Commit 6bde3b00 authored by pfreon's avatar pfreon
Browse files

Major changes on Arbre_decision, QuestionReponse, TexteRegles, about stock...

Major changes on Arbre_decision, QuestionReponse, TexteRegles, about stock structure and level of exploitation.

Major changes to incorporate new messages regarding the stock structure and the level of explotation relative to MSY-MSE. Introduction of the metapopulation concept. Elimination of a redondant questions regarding stock structure when chosing between linear (Schaefer) and exponential (Fox) models.
Minor changes: Comment.csv, comments into .java files, new CLI test file.
parent 461b77fb
Years;Production;Effort;Environment
1969; 332.4; 146.5; 4.40
1970; 285.5; 127.6; 4.32
1971; 306.7; 130.34; 4.70
1972; 537.2; 208.06; 5.63
1973; 599.4; 208.06; 5.53
1974; 692.5; 208.06; 5.76
1975; 612.9; 208.06; 5.66
1976; 809.4; 208.06; 5.79
1977; 776.0; 208.06; 5.72
1978; 764.0; 208.06; 5.21
1979; 694.7; 208.06; 4.68
1980; 702.4; 208.06; 4.98
1981; 788.7; 208.06; 5.09
1982; 688.0; 208.06; 4.86
1983; 719.7; 208.06; 4.60
1984; 677.3; 208.06; 4.67
1985; 845.03; 208.06; 5.38
1986; 958.43; 208.06; 5.44
1987; 1203.9; 208.06; 4.92
......@@ -405,7 +405,7 @@ public class Cadre_Question extends JFrame
modele = new DefaultListModel<String>();
numQ = QuestionReponse.getNum();
numR = QuestionReponse.getNumRegle();
System.out.println("Dans Cadre_Question ligne 406: n° de question numQ = " + numQ + " n° de règle numR = " +numR);
//System.out.println("Dans Cadre_Question ligne 406: n° de question numQ = " + numQ + " n° de règle numR = " + numR);
if (numQ == -1)
{
String m$ = ""; // Modif. 2020
......@@ -419,7 +419,7 @@ public class Cadre_Question extends JFrame
stopProcess();
return;
}
else
else
if (numQ == -2 || numQ == -3)
{
new MsgDialogBox(0, "Problem in Jackknife computation \ndue to CPUE values <1. \nPlease modifiy your units of production (catches) and/or effort.", 0, this.parent);//System.out.println("Texte_erreur_jackknife$1 = "); // + Texte_erreur_jackknife$[1]
......@@ -433,7 +433,7 @@ public class Cadre_Question extends JFrame
}
return;
}
else
else
if (numQ == -4)
{
if (dlgSp != null)
......@@ -452,19 +452,21 @@ public class Cadre_Question extends JFrame
if (numR >= 0)
{
//TexteRegles.loadRegles(numR);
System.out.println("Dans Cadre_Question ligne 455: n° de question numQ = " + numQ + " n° de règle numR = " + numR);
jTextAreaRegle.setText(TexteRegles.getScript());
String[] itemR = TexteRegles.getItem();
for (int i = 0; i < itemR.length; i++)
{
for (int i = 0; i < itemR.length; i++) // Item.length = nombre d'item (questions) associés à la règle. Commentaire 2020.
{
jTextAreaRegle.append("\n\t");
jTextAreaRegle.append(itemR[i]);
}
jTextAreaRegle.setCaretPosition(0);
}
else { jTextAreaRegle.setText("");}
else { jTextAreaRegle.setText("");// Ne passe ici que pour question "Does the data-set apply to a single stock?" réponse oui et règle -1 (décision 5).
}
QuestionReponse.loadQuestion();
Script = QuestionReponse.getScript();
Script = QuestionReponse.getScript(); // Script = texte question (if any). Commentaire 2020.
if (Script != null) {
jTextAreaQuestion.setText(QuestionReponse.getScript());
} else {
......@@ -472,8 +474,7 @@ public class Cadre_Question extends JFrame
}
jTextAreaQuestion.setCaretPosition(0);
item = QuestionReponse.getItem();
item = QuestionReponse.getItem(); // Contenu question codé (ex: [Ljava.lang.String;@7ba4500a)
jlstItem.setModel(modele);
if (item != null) {
for (int i = 0; i < item.length; i++) {
......@@ -496,8 +497,8 @@ public class Cadre_Question extends JFrame
} else {
cmdPrevious.doClick();
}
// Passe ici uniquement si pas de commentaire
return;
}
}
......@@ -604,7 +605,7 @@ public class Cadre_Question extends JFrame
} else {
UtilCadre.Size(this, 60, 60); // remplace 60, 60 par 30, 30 Test 2020
System.out.println("Définition dans ligne 606 de Cadre_Question.java des Facteurs de réduction (30, 30) (JFrame) par rapport à max (sx et sy) ligne 73 UtilCadre.java. Test 2020");// Test 2020
// System.out.println("Définition dans ligne 606 de Cadre_Question.java des Facteurs de réduction (30, 30) (JFrame) par rapport à max (sx et sy) ligne 73 UtilCadre.java. Test 2020");// Test 2020
UtilCadre.Centrer(this);
}
......
......@@ -227,9 +227,11 @@ public class QuestionReponse {
//System.out.println("AAA question number : "+numEnCours);
//System.out.println("AAA question : "+questxt);
//System.out.println("BBB i guess answer is : "+reptxt);
Global.questionDic.put(numEnCours, questxt);
Global.answerDic.put(numEnCours, reptxt);
Global.warningDic.put(numEnCours, commentTxt);
Global.questionDic.put(numEnCours, questxt); // Texte de la question.
Global.answerDic.put(numEnCours, reptxt); // Réponse à la question.
System.out.println("Dans QuestionReponse.java ligne 232, numEnCours: " + numEnCours + " questxt: " + questxt + " reptxt: " + reptxt + " commentTxt: " + commentTxt);
Global.warningDic.put(numEnCours, commentTxt);
// System.out.println("Dans QuestionReponse.java ligne 234, Global.warningDic: " + Global.warningDic + " commentTxt: " + commentTxt);
try {
switch (numEnCours) {
case 1:
......@@ -245,7 +247,7 @@ public class QuestionReponse {
Global.stock_unique = index;
break;
case 6:
Global.sous_stock = index;
Global.metapopulation = index; // Avant stock_divise. Modif. 2020
break;
case 7:
Global.sous_stock_isole = index;
......@@ -320,10 +322,10 @@ public class QuestionReponse {
case 73:
Global.rapport_vie_exploitee_inferieur_deux = index;
break;
case 25:
case 74:
Global.stock_divise = index;
break;
// case 25: // Cas supprimé car doublon avec metapopulation
// case 74: // Cas supprimé car doublon avec metapopulation
// Global.stock_divise = index;
// break;
case 26:
case 75:
Global.reserves_naturelles = index;
......@@ -514,7 +516,7 @@ public class QuestionReponse {
@return boolean
*/
public static boolean displayQuestion() {
String tc = TexteRegles.getComment(); // Commentaire dans "Current known facts" de la fenêtre principale.
String tc = TexteRegles.getComment(); // Commentaire dans "Current known facts" de la fenêtre principale.
if (scriptEnCours != null) {
return true;
} else return (type[indexEnCours] == Global.fixationM && (!(tc == null) && !tc.equals("")));
......
/**
* Titre : Climprod<p>
* Gestion des messages de la fenetre "Climprod: select the appropriate model and fit it". Commentaire 2020.
* en relation avec regles.csv et comment.csv
*/
package fr.ird.climprod;
import java.io.InputStream;
......@@ -91,7 +92,7 @@ public class TexteRegles {
public static void loadRegles(int number)
{
numEnCours=number;
System.out.println("on charge la règle " + numEnCours );
System.out.println("on charge la règle (dans TexteRegles, ligne 94) " + numEnCours );
commentaireEnCours="";
if (numEnCours !=-1)
{
......@@ -133,6 +134,11 @@ public static void initRegles()
/*
Teste la règle
@return boolean true si règle vraie.
IMPOSSIBLE DE PRESENTER MESSAGE DE WARNING (lu dans Comments.csv) DANS FENETRE QUESTION SI:
1) Pas de règle associée (ex: décision n°5;
2)¨result (boléen) = true;
3) si décision aboutit sur -1 (on a alors un message d'arrêt de la procedure de sélection STOP).
Seule solution trouvée (uniquement lorsque result != true): rajouter un if et donner ici le commentaire.
*/
public static boolean isTrue(){
boolean result=false;
......@@ -157,7 +163,7 @@ public static boolean isTrue(){
double[] effort=Data.getF();
double[] ext=Stat1.Extremas(effort);
temp=((ext[1]-ext[0])/ext[0]);
result = temp<0.4d;
result = temp<1.0d; // Avant <0.4d. Modif. 2020.
if(!result)
commentaireEnCours="The range of fishing effort variation of your data set is " + (temp);
break;
......@@ -165,19 +171,30 @@ public static boolean isTrue(){
result = (Global.effet_delais_abundance_negligeable!=1);
break;
case 46:
result = (Global.stock_unique!=1 && Global.sous_stock!=1);
result = (Global.stock_unique!=1 && Global.metapopulation!=1); // Changement de nom variable. Modif. 2020
System.out.println("Dans TexteRegles.java ligne 169 case 46, result = " + result);
if(!result){
commentaireEnCours="Metapopulations are special cases that difficult the application of any kind of population dynamics model. \nAccording to the level connectivity between sub-stocks, modelization might be borderline or not recommended as you will see \nafter answering the next question.";
}
break;
case 45:
result = (Global.stock_unique!=1 && Global.sous_stock==1 && Global.sous_stock_isole!=1);
result = (Global.stock_unique!=1 && Global.metapopulation==1 && Global.sous_stock_isole!=1); // Global.metapopulation==1
if(!result){
commentaireEnCours="Your case is a borderline one either because you deal only with a sub-stock or with a full metapopulation \n(and the lower is the connectivity between sub-stocks, the more borderline you are).";
}
break;
case 34:
result = (Global.stock_unique!=1 && Global.sous_stock==1 && Global.sous_stock_isole==1);
result = (Global.stock_unique!=1 && Global.metapopulation==1 && Global.sous_stock_isole==1); // Pas trouvé de solution pour afficher un message associé à cette règle lorsque result = true. Modif. 2020
break;
case 35:
result = (Global.under_and_over_exploited!=1 && Global.under_and_optimaly==1);
result = (Global.under_and_over_exploited!=1);// Avant Global.under_and_over_exploited!=1 && Global.under_and_optimaly==1). Modif 2020.
System.out.println("Dans TexteRegles.java ligne 182, case 35, result = " + result);
break;
case 49:
result = (Global.under_and_over_exploited!=1 && Global.under_and_optimaly!=1);
result = (Global.under_and_optimaly!=1); // Avant (Global.under_and_over_exploited!=1 && Global.under_and_optimaly!=1). Modif 2020.
if(!result){
commentaireEnCours="Your can still go on but your case is a borderline one. Model results will be uncertain (particularly maximum production that could be underestimated) owing to the lack of exploitation above MSY/MSE levels.";
}
break;
case 37:
result = (Global.statistiques_anormales==1);
......@@ -218,11 +235,11 @@ public static boolean isTrue(){
if(result) Flag_Modele_Exponentiel_deja_recherche=1;
break;
case 14:
result = (Global.relationCPU_E==RechercheModele.exponentiel && Global.pessimiste!=1 && Global.stock_deja_effondre!=1 && Global.lifespan>4 && Global.lifespan<11 && Global.fecondite_faible!=1 && Global.stock_divise==1);
result = (Global.relationCPU_E==RechercheModele.exponentiel && Global.pessimiste!=1 && Global.stock_deja_effondre!=1 && Global.lifespan>4 && Global.lifespan<11 && Global.fecondite_faible!=1 && Global.metapopulation==1); // metapopulation remplace ici stock_subdivise car redondant. Modif 2020.
if(result) Flag_Modele_Exponentiel_deja_recherche=1;
break;
case 16:
result = (Global.relationCPU_E==RechercheModele.exponentiel && Global.pessimiste!=1 && Global.stock_deja_effondre!=1 && Global.rapport_vie_exploitee_inferieur_deux==2 && Global.premiere_reproduction_avant_recrutement==1 && Global.fecondite_faible!=1 && Global.reserves_naturelles==1 && Global.stock_divise==1);
result = (Global.relationCPU_E==RechercheModele.exponentiel && Global.pessimiste!=1 && Global.stock_deja_effondre!=1 && Global.rapport_vie_exploitee_inferieur_deux==2 && Global.premiere_reproduction_avant_recrutement==1 && Global.fecondite_faible!=1 && Global.reserves_naturelles==1 && Global.metapopulation==1); // metapopulation remplace ici stock_subdivise car redondant. Modif 2020.
if(result) Flag_Modele_Exponentiel_deja_recherche=1;
break;
case 17:
......@@ -282,7 +299,7 @@ public static boolean isTrue(){
}
break;
case 22:
result = (Global.lifespan<5 && Global.rapport_vie_exploitee_inferieur_deux==1 && Global.reserves_naturelles==2 && Global.stock_divise==2 && Global.cpue_unstable==2);
result = (Global.lifespan<5 && Global.rapport_vie_exploitee_inferieur_deux==1 && Global.reserves_naturelles==2 && Global.metapopulation==2 && Global.cpue_unstable==2); // metapopulation remplace ici stock_subdivise car redondant. Modif 2020.
if(result)
{
Flag_Modele_Lineaire_deja_recherche=1;
......@@ -456,20 +473,21 @@ public static boolean isTrue(){
if(result)
commentaireEnCours="From the current rule the model " + RechercheModele.getEquation()+ " is validated";
break;
case 32:
case 32:
result= (Global.environmental_influence.equals(Global.influenceEnv[2]));
break;
}
if(result && commentaireEnCours.equals(""))
commentaireEnCours=(String)htComment.get(Integer.toString(numEnCours));
System.out.println("Le commentaire est "+commentaireEnCours);
System.out.println("On teste " + numEnCours + " elle est "+ result );
return result;
//System.out.println("Le commentaire du numEnCours " + numEnCours + "dans TexteRegles.java ligne 466) est: " + commentaireEnCours + "result = " + result);
if (result && commentaireEnCours.equals(""))
{ commentaireEnCours=(String)htComment.get(Integer.toString(numEnCours));
//System.out.println("Le commentaire est (dans TexteRegles.java ligne 468) " + commentaireEnCours);
System.out.println("On teste la règle (dans TexteRegles.java ligne 469) " + numEnCours + " elle est "+ result );
}
return result;
}
public static String getComment(){
return commentaireEnCours;
}
}
\ No newline at end of file
......@@ -3,12 +3,12 @@
2;3;-1;43;1;unite_standardisee;Is the fishing effort unit standardized and is the CPUE proportional to abundance?;standard.hlp ;
3;-1;4;47;1;;;;
4;5;-1;44;1;effet_delais_abundance_negligeable;Do time-lags and deviations from the stable age structure have negligible effects on production rate?; lageffe1.hlp ;
5;9;6;-1;1;stock_unique;Does the data-set apply to a single stock?; singlest.hlp ;
6;7;-1;46;1;sous_stock;Does the data-set apply to a sub-stock?; substock.hlp ;
7;8;-1;45;1;sous_stock_isole;Is the sub-stock well isolated (i.e. with few exchanges) from others?; isostock.hlp ;
8;9;9;34;1;;;;
9;11;10;-1;1;under_and_over_exploited;Do you think that the data-set covers periods both of overexploitation and of underexploitation?; undover.hlp ;
10;11;11;35;1;under_and_optimaly;Do you think that the data-set cover periods both of underexploitation and optimal exploitation?; undopt.hlp ;
5;9;6;-1;1;stock_unique;Does the data-set apply to a unit stock?; singlest.hlp ;
6;7;-1;46;1;metapopulation;Does the data-set applies to a metapopulation?; metapopulation.hlp ;
7;8;-1;45;1;sous_stock_isole;Does the data applies to the full metapopulation or at least to only one of its sub-stock with limited connectivity?; isostock.hlp ;
8;9;-1;34;1;;;;
9;11;10;35;1;under_and_over_exploited;Do you think that the data-set covers periods of both overexploitation and of underexploitation?; undover.hlp ;
10;11;-1;49;1;under_and_optimaly;Do you think that the data-set cover periods of both underexploitation and optimal exploitation?; undopt.hlp ;
11;12;12;37;1;statistiques_anormales;Do you see any abnormal statistics in the statistical data table?(see the second table in the Climprod frame); abnormal.hlp ;
12;13;13;36;1;unstability;Is interannual variability too large?; unstabil.hlp ;
13;14;14;38;1;abnormal_points_dist;Do you see outlier points?; outlier.hlp ;
......@@ -16,18 +16,17 @@
15;16;16;50;1;effort_increasing;Constantly increasing effort?; increasf.hlp ;
16;17;17;40;1;independance;Are the two variables dependent?; independ.hlp ;;;;;;;;;;;
17;18;18;-1;1;nb_classes_exploitees;Number of significantly exploited year-classes; nbclass.hlp ;1;2;3;4;5;6;7;8;9;10;>10
18;19;57;-1;1;effort_preponderant;Is the influence of fishing effort on CPUE more important than environmental influence?; fishmore.hlp ;;;;;;;;;;;
18;19;57;-1;1;effort_preponderant;Is the influence of fishing effort on CPUE more important than the environmental influence?; fishmore.hlp ;;;;;;;;;;;
19;20;-1;48;1;decreasing_relationship;Does this plot appear to be decreasing?; decreas.hlp ;;;;;;;;;;;
20;40;21;17;1;obviously;Does this plot look obviously linear?; obvious.hlp ;;;;;;;;;;;
21;40;22;18;1;pessimiste;Do you have any (additional) reason to expect highly unstable behaviour or collapse of the stock?; pessimis.hlp ;;;;;;;;;;;
22;40;23;19;1;stock_deja_effondre;Did the stock already collapse or exhibit drastic decrease(s) in catches?; collapse.hlp ;;;;;;;;;;;
21;40;22;18;1;pessimiste;Do you have any (additional) reason to expect a highly unstable behaviour or a collapse of the stock?; pessimis.hlp ;;;;;;;;;;;
22;40;23;19;1;stock_deja_effondre;Did the stock already collapse or did it exhibit drastic decrease(s) in catches?; collapse.hlp ;;;;;;;;;;;
23;24;24;-1;1;lifespan;What is the life span of the species?; lifespan.hlp ;1;2;3;4;5;6;7;8;9;10;>10
24;25;25;-1;1;rapport_vie_exploitee_inferieur_deux;Is the ratio (lifespan/number of exploited year-classes) lower than 2?; ratio.hlp ;;;;;;;;;;;
25;26;26;-1;1;stock_divise;Is the single stock subdivided into various geographical sub-stocks (all must be exploited by the fleet)?; stockdiv.hlp ;;;;;;;;;;;
24;26;26;-1;1;rapport_vie_exploitee_inferieur_deux;Is the ratio (lifespan/number of exploited year-classes) lower than 2?; ratio.hlp ;;;;;;;;;;;
26;27;27;-1;1;reserves_naturelles;Are there natural protected areas for the stock or constantly inacessible adult biomass?; protect.hlp ;;;;;;;;;;;
27;28;28;-1;1;premiere_reproduction_avant_recrutement;Are there one or several non negligible spawnings before recruitment?; firstspa.hlp ;;;;;;;;;;;
28;29;29;-1;1;fecondite_faible;Is the fecundity of the species very low (sharks mammals etc.)?; fecundit.hlp ;;;;;;;;;;;;;;;;;;;;;
29;30;30;-1;1;cpue_unstable;Is there a strong instability in the cpue time series?; unstabil.hlp ;;;;;;;;;;;
29;30;30;-1;1;cpue_unstable;Is there a strong instability in the cpue time series?; pueunsta.hlp ;;;;;;;;;;;
30;42;31;10;1;;;;;;;;;;;;;;
31;42;32;11;1;;;;;;;;;;;;;;
32;42;33;12;1;;;;;;
......
0;-1;1;41;1;;;;
1;-1;2;42;1;changement_exploitation; Have there been changes in the fishing pattern during the period (effort allocation quota mesh-size ...)?;changes.hlp ;
2;3;-1;43;1;unite_standardisee;Is the fishing effort unit standardized and is the CPUE proportional to abundance?;standard.hlp ;
3;-1;4;47;1;;;;
4;5;-1;44;1;effet_delais_abundance_negligeable;Do time-lags and deviations from the stable age structure have negligible effects on production rate?; lageffe1.hlp ;
5;9;6;-1;1;stock_unique;Does the data-set apply to a single stock?; singlest.hlp ;
6;-1;7;46;1;sous_stock;Are the different stocks independant from each other (not a metapopulation)?; substock.hlp ;
7;8;-1;45;1;sous_stock_isole;Does the data apply to the full metapopulation or at least to only one of its sub-stock well isolated (i.e. with few exchanges) from others?; isostock.hlp ;
8;9;-1;34;1;;;;
9;11;10;35;1;under_and_over_exploited;Do you think that the data-set covers periods both of overexploitation and of underexploitation?; undover.hlp ;
10;11;-1;49;1;under_and_optimaly;Do you think that the data-set cover periods both of underexploitation and optimal exploitation?; undopt.hlp ;
11;12;12;37;1;statistiques_anormales;Do you see any abnormal statistics in the statistical data table?(see the second table in the Climprod frame); abnormal.hlp ;
12;13;13;36;1;unstability;Is interannual variability too large?; unstabil.hlp ;
13;14;14;38;1;abnormal_points_dist;Do you see outlier points?; outlier.hlp ;
14;15;15;39;1;abnormal_points_scatt;Do you see outlier points?; outlier.hlp ;
15;16;16;50;1;effort_increasing;Constantly increasing effort?; increasf.hlp ;
16;17;17;40;1;independance;Are the two variables dependent?; independ.hlp ;;;;;;;;;;;
17;18;18;-1;1;nb_classes_exploitees;Number of significantly exploited year-classes; nbclass.hlp ;1;2;3;4;5;6;7;8;9;10;>10
18;19;57;-1;1;effort_preponderant;Is the influence of fishing effort on CPUE more important than environmental influence?; fishmore.hlp ;;;;;;;;;;;
19;20;-1;48;1;decreasing_relationship;Does this plot appear to be decreasing?; decreas.hlp ;;;;;;;;;;;
20;40;21;17;1;obviously;Does this plot look obviously linear?; obvious.hlp ;;;;;;;;;;;
21;40;22;18;1;pessimiste;Do you have any (additional) reason to expect highly unstable behaviour or collapse of the stock?; pessimis.hlp ;;;;;;;;;;;
22;40;23;19;1;stock_deja_effondre;Did the stock already collapse or exhibit drastic decrease(s) in catches?; collapse.hlp ;;;;;;;;;;;
23;24;24;-1;1;lifespan;What is the life span of the species?; lifespan.hlp ;1;2;3;4;5;6;7;8;9;10;>10
24;25;25;-1;1;rapport_vie_exploitee_inferieur_deux;Is the ratio (lifespan/number of exploited year-classes) lower than 2?; ratio.hlp ;;;;;;;;;;;
25;26;26;-1;1;stock_divise;Is the single stock subdivided into various geographical sub-stocks (all must be exploited by the fleet)?; stockdiv.hlp ;;;;;;;;;;;
26;27;27;-1;1;reserves_naturelles;Are there natural protected areas for the stock or constantly inacessible adult biomass?; protect.hlp ;;;;;;;;;;;
27;28;28;-1;1;premiere_reproduction_avant_recrutement;Are there one or several non negligible spawnings before recruitment?; firstspa.hlp ;;;;;;;;;;;
28;29;29;-1;1;fecondite_faible;Is the fecundity of the species very low (sharks mammals etc.)?; fecundit.hlp ;;;;;;;;;;;;;;;;;;;;;
29;30;30;-1;1;cpue_unstable;Is there a strong instability in the cpue time series?; unstabil.hlp ;;;;;;;;;;;
30;42;31;10;1;;;;;;;;;;;;;;
31;42;32;11;1;;;;;;;;;;;;;;
32;42;33;12;1;;;;;;
33;42;34;13;1;;;;;;
34;42;35;14;1;;;;;;
35;42;36;16;1;;;;;;
36;40;37;20;1;;;;;;
37;40;38;22;1;;;;;;
38;40;39;21;1;;;;;;
39;44;44;23;1;;;;;;
40;41;46;24;2;;;;;;
41;102;43;51;2;;;;;;
42;43;46;25;2;;;;;;
43;102;102;52;2;;;;;;
44;102;45;51;2;;;;;;
45;102;103;52;2;;;;;;
46;97;47;6;2;;;;;;
47;48;49;-1;1;environmental_influence;Does the environment influence:; Influenc.hlp ;abundance;catchability;both
48;51;49;-1;1;cpue_sous_sur_production;May the stock present large fluctuations in CPUE when overexploited?; additif.hlp ;;;;;;;;;;;;
49;52;50;17;1;linear_relationship;Does this plot look linear; linear.hlp ;;;;;;;;;;;;
50;52;52;-1;1;monotonic_relationship;Does this plot look monotonic?; monotoni.hlp ;;;;;;;;;;;;
51;52;105;-1;1;linear_relationship;Does this plot look linear?; linear.hlp ;;;;;;;;;;;;
52;53;53;-1;1;recruitment_age;Age at recruitment; Agerec.hlp ;1;2;3;4;5;6;7;8;9;10;>10;
53;54;54;-1;1;begin_influence_period;Age at the begining of environmental influence; begin.hlp ;0;1;2;3;4;5;6;7;8;9;10;>10
54;55;55;-1;1;end_influence_period;Age at the end of environmental influence; end.hlp ;0;1;2;3;4;5;6;7;8;9;10;>10
55;97;56;4;2;;;;;;;;;;;;;;;
56;97;-1;5;2;;;;;;;;;;;;;;;
57;58;58;-1;1;recruitment_age;Age at recruitment; Agerec.hlp ;1;2;3;4;5;6;7;8;9;10;>10;
58;59;59;-1;1;begin_influence_period;Age at the begining of environmental influence; begin.hlp ;0;1;2;3;4;5;6;7;8;9;10;>10
59;60;60;-1;1;end_influence_period;Age at the end of environmental influence; end.hlp ;0;1;2;3;4;5;6;7;8;9;10;>10
60;62;61;-1;1;linear_relationship;Does_this_plot_look_linear?; linear.hlp ;;;;;;;;;;;;
61;63;64;-1;1;monotonic_relationship;Does this plot look monotonic?; monotoni.hlp ;;;;;;;;;;;;
62;65;63;26;1;;;;;;;;;;;;;;;
63;65;64;28;1;;;;;;;;;;;;;;;
64;65;65;29;1;;;;;;;;;;;;;;
65;97;66;9;2;;;;;;;;;;;;;;
66;-1;67;53;2;;;;;;;;;;;;;;
67;68;69;-1;1;environmental_influence;Does the environment influence:; Influenc.hlp ;abundance;catchability;both;;;;;;;;
68;69;69;-1;1;cpue_sous_sur_production;May the stock present large fluctuations in CPUE when overexploited?; additif.hlp;;;;;;;;;;;
69;89;70;17;1;obviously;Does this plot look obviously linear?; obvious.hlp ;;;;;;;;;;;
70;89;71;18;1;pessimiste;Do you have any (additional) reason to expect highly unstable behaviour or collapse of the stock?; pessimis.hlp ;;;;;;;;;;;
71;89;72;19;1;stock_deja_effondre;Did the stock already collapse or exhibit drastic decrease(s) in catches?; collapse.hlp ;;;;;;;;;;;
72;73;73;-1;1;lifespan;What is the life span of the species?; lifespan.hlp ;1;2;3;4;5;6;7;8;9;10;>10
73;74;74;-1;1;rapport_vie_exploitee_inferieur_deux;Is the ratio (lifespan/number of exploited year-classes) lower than 2?; ratio.hlp ;;;;;;;;;;;
74;75;75;-1;1;stock_divise;Is the single stock subdivided into various geographical sub-stocks (all must be exploited by the fleet)?; stockdiv.hlp ;;;;;;;;;;;
75;76;76;-1;1;reserves_naturelles;Are there natural protected areas for the stock or constantly inacessible adult biomass?; protect.hlp ;;;;;;;;;;;
76;77;77;-1;1;premiere_reproduction_avant_recrutement;Are there one or several non negligible spawnings before recruitment?; firstspa.hlp ;;;;;;;;;;;
77;78;78;-1;1;fecondite_faible;Is the fecundity of the species very low (sharks mammals etc.)?; fecundit.hlp ;;;;;;;;;;;;;;;;;;;;;
78;79;79;-1;1;cpue_unstable;Is there a strong instability in the cpue time series?; unstabil.hlp ;;;;;;;;;;;
79;91;80;10;1;;;;;;;;;;;;;;
80;91;81;11;1
81;91;82;12;1
82;91;83;13;1
83;91;84;14;1
84;91;85;16;1
85;89;86;20;1
86;89;87;22;1
87;89;88;21;1
88;93;93;23;1
89;90;95;24;2
90;92;92;51;2
91;92;95;25;2
92;95;95;52;2
93;97;94;51;2
94;95;95;52;2
95;97;96;7;2
96;97;-2;8;2;;;;
97;98;-3;0;3;good_results;Is this an acceptable model?; acceptab.hlp ;
98;99;-3;15;3;trend_residuals;Are there a good fit and no trend or strong autocorrelation in residuals?; fitresid.hlp ;
99;104;100;2;3;;;;
100;101;-3;1;3;jackknife;Is there a reasonable jackknife coefficient R2 (>65% recommended) no extreme yearly regression coefficients, an acceptable F test (p<0.01 recommended) and acceptable MSY graph ?; valide.hlp ;;;;;;;;;;;;
101;-4;-4;3;3;;;;
102;-1;47;54;2
103;46;102;55;2
104;-3;-3;56;2
105;-1;-1;57;2
\ No newline at end of file
34;Your case is a borderline case for use with these models because you deal with a sub-stock.;You must not extrapolate your results beyond the interval of observation of the different variables (effort and/orenvironment), when using the model for predictions.;Moreover, any surplus production model using effort will implicitly make the assumption that novariation in recruitment due to other sub-stocks will occur.
35;Model results will be uncertain (particularly maximum production) owing to the low range of exploitation levels.
34;When Your case is a borderline case for use with these models because you deal with a sub-stock or a metapopulation.;You must not extrapolate your results beyond the interval of observation of the different variables (effort and/orenvironment), when using the model for predictions.;Moreover, any surplus production model using effort will implicitly make the assumption that novariation in recruitment due to other sub-stocks will occur.
35;Surplus production models results are sensitive to the location of the higher level exploitation reached with respect of the Maximum Sustainable Effort (MSE).; According to your assessment of the maximum level of exploitation reached, modelization might be borderline or not recommended as you will see after answering the next question.
36;When the time-series is unstable, especially when effort or environment is concerned, the models are unable to take into account the transitional situations because the past-effort-averaging and the past-environment-averaging approaches are used in this software.;Of course this comment does not apply in the case of short lived species where effort and environment only concern one year of a single year-class.
37;Modelization will not be reliable owing to the data-series structure.
38;Your case is a borderline case for use with these models because your data-set probably contains a few outlier points which may strongly force the structure of any model. The jackknife results will probably confirm of the model (if any selected by the software) will be poor.
......@@ -10,8 +10,8 @@
43;Your data-set is not appropriate because you have first to standardize your fishing effort unit.;Sorry, I stop the model selection routine here.
44;Your data-set is not appropriate for use with these models on account of the population dynamics of your stock.;Sorry, I stop the model selection routine here.
45;Your data-set is not appropriate for use with these models on account of the stock structure.; Sorry, I stop the model selection routine here.
46;Your data-set is not appropriate for use with these models on account of the stock structure.; Sorry, I stop the model selection routine here.
47;"Your data-set is not appropriate for use with surplus production models using fishing effort because the range of fishing effort variation is lower than 100% (factor x2).;If you think that environment is the main variable driving CPUE variation and if you suppose that fishing effort will continue to stay at the same level,;you may apply a simple regression using only environment as an independent variable (choose the 'fit_a_model_directly' menu or answer NO to the question: ""Is the influence of effort on CPUE more important than the environmental influenceÿ?"". Note that this regression is not a model and that any prediction will be poor since the fishing effort level may change without influence on the regression."
48;"There is a contradiction between your answers, or your data-set is not appropriate for use with surplus production models because the relationship between CPUE (or CPUE residuals) and effort is expected to be decreasing.;This means that fishing effort was probably not the key variable driving the stock during the period of observation.;If you think that environment is the main variable driving CPUE variations and if you suppose that fishing effort will continue to stay at the same level, you may apply a simple regression using only environment as independent variable (choose the ""fit_a_model_directly"" menu or answer NO to the question: ""Is the influence of effort on CPUE more important than the environmental influence?"".; Note that this regression is not a model and that any prediction will be poor since the fishing effort level may change without influence on the regression.;Sorry, I stop the model selection routine here."
49;Model results will be inappropriate for stock assessment owing to the low, range of exploitation levels
50;Maximum production(s) will be overestimated owing to the dynamics of exploitation: when the effort is constantly increasing, the equilibrium state is not respected, and owing to the past-effort-averaging method which was retained in transitional state cases MSY is overestimaded (see Appendix B of the manual for discussion).
46;Your data-set is not appropriate on account of the stock structure.; Sorry, I stop the model selection routine here.
47;"Your data-set is not appropriate for use with surplus production models using fishing effort because the range of fishing effort variation is lower than 100% (factor x2).;If you think that environment is the main variable driving CPUE variation and if you suppose that fishing effort will continue to stay at the same level,;you may apply a simple regression using only environment as an independent variable (choose the 'fit_a_model_directly' menu or answer NO to the question: "Is the influence of effort on CPUE more important than the environmental influenceÿ?"; \nNote that this regression is not a model and that any prediction will be poor since the fishing effort level may change without influence on the regression."
48;There is a contradiction between your answers, or your data-set is not appropriate for use with surplus production models because the relationship between CPUE (or CPUE residuals) and effort is expected to be decreasing.;This means that fishing effort was probably not the key variable driving the stock during the period of observation.;If you think that environment is the main variable driving CPUE variations and if you suppose that fishing effort will continue to stay at the same level, you may apply a simple regression using only environment as independent variable (choose the "fit_a_model_directly" menu or answer NO to the question: "Is the influence of effort on CPUE more important than the environmental influence?".; Note that this regression is not a model and that any prediction will be poor since the fishing effort level may change without influence on the regression.;Sorry, I stop the model selection routine here.
49;Model results would be inappropriate for stock assessment owing to the low range of exploitation levels.;Sorry, I stop the model selection routine here.
50;Maximum production(s) will be overestimated owing to the dynamics of exploitation: when the effort is constantly increasing, the equilibrium state is not respected, and owing to the past-effort-averaging method which was retained in transitional state cases MSY is overestimaded (see Appendix B of the manual for discussion).
......@@ -14,13 +14,13 @@
12;0;A simple model CPUE=f(E) or Residuals=f(E) of exponential type is deduced if:; -the graphic relation CPUE/E is not obviously linear ; -you have no reason to be pessimistic; -stock did not collapse; -lifespan of species lies between 5 and 11; there is first reproduction before recruitment; fecundity is not very low. ;;;
13;0;A simple model CPUE=f(E) or Residuals=f(E) of exponential type is deduced if:; -the graphic relation CPUE/E is not obviously linear ; -you have no reason to be pessimistic; -stock did not collapse; -lifespan of species lies between 5 and 11; -there are natural protected areas; fecundity is not very low. ;;;
14;0;A simple model CPUE=f(E) or Residuals=f(E) of exponential type is deduced if:; -the graphic relation CPUE/E is not obviously linear ; -you have no reason to be pessimistic; -stock did not collapse; -lifespan of species lies between 5 and 11; -stock is subdivided in sub-stocks; fecundity is not very low. ;;;
16;0;A simple model CPUE=f(E) or Residuals=f(E) of exponential type is deduced if:; -the graphic relation CPUE/E is not obviously linear ; -you have no reason to be pessimistic; -stock did not collapse; -lifespan/number of exploited years classes > 2; -there is first reproduction before recruitment; -there are natural protected areas; -stock is subdivided in sub-stocks; -fecundity is not very low.
16;0;A simple model CPUE=f(E) or Residuals=f(E) of exponential type is deduced if:; -the graphic relation CPUE/E is not obviously linear ; -you have no reason to be pessimistic; -stock did not collapse; -lifespan/number of exploited years classes > 2; -there is first reproduction before recruitment; -there are natural protected areas; -your data-set deals with a metapopulation or at least one of its substocks; -fecundity is not very low.
17;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; -the graphic relation CPUE/E is obviously linear.;;;;;;;
18;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; -you have reason to be pessimistic.;;;;;;;
19;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; -stock collapsed.;;;;;;;
20;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; lifespan < 5 ; lifespan/number of exploited years classes < 2; there is not first reproduction before recruitment. ;;;;;
20;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; lifespan < 5 ; -lifespan/number of exploited years classes < 2; -there is not first reproduction before recruitment. ;;;;;
21;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; -fecondity is low.;;;;;;;
22;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; -lifespan < 5 ; -lifespan/number of exploited years classes < 2; -there are natural protected areas; -stock is not subdivided in sub-stocks; -CPUE is not unstable. ;;;
22;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; -lifespan < 5 ; -lifespan/number of exploited years classes < 2; -there are natural protected areas; -your data-set does not deal with a metapopulation or at least one of its substocks; -CPUE is not unstable. ;;;
23;0;A simple model CPUE=f(E) or Residuals=f(E) of generalized type is deduced if:; -neither an exponential ; -nor a linear model has been deduced ;;;;;;
24;0;A simple model CPUE=f(E) or Residuals=f(E) of generalized type is deduced if:; -a linear model has been deduced ; -this model has a coefficient of determination R2 < 40 ;;;;;;
25;0;A simple model CPUE=f(E) or Residuals=f(E) of generalized type is deduced if:; -an exponential model has been deduced ; -this model has a coefficient of determination R2 < 40 ;;;;;;
......@@ -30,7 +30,7 @@
31;0;Effect is abundance if:; -you answer abundance to the environmental influence question.;;;;;;;
32;0;Effect is catchability if:; -you answer catchability to the environmental influence question.;;;;;;;
33;0;Effect is abundance catchability if:; -you answer both or I do not know to the environmental influence question.;;;
34;0;stock assessment is uncertain if:; stock is not single ; -there is a sub-stock; -this sub-stock is well isolated from the others ;
34;0;stock assessment is uncertain if:; -stock is not single ; -there is a metapopulation; -either the a metapopulation displays a high connectivity between its sub-stocks or only a sub-stock of it with low connectivity. ;
35;0;Model results are uncertain -particularly maximum productions- if:; -the data-series does not cover periods of both underexploitation and overexploitation ;
49;0;Model results are inappropriate for assessment and predicition if:; -the data-series does not cover periods of both under exploitation and overexploitation; -the data-series does not cover periods of both underexploitation and of optimal exploitation;
36;0;Modelization is not reliable if:; -you graphically detect unstability in the time plots .;;;
......@@ -42,9 +42,9 @@
42;1;A basic assumption is not verified if:; -there have been changes in fishing pattern.;;;
43;1;A basic assumption is not verified if:; -fishing effort unit is not standardized ; -the CPUE is not a good index of abundance variations ;;
44;1;A basic assumption is not verified if:; -time lags have effects on production rate.;;;
45;1;A basic assumption is not verified if:; -stock is not single ; -there is a sub-stock; this sub-stock is not well isolated ;
46;1;A basic assumption is not verified if:; -stock is not single ; -this stock is not a sub-stock ;;
47;1;Model results are not usable if:; -the relative range of observed effort values (Max-Min)/Min is < 0.4.;;;
45;1;A basic assumption is not verified if:; -stock is not single ; -there is a metapopulation; -either the a metapopulation displays a low connectivity between its sub-stocks or only a sub-stock of it with high connectivity with the rest of the sub-stocks.;
46;1;A basic assumption is not verified if:; -stock is not single ; -there is no metapopulation ;;
47;1;Model results are not usable if:; -the relative range of observed effort values (Max-Min)/Min is < 1.0 (factor x2).;;;
48;1;Your assumption on preponderance of fishing effort on CPUE is not verified if:; -you stated that effort is preponderant ; -and the graph CPUE/E is not decreasing ;
50;0;Maximum productions are overestimated if:; -you graphically detect a constantly increasing effort.;;
51;0;A simple model CPUE=f(E) or Residuals=f(E) of linear type is deduced if:; -a generalized model was fitted and coefficient c (m in the Pella and Tomlinson notation) value was lying between 1.8 and 2.2 ; -this model has a coefficient of determination R2 > 40.;
......
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