|
198 : |
|
|
maxl = min(CI.maxPos(v[area]->maxLength(age) - 1) + 1, Addition[area].maxLength(age));
|
199 : |
|
|
if (maxl > minl && CI.getPos(maxl - 1) < v[area]->maxLength(age)
|
200 : |
|
|
&& CI.getPos(minl) >= v[area]->minLength(age)) {
|
201 : |
|
|
|
202 : |
|
|
for (l = minl; l < maxl; l++) {
|
203 : |
|
|
for (tagid = 0; tagid < numtags; tagid++) {
|
204 : |
|
|
numfish = *(Addition[area][age][l][tagid].N) * ratio;
|
205 : |
|
|
*((*v[area])[age][CI.getPos(l)][tagconversion[tagid]].N) += numfish;
|
206 : |
|
|
}
|
207 : |
|
|
}
|
208 : |
|
|
}
|
209 : |
|
|
}
|
210 : |
|
|
}
|
211 : |
|
|
}
|
212 : |
|
|
}
|
213 : |
|
|
|
214 : |
|
|
void AgeBandMatrixRatioPtrVector::Migrate(const DoubleMatrix& MI, const AgeBandMatrixPtrVector& Total) {
|
215 : |
|
|
|
216 : |
|
|
DoubleVector tmp(size, 0.0);
|
217 : |
|
|
int i, j, age, length, tag;
|
218 : |
|
|
int numTagExperiments = tagID.Size();
|
219 : |
|
|
if (numTagExperiments > 0) {
|
220 : |
|
|
for (age = v[0]->minAge(); age <= v[0]->maxAge(); age++) {
|
221 : |
|
|
for (length = v[0]->minLength(age); length < v[0]->maxLength(age); length++) {
|
222 : |
|
|
for (tag = 0; tag < numTagExperiments; tag++) {
|
223 : |
|
|
tmp.setToZero();
|
224 : |
|
|
for (j = 0; j < size; j++)
|
225 : |
|
|
for (i = 0; i < size; i++)
|
226 : |
|
|
tmp[j] += *((*v[i])[age][length][tag].N) * MI[j][i];
|
227 : |
|
|
|
228 : |
|
|
for (j = 0; j < size; j++)
|
229 : |
|
|
*((*v[j])[age][length][tag].N) = tmp[j];
|
230 : |
|
|
}
|
231 : |
|
|
}
|
232 : |
|
|
}
|
233 : |
|
|
for (i = 0; i < size; i++)
|
234 : |
|
|
v[i]->updateRatio(Total[i]);
|
235 : |
|
|
}
|
236 : |
|
|
}
|