Commit 6e2144a4 authored by pfreon's avatar pfreon
Browse files

Minor changes

Correction of time series display associated to the question  related to fishing effort stability.
Enlargement of the row height in the tables of new data manual entry and predictions.
Correction of the range of years (only used for setting the lable intervals on the X axis of time series).
Addition of the Climprod.jpg file in resources\images
Removal of special characters " and ' in the HLP files because incorrectly displayed.
parent 771b393a
......@@ -372,7 +372,7 @@ public class CadreMain extends JFrame {
});
menuModelsPrediction.setEnabled(false);
menuModelsPrediction.setText("Use the model for prediction");
menuModelsPrediction.setText("Intent prediction (allowed if good jackknife test) ");
menuModelsPrediction.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_P,InputEvent.CTRL_DOWN_MASK));
menuModelsPrediction.addActionListener(new java.awt.event.ActionListener() {
......
......@@ -79,7 +79,7 @@ public class CadreMain_HowToBox extends JDialog implements ActionListener {
"will be able to display additional graphs related to the validation of the model.\n\n" +
"At the end of any of the two ‘Modelization’ options you will be able to use the ‘Display the results " +
"tables’ related to modelization and validation. If the model was validated, you will also access to " +
"the sub-menu ‘Use the model for prediction’. In any case you will be allowed to build and display a " +
"the sub-menu ‘Intent prediction (allowed if good jackknife test)’. In any case you will be allowed to build and display a " +
"history html & graphs folder by using the corresponding sub-menu in the 'Files' main menu.\n\n");
jTextAreaCopyRight.setLineWrap(true);
jTextAreaCopyRight.setWrapStyleWord(true);
......
......@@ -185,6 +185,7 @@ public class Cadre_Prediction extends JDialog implements DocumentListener {
}
ModeleDeTablePredict mdt = new ModeleDeTablePredict(data$, title$);
jTablePrediction.setModel(mdt);
jTablePrediction.setRowHeight(25);
editorComponent.selectAll();
TableCellEditor jtce = new DefaultCellEditor(editorComponent);
TableCellRenderer jtcr = new editTableCellRenderer();
......
/**
/*****
* Titre : Climprod<p>
* Gère les fenêtres de "Select the appropriate model and fit it" (=Questions)
* y compris les messages de résultats de la sélection, dont ceux
......@@ -562,7 +562,7 @@ public class Cadre_Question extends JFrame
dlgSp = new Cadre_SplitPlot(Global.scatterPlot);
break;
case 15:
dlgSp = new Cadre_SplitPlot(Global.timePlot[0]);
dlgSp = new Cadre_SplitPlot(Global.timePlot[2]);
break;
case 16:
dlgSp = new Cadre_SplitPlot(Global.indePlot);
......
......@@ -58,8 +58,9 @@ public class CreateNewFile extends JDialog{
}
private void initWindow() throws Exception {
jScrollPane1.getViewport().add(jTableData, null);
jPanData.add(jScrollPane1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0
,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(5, 2, 5, 2), 0, 200));
jPanData.add(jScrollPane1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(5, 2, 5, 2), 0, 200));
//Assignations des variables de GridBagConstraints(gridx, gridy, gridwidth, gridheight, 1.0, 1.0, anchor, fill, insets, 0, 0)
//Assignations des variables de Insets(int top, int left, int bottom, int right)
this.getContentPane().add(jPanData, BorderLayout.CENTER);
jPanCmd.add(cmdOk);
......@@ -104,6 +105,7 @@ public class CreateNewFile extends JDialog{
jTableData.setModel(mdt);
jTableData.setColumnSelectionAllowed(false);
jTableData.setRowSelectionAllowed(false);
jTableData.setRowHeight(25);
// jTableData.setTableHeader(new JTableHeader tableHeader());
TableColumn tmcolumn = null;
floatTextField ftf =new floatTextField();
......
......@@ -391,7 +391,7 @@ public class Global {
public static double RangeYear(){ // Computes year range.
double[] year=Data.getYears();
double[] ext=Stat1.Extremas(year);
return (ext[1]-ext[0]);
return (ext[1]-ext[0]+1);
}
public static double fF(double R2, double p, double n){ // Fisher Fcalc; p = nombre de paramètres autres que constante (a en général)
......
......@@ -5,5 +5,5 @@ the exceptionally young individuals (at least 50% of the year-class must
be recruited).
The limits of year 1 are the spawning time (or birth date) and the first
"birthday" one year later. The limits of year 2 are the first and
birthday one year later. The limits of year 2 are the first and
the second birthday, etc. 
\ No newline at end of file
Do you wish to see again this special warning about the double click use in CLIMPROD when you will re-open the software?
Answer 'No' if you already read the message about the use of the double click in CLIMPROD and that you are sure that you will remind it.
Answer No if you already read the message about the use of the double click in CLIMPROD and that you are sure that you will remind it.
If you answer 'Yes' or 'Don't know' you will see this message again next time you will use the software.
If you answer Yes or Don't know you will see this message again next time you will use the software.

\ No newline at end of file
Did the stock already collapse or did it exhibit drastic decrease(s) in
catches?
Answer YES if a collapse of the stock occurred in the past, even out of
Answer Yes if a collapse of the stock occurred in the past, even out of
your data-set period.
You have also to answer YES if the production of the stock exhibits strong
You have also to answer Yes if the production of the stock exhibits strong
and fast unexpected decrease(s).
In such instances, the program will choose a linear production model, which
......
Does this plot appear to be decreasing?
You have to answer YES if the scatter-plot of the relationship between
You have to answer Yes if the scatter-plot of the relationship between
fishing effort E and catch per unit of effort (CPUE or CPUE residuals)
seems to be decreasing. If not, that means that fishing effort is not a key
variable for explaining CPUE variability, except if E is not independent
......
Are there a good fit and no trend or strong autocorrelation in residuals?
Answer YES if the comparison between the time-series of observed and
Answer Yes if the comparison between the time-series of observed and
predicted values of CPUE seems acceptable and if you do not observe any
trend and/or strong autocorrelation in the bottom graph presenting
residuals versus year-index.
......
Constantly increasing effort?
From the observation of this time-series of fishing effort, answer
YES if you note a relatively constant increase of the effort from
Yes if you note a relatively constant increase of the effort from
the beginning of the data-series to recent years.

\ No newline at end of file
Are the two variables independent?
A scatter plot of fishing effort E versus the environmental variable V
is presented. These two "independent variables" (or predictor variables)
is presented. These two independent variables (or predictor variables)
are supposed to be independent. If not, the resulting model would be
difficult to use for many reasons among which the difficulty of estimating
the individual effect of each variable.
......
Does the environment influence : abundance, catchability, both ?
Does the environment influence : abundance, catchability, both?
According to your knowledge of the stock, you have to say if the
environmental variable retained in your data-set has an influence
......@@ -24,7 +24,4 @@ where the environmental variable influences either the abundance or the
catchability. This is due to the limit of the maximum number of parameters
set to four in order to avoid overparameterization of the model (and the
former case is demanding in parameters, even after reparameterization).

\ No newline at end of file
......@@ -7,7 +7,7 @@ to answer this question. Connectivity patterns range from a well-mixed larval po
(minimal connectivity) at the other. However, most situations are intermediate to these
two extremes (MSC, 2020).
Answer YES if the considered stock exploited by the fleet(s) is either:
Answer Yes if the considered stock exploited by the fleet(s) is either:
1) a full metapopulation with reasonably high connectivity. Note that according to
your previous answers, all these eventual sub-stocks must be exploitedby the fleet(s)
corresponding to your data-set. This case is not in contradiction with the fact that
......
Do the time-lags and deviation from the stable age structure have
negligible effects on production rate?
Answer YES if "it is assumed that the total catch and stock production in
Answer Yes if it is assumed that the total catch and stock production in
weight are independant of age, and that time lags in recruitment or in
density-dependant growth, natural mortality and reproduction do not occur"
density-dependant growth, natural mortality and reproduction do not occur
(Fox, 1974).

\ No newline at end of file
Does this plot look linear?
You have to answer YES if the relationship between the two variables seems
You have to answer Yes if the relationship between the two variables seems
linear. These variables are: fishing effort E versus catch per unit of effort
(CPUE or CPUE residuals) or environment V versus CPUE or CPUE residuals.

\ No newline at end of file
MAIN MENU
From this main menu you can:
- Open or select a data file : this is the first step to take
before attempting any other option.
- Update a data file: this allows you to correct or add new data to a data
file.
- Select the appropriate model and fit it: an expert-system will help
you to choose the appropriate model according to your case.
- See the chain of reasoning : after selecting the model, you are allowed
to look at the chain of reasoning used by the expert-system for its choice.
- Fit a model directly : among the 31 models available, you are allowed to
choose directly which one you want to fit, without using the expert-system.
- Plot the model : this displays the time-plots of observed and predicted
CPUE values, the time-plot of CPUE residuals, the relationship between
production, effort and environment (three-variate graphics).
- Validate the model : this assesses the quality of the fit using the
jackknife method.
- Use carefully the model for prediction : this allows to predict the
CPUE of the two next years according to estimated values of effort
and environment.
- Make EXCEL file for editing graphs : you can create a Microsoft-EXCEL*
(XL) file and use for graphs edition and printing under EXCEL/WINDOWS*.
The interface programme is run when you open the CLIMPROD.XLS file which
is already included in our CLIMPROD\XL directory. In order to get all the
graphs seen in this DOS application automatically redrawn by XL you just
need to double click on the XL-interface icone in your CLIMPROD Program
Group.
- Stop : to exit from the program.
*EXEL (XL) and WINDOWS are registered Microsoft softwares.
......@@ -2,12 +2,12 @@ Does the data-set apply to metapopulation?
The concept of metapopulation was first proposed by Levins (1968).
It was then enriched with new ideas and summarised by McQuinn (1997) and
can be defined as : The population structure of many species can be
can be defined as follows: The population structure of many species can be
considered as an array of local populations linked by variable degrees
of gene flow.
of gene flow.
According to Sale et al. (2006), in some cases, stocks may be structured
as metapopulations – systems in which local populations (namded sub-
as metapopulations – systems in which local populations (namded sub-
populations or sub-stocks, or components) inhabit discrete habitat patches
and inter-patch dispersal is neither so low as to negate significant demographic
connectivity, nor so high as to eliminate any independence of local population
......
Does this plot look monotonic?
You have to answer YES if the relationship between the two variables
You have to answer Yes if the relationship between the two variables
seems monotonic, permanently increasing or decreasing, but not dome-shaped.
These variables are: fishing effort E versus catch per unit of effort
(CPUE or CPUE residuals) or environment V versus CPUE or CPUE residuals.
......
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