Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population

Script

library(popbio)
trans<-subset(merge(table, table, by = "plant", sort = FALSE), year.x == year.y - 1)
rownames(trans) <- 1:nrow(trans)
colnames(trans)[2:9] <- c("year", "stage", "reprstr", "recruitment", "year2", "fate", "reprstr2", "recruitment2")
trans01 <- subset(trans, year==start_year, c(plant, stage, reprstr, fate, recruitment))
# foreach value in recruited run this
# check if recruitment value is non-empty
for (stage1 in recruited) {
   new_individuals <- nrow(subset(table, year==start_year+1 & stage==stage1 & recruitment!=""))
   trans01[[stage1]] <- trans01$reprstr/sum(trans01$reprstr) * new_individuals	
}
matrix <- projection.matrix(trans01, sort=stages)

R Server

Script

table<-read.table(tablein, header=TRUE, fill=TRUE)

R Server

Script

sink(output)
print(input)

R Server

Script

write.csv(input, file=output)

R Server

Script

sink(output)
print(input)

R Server

Script

stagef <- factor(tab[["stage"]])
stages <- levels(stagef)

R Server

Script

import javax.swing.*;

if ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {
    throw new RuntimeException("selectionValues must be specified and non-empty");
}

Vector included = new Vector();
Vector excluded = new Vector(selectionValues);

// Create a scrollable list view of excluded items
JList excludeList = new JList(excluded);
JScrollPane excludeScroll = new JScrollPane(excludeList);

// Create a scrollable list view of included items
JList includeList = new JList(included);
JScrollPane includeScroll = new JScrollPane(includeList);

moveButton( label, fromList, fromVector, toList, toVector ) {
    JButton button = new JButton(label);
	button.addActionListener( this );
	actionPerformed( e ) {
        // when button is clicked, remove selected items from source list
		// and add them to the target list
        int nremoved = 0;
    	for (int i : fromList.getSelectedIndices()) {
		    String s = fromVector.remove(i - nremoved);
			toVector.add(s);
			++nremoved;
        }
		if (nremoved > 0) {
	        fromList.setListData(fromVector);
			toList.setListData(toVector);
        }	    
	}
	return button;
}

JPanel leftRightArrowsPanel = new JPanel();
leftRightArrowsPanel.setLayout(new BoxLayout(leftRightArrowsPanel, BoxLayout.Y_AXIS));
leftRightArrowsPanel.add(moveButton("<", includeList, included, excludeList, excluded)); 
leftRightArrowsPanel.add(moveButton(">", excludeList, excluded, includeList, included)); 

upButton( label ) {
    JButton button = new JButton(label);
	button.addActionListener( this );
	actionPerformed( e ) {
		int min = 0;
    	for (int i : includeList.getSelectedIndices()) {
			if (i == min) {
                // ignore first items that are selected
                ++min;
            }
            else {
		        String s = included.remove(i);
			    included.add(i - 1, s);
				min = -1;
            }
        }
		if (min < 0) {
	        includeList.setListData(included);
        }	    
	}
	return button;
}

JPanel upDownArrowsPanel = new JPanel();
upDownArrowsPanel.setLayout(new BoxLayout(upDownArrowsPanel, BoxLayout.Y_AXIS));
upDownArrowsPanel.add(upButton("Move Up"));
//downButton = new JButton("V");
//upDownArrowsPanel.add(downButton);

JPanel mainPanel = new JPanel();
mainPanel.setLayout(new BoxLayout(mainPanel, BoxLayout.Y_AXIS));

mainPanel.add(new JLabel((message == void ? null : message)));

JPanel selectionPanel = new JPanel();
selectionPanel.setLayout(new BoxLayout(selectionPanel, BoxLayout.X_AXIS));

selectionPanel.add(excludeScroll);

selectionPanel.add(leftRightArrowsPanel);

selectionPanel.add(includeScroll);

selectionPanel.add(upDownArrowsPanel);

mainPanel.add(selectionPanel);

JOptionPane.showMessageDialog(
  null, mainPanel, (title == void ? null : title), JOptionPane.PLAIN_MESSAGE);

List answer = included;

Value

Value

Script

import javax.swing.*;

if ((selectionValues == void) || (selectionValues == null) || (selectionValues.isEmpty())) {
    throw new RuntimeException("selectionValues must be specified and non-empty");
}

Vector included = new Vector();
Vector excluded = new Vector(selectionValues);

// Create a scrollable list view of excluded items
JList excludeList = new JList(excluded);
JScrollPane excludeScroll = new JScrollPane(excludeList);

// Create a scrollable list view of included items
JList includeList = new JList(included);
JScrollPane includeScroll = new JScrollPane(includeList);

moveButton( label, fromList, fromVector, toList, toVector ) {
    JButton button = new JButton(label);
	button.addActionListener( this );
	actionPerformed( e ) {
        // when button is clicked, remove selected items from source list
		// and add them to the target list
        int nremoved = 0;
    	for (int i : fromList.getSelectedIndices()) {
		    String s = fromVector.remove(i - nremoved);
			toVector.add(s);
			++nremoved;
        }
		if (nremoved > 0) {
	        fromList.setListData(fromVector);
			toList.setListData(toVector);
        }	    
	}
	return button;
}

JPanel leftRightArrowsPanel = new JPanel();
leftRightArrowsPanel.setLayout(new BoxLayout(leftRightArrowsPanel, BoxLayout.Y_AXIS));
leftRightArrowsPanel.add(moveButton("<", includeList, included, excludeList, excluded)); 
leftRightArrowsPanel.add(moveButton(">", excludeList, excluded, includeList, included)); 

upButton( label ) {
    JButton button = new JButton(label);
	button.addActionListener( this );
	actionPerformed( e ) {
		int min = 0;
    	for (int i : includeList.getSelectedIndices()) {
			if (i == min) {
                // ignore first items that are selected
                ++min;
            }
            else {
		        String s = included.remove(i);
			    included.add(i - 1, s);
				min = -1;
            }
        }
		if (min < 0) {
	        includeList.setListData(included);
        }	    
	}
	return button;
}

JPanel upDownArrowsPanel = new JPanel();
upDownArrowsPanel.setLayout(new BoxLayout(upDownArrowsPanel, BoxLayout.Y_AXIS));
upDownArrowsPanel.add(upButton("Move Up"));
//downButton = new JButton("V");
//upDownArrowsPanel.add(downButton);

JPanel mainPanel = new JPanel();
mainPanel.setLayout(new BoxLayout(mainPanel, BoxLayout.Y_AXIS));

mainPanel.add(new JLabel((message == void ? null : message)));

JPanel selectionPanel = new JPanel();
selectionPanel.setLayout(new BoxLayout(selectionPanel, BoxLayout.X_AXIS));

selectionPanel.add(excludeScroll);

selectionPanel.add(leftRightArrowsPanel);

selectionPanel.add(includeScroll);

selectionPanel.add(upDownArrowsPanel);

mainPanel.add(selectionPanel);

JOptionPane.showMessageDialog(
  null, mainPanel, (title == void ? null : title), JOptionPane.PLAIN_MESSAGE);

List answer = included;

Value