JavaGrinders.spatial
Class CaptureVariable

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.Vector
              JavaGrinders.Variable
                  JavaGrinders.spatial.CaptureVariable

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

Direct Known Subclasses:

Animal, MoveVariable

public class CaptureVariable
extends Variable
implements java.lang.Cloneable

handles a variable of Captures (capture localities and time of capture).

See Also:

Serialized Form

Field Summary

boolean

latlong

Fields inherited from class JavaGrinders.Variable

allData, autoExtracted, df, itsDescriptives, itsHighlitedColor, itsLineColor, itsLocationColor, rand

Fields inherited from class java.util.Vector

capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

CaptureVariable(java.lang.String varName, VariableOrganizer theOrganizer)
Standard constructor for the CaptureVariable class using a VariableOrganizer

Method Summary

void	addMove(MoveVector aMove) makes the animal move from the last recorded position
MoveVector	applyRandomMoveFromDistribution(Capture StartCapture) generates a single move from a Distribution of Moves
void	asCircularGraph() Creates a circular presenter
void	asCircularGraph(boolean relative) Creates a circular presenter
void	asSpatialMap() Creates a presenter and plots and connects the locations
void	asSpatialMap(boolean xDirection, boolean yDirection) Creates a presenter and plots the locations
void	asSpatialMap(boolean xDirection, boolean yDirection, int view) Creates a presenter and plots the locations
void	asSpatialSpeedMap() Creates a presenter and plots and connects the locations
void	asSpatialSpeedMap(boolean xDirection, boolean yDirection) Creates a presenter and plots the locations
boolean	checkConnectedCoords() assures that coordinates are connected
Variable	cloneSelectedRowsOnly() returns a copy of the CaptureVariable contianing only the selected rows
SpatialDescriptives	copySpatialDescriptives() fills the descriptive statistics for the variable and returns the results
double	estimateD(double maxPathLength, double stepSize, double pathLength) returns the fractal dimension of the coordinates
void	fill(NumberVariable x, NumberVariable y) Fills the variable with captures, x and y variable from the same row are assumed to belong together
void	fill(NumberVariable x, NumberVariable y, NumberVariable z, TimeVariable time) Fills the variable with captures, x and y variable from the same row are assumed to belong together
void	fill(NumberVariable x, NumberVariable y, TimeVariable time) Fills the variable with captures, x and y variable from the same row are assumed to belong together
void	fill(PolarVector[] aVecs) fills the variable with captures
void	fill(java.awt.Polygon poly) fills the variable with locations from x and y coordinates that mark the corners of a polygon.
void	fill(SpatialVector[] aVecs) fills the variable with captures
void	fillDescriptives(java.lang.Double hypVal) fills the descriptive statistics for the variable - locations
void	fillWithGaussRandom(Capture StartCapture, double theMean, double theSD, boolean is3D) fills the variable with random values from a uniform distribution between 0 and 1
void	fillWithRandomFromDistribution(Capture StartCapture) fills the variable with random values from a Distribution of Moves
NumberVariable	getAnglesFromCenter() returns the distances to one specific location
Capture	getCapture(int row) returns the capture stored at a given row of the Vector
SpatialVector	getCenterLocation() returns the average neighbor distance
boolean	getConnect() returns whether the Capture should be visually connected
Constraint	getConstraint() returns the spatial constraint for the population
SpatialVector	getCurrentLocation() returns the current location for the animal
DataTable	getDistanceMatrix(int DistanceMeasure) calculates a matrix of distances between all valid (i.e., selected and non-missing) locations
NumberVariable	getDistancesToLocation(SpatialVector aLocation) returns the distances to one specific location
Capture	getEndCapture() returns the end capture for the animal
double	getEndTime() returns the start time for the animal
double	getFractalDimension() returns the fractal dimension of the coordinates
double	getFractalDimension(double stepSize) returns the fractal dimension of the coordinates
Descriptives[]	getGroupDescriptives(Variable theXVar) returns the descriptives for the groups identified by X
java.awt.Polygon	getHomeRange_MinimumPolygon() returns the average neighbor distance
ANOVAResults	getHotellingFResults(Variable theXVar) lists the results from an analysis of differences in mean angles for a variable of locations
CaptureVariable	getLatLongAsDistances() if the Captures are defined in longitude and latitude then this function converts these to distanced measures in meters using Haversines
double	getMeanDistanceToLocation(SpatialVector meanVec) returns the average neighbor distance
double	getMinNeighborDistance() returns the minimum neighbor distance
NumberVariable	getMoveDistances() creates and returns a variable containing the series of distances between captures
MoveVariable	getMoves() creates and returns a variable containing the series of absolute moves between captures
MoveVariable	getMoves(boolean relative) creates and returns a variable containing the series of absolute moves between captures
double	getNetDisplacement() returns the time difference between first and last capture
MoveVector	getNetMove() returns the time difference between first and last capture
double	getNetTime() returns the time difference between first and last capture
SpatialDescriptives	getSpatialDescriptives() fills the descriptive statistics for the variable and returns the results
SpatialVector	getSpatialVector(int row) returns the capture stored at a given row of the Vector
NumberVariable	getSpeeds() creates and returns a variable containing the series of speeds between captures
SquaresCrossproducts	getSSCP() returns the sums of squares and crossproducts for the variable
Capture	getStartCapture() returns the start capture for the animal
double	getStartTime() returns the start time for the animal
java.lang.String	getStringValue(int row) returns the capture stored at a given row of the Vector as a String
NumberVariable	getTimeBetweenFrames() creates and returns a variable containing the series of time distances between captures
TimeVariable	getTimeRefs() creates and returns a variable containing the times for these captures
IntegerVariable	getTimes() creates and returns a variable containing the times for these captures
CaptureVariable	getTinyStepPath(int nSteps) traces the current selected path in small increments
NumberVariable	getXs() returns the x coordinates as a Vector
NumberVariable	getYs() returns the x coordinates as a Vector
NumberVariable	getZs() returns the x coordinates as a Vector
void	listCircularDescriptives(boolean relative) lists the descriptive statistics for the angles of the moves using the currently selected set of rows
void	listDistanceMatrix(int DistanceMeasure) lists a matrix of distances between all valid (i.e., selected and non-missing) locations
void	listFractalDimension() lists the fractal dimension for the variable using the currently selected set of rows
void	listFractalDimension(double stepSize) lists the fractal dimension for the variable using the currently selected set of rows
void	listGroupDescriptives(Variable theXVar) lists the descriptives for the groups identified by X
void	listMoveDescriptives(boolean relative) lists the descriptive statistics for the moves using the currently selected set of rows
void	makeNewDescriptives() create a new set of descriptives for the variable the object
SpatialVector	reMapInConstraint(SpatialVector aCapture) remaps a capture for a given constraint
CaptureVariable[]	resamplePath(double[] distUnits) retraces the path with different step lengths
void	selectAbove(double cutoffX, double cutoffY, double cutoffZ, boolean fromPrevSelected) select all rows with a value greater than the one provided
void	selectAboveDistance(double distanceCutoff, boolean fromPrevSelected) select all rows with a value less than the one provided
void	selectAboveEqual(double cutoffX, double cutoffY, double cutoffZ, boolean fromPrevSelected) select all rows with a value greater than the one provided
void	selectAboveSpeed(double speedCutoff, boolean fromPrevSelected) select all rows with a value less than the one provided
void	selectAfter(long cutoffTime, boolean fromPrevSelected) select all rows with a value greater than the one provided
void	selectAfterEqual(long cutoffTime, boolean fromPrevSelected) select all rows with a value greater than the one provided
void	selectBefore(long cutoffTime, boolean fromPrevSelected) select all rows with a value greater than the one provided
void	selectBeforeEqual(long cutoffTime, boolean fromPrevSelected) select all rows with a value greater than the one provided
void	selectBelow(double cutoffX, double cutoffY, double cutoffZ, boolean fromPrevSelected) select all rows with a value less than the one provided
void	selectBelowDistance(double distanceCutoff, boolean fromPrevSelected) select all rows with a value less than the one provided
void	selectBelowEqual(double cutoffX, double cutoffY, double cutoffZ, boolean fromPrevSelected) select all rows with a value less or equal than the one provided
void	selectBelowSpeed(double speedCutoff, boolean fromPrevSelected) select all rows with a value less than the one provided
void	selectBetween(long sCutoffTime, long eCutoffTime, boolean fromPrevSelected) select all rows with a value greater equal the start time and less or equal the end time
void	selectInArea(GridSpace3D a3DBox, boolean fromPrevSelected) select all rows with a value locatad within the 3D box
void	selectXAbove(double cutoffX, boolean fromPrevSelected) select all rows with an X value greater than the one provided
void	selectXAboveEqual(double cutoffX, boolean fromPrevSelected) select all rows with an X value greater or equal than the one provided
void	selectXBelow(double cutoffX, boolean fromPrevSelected) select all rows with an X value less than the one provided
void	selectXBelowEqual(double cutoffX, boolean fromPrevSelected) select all rows with an X value less or equal than the one provided
void	selectYAbove(double cutoffY, boolean fromPrevSelected) select all rows with a Y value greater than the one provided
void	selectYAboveEqual(double cutoffY, boolean fromPrevSelected) select all rows with a Y value greater or equal than the one provided
void	selectYBelow(double cutoffY, boolean fromPrevSelected) select all rows with a Y value less than the one provided
void	selectYBelowEqual(double cutoffY, boolean fromPrevSelected) select all rows with a Y value less or equal than the one provided
void	selectZAbove(double cutoffZ, boolean fromPrevSelected) select all rows with a Z value greater than the one provided
void	selectZAboveEqual(double cutoffZ, boolean fromPrevSelected) select all rows with a Z value greater or equal than the one provided
void	selectZBelow(double cutoffZ, boolean fromPrevSelected) select all rows with a Z value less than the one provided
void	selectZBelowEqual(double cutoffZ, boolean fromPrevSelected) select all rows with a Z value less or equal than the one provided
void	setConnect(boolean connect) sets whether the Captures should be visually connected
void	setConstraint(Constraint aConstraint) install a spatial constraint for the variable
void	setExternalMovesDistribution(MoveVariable theMoves) install an external distribution of Moves to sample from
void	setMaxMovingThreshold(float maxMovingThreshold) sets the maximum threshold for the distance an animal may move to be considered a valid travel
void	setMinMovingThreshold(float minMovingThreshold) sets the threshold for the distance an animal may move to be considered a valid travel
void	writeKMLCoords(java.io.Writer output) export the CaptureVariable's LineStyle into a KML file for display in Google Earth
void	writeKMLFile() export the coordinates into a KML file for display in Google Earth
void	writeKMLFile(java.lang.String name) export the coordinates into a KML file for display in Google Earth
void	writeKMLIntro(java.io.Writer output) export the CaptureVariable's LineStyle into a KML file for display in Google Earth
void	writeKMLLine(java.io.Writer output) export the CaptureVariable's coordinates into a KML file for display in Google Earth
void	writeKMLLineStyle(java.io.Writer output) export the CaptureVariable's LineStyle into a KML file for display in Google Earth
void	writeKMLOutro(java.io.Writer output) export the CaptureVariable's LineStyle into a KML file for display in Google Earth
void	writeKMLPoints(java.io.Writer output) export the CaptureVariable's coordinates into a KML file for display in Google Earth

Methods inherited from class JavaGrinders.Variable

addValue, append, appendVariable, asJAMAMatrix, asVariableOrganizer, checkMatchingRows, checkMinUseRows, checkNumberIDs, checkSameIDs, checkSameSelectRows, checkSameSelectRows, checkSameUseRows, checkSameUseRows, checkValidRowRange, clone, cloneVariableFrom, combineSelectedWithSavedSelectedRows, copyDescriptives, copySelectStateFrom, customColorSelectedRows, deleteAllRows, deleteDuplicateRows, deleteMissingRows, deleteNonSelectedRows, deleteRow, deleteSelectedRows, deselectAllRows, fill, fill, fill, fill, fill, fill, fillDescriptives, fillIDs, fillWithParser, fillWithParser, fillWithVariable, findFirstValidRow, findLastValidRow, findNextNonMissingRow, findNextValidRow, findNextValue, findPreviousValidRow, getabasedintValue, getAbasedintValue, getArray, getbooleanValue, getcharValue, getCombinedIDs, getCrossTabulation, getCrossTabulation, getCustomColorRow, getDescriptives, getdoubleArray, getdoubleValue, getfloatValue, getFrequencies, getHighliteColor, getHighlitedRow, getIDMap, getIDs, getIDString, getIDStrings, getInteractions, getintValue, getJaccard, getLineColor, getLocationColor, getlongValue, getManhattan, getMissingRow, getName, getNIDs, getNMissingRows, getNotes, getNRows, getNSelectRows, getNUseRows, getNValidRows, getOrganizer, getProximity, getProximity, getRandomValue, getRowOrder, getRowOrderRow, getSelectRow, getSquEuclidian, getStringArray, getTransitions, getUseRow, getValue, getVariableDesignRole, getVariableDesignRoleString, getVariableFormat, getVariableType, highliteSelectedRows, highliteSelectedRows, invalidDescriptives, invertSelectedRows, isAngleType, isContinuousType, isLocationType, isLocked, isNominalType, isOrdinalType, isXVariable, isYVariable, listDescriptives, listDescriptives, listGroupDescriptivesNoDia, listRowOrder, listRows, listRows, listRows, listSelectedRows, listSelectState, listSelectState, listUseRows, makeTableSubSet, matchedIDs, replaceSelectedRows, restoreSelectedRows, restrictToMatchingUseRows, restrictToMatchingUseRows, restrictToValidRowsOnly, reverseRows, saveSelectedRows, selectAllRows, selectDuplicateRows, selectRows, selectUseRows, selectValue, setAnglesType, setCustomColorRow, setFormula, setHighliteColor, setHighlitedRow, setLineColor, setLocationColor, setLocationsType, setLock, setMissingRow, setName, setNominalType, setNotes, setNRows, setOrdinalType, setOrganizer, setRowOrder, setRowOrderRow, setSelectRow, setSelectRows, setSelectRowsToMissing, setValue, setValue, setValue, setValue, setValue, setValue, setVariableDesignRole, setVariableFormat, setVariableType, sort, sort, sort2, updateRowOrder

Methods inherited from class java.util.Vector

add, add, addAll, addAll, addElement, capacity, clear, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeRange, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, toString, trimToSize

Methods inherited from class java.util.AbstractList

iterator, listIterator, listIterator

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

iterator, listIterator, listIterator

Field Detail

latlong

public boolean latlong

Constructor Detail

CaptureVariable

public CaptureVariable(java.lang.String varName,
                       VariableOrganizer theOrganizer)
                throws java.lang.Exception

Standard constructor for the CaptureVariable class using a VariableOrganizer

Parameters:

varName - assigns a name (String) to the variable

theOrganizer - an instance of VariableOrganizer class coordinates a set of variables with respect to number of data points available and the rows that are currently selected

Throws:

java.lang.Exception

Method Detail

setConnect

public void setConnect(boolean connect)

sets whether the Captures should be visually connected

Parameters:

connect - should the Captures be connected?

getConnect

public boolean getConnect()

returns whether the Capture should be visually connected

checkConnectedCoords

public boolean checkConnectedCoords()
                             throws java.lang.Exception

assures that coordinates are connected

Throws:

java.lang.Exception

addMove

public void addMove(MoveVector aMove)

makes the animal move from the last recorded position

Parameters:

aMove - the next move

fill

public void fill(java.awt.Polygon poly)
          throws java.lang.Exception

fills the variable with locations from x and y coordinates that mark the corners of a polygon. Captures have time stamp 0

Parameters:

poly - Polygon containing x,y coordinates

Throws:

java.lang.Exception

fill

public void fill(NumberVariable x,
                 NumberVariable y)
          throws java.lang.Exception

Fills the variable with captures, x and y variable from the same row are assumed to belong together

Parameters:

x - the x coordinates

y - the y coordinates

Throws:

java.lang.Exception

fill

public void fill(NumberVariable x,
                 NumberVariable y,
                 NumberVariable z,
                 TimeVariable time)
          throws java.lang.Exception

Fills the variable with captures, x and y variable from the same row are assumed to belong together

Parameters:

x - the x coordinates

y - the y coordinates

z - the z coordinates

time - the time stamp for the capture

Throws:

java.lang.Exception

fill

public void fill(NumberVariable x,
                 NumberVariable y,
                 TimeVariable time)
          throws java.lang.Exception

Fills the variable with captures, x and y variable from the same row are assumed to belong together

Parameters:

x - the x coordinates

y - the y coordinates

time - the time stamp for the capture

Throws:

java.lang.Exception

fill

public void fill(PolarVector[] aVecs)
          throws java.lang.Exception

fills the variable with captures

Parameters:

aVecs - an array of polar vectors

Throws:

java.lang.Exception

fill

public void fill(SpatialVector[] aVecs)
          throws java.lang.Exception

fills the variable with captures

Parameters:

aVecs - an array of spatial vectors

Throws:

java.lang.Exception

fillWithGaussRandom

public void fillWithGaussRandom(Capture StartCapture,
                                double theMean,
                                double theSD,
                                boolean is3D)
                         throws java.lang.Exception

fills the variable with random values from a uniform distribution between 0 and 1

Parameters:

StartCapture - the Capture that describes the starting point

theMean - the mean distance

theSD - the standard deviation for distances

is3D - are all 3 dimensions used?

Throws:

java.lang.Exception

fillWithRandomFromDistribution

public void fillWithRandomFromDistribution(Capture StartCapture)
                                    throws java.lang.Exception

fills the variable with random values from a Distribution of Moves

Parameters:

StartCapture - first position at which the animal is captured

Throws:

java.lang.Exception

cloneSelectedRowsOnly

public Variable cloneSelectedRowsOnly()
                               throws java.lang.Exception

returns a copy of the CaptureVariable contianing only the selected rows

Overrides:

cloneSelectedRowsOnly in class Variable

Throws:

java.lang.Exception

selectBefore

public void selectBefore(long cutoffTime,
                         boolean fromPrevSelected)
                  throws java.lang.Exception

select all rows with a value greater than the one provided

Parameters:

cutoffTime - lists the comparison value for the time

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectBeforeEqual

public void selectBeforeEqual(long cutoffTime,
                              boolean fromPrevSelected)
                       throws java.lang.Exception

select all rows with a value greater than the one provided

Parameters:

cutoffTime - lists the comparison value for the time

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectAfter

public void selectAfter(long cutoffTime,
                        boolean fromPrevSelected)
                 throws java.lang.Exception

select all rows with a value greater than the one provided

Parameters:

cutoffTime - lists the comparison value for the time

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectAfterEqual

public void selectAfterEqual(long cutoffTime,
                             boolean fromPrevSelected)
                      throws java.lang.Exception

select all rows with a value greater than the one provided

Parameters:

cutoffTime - lists the comparison value for the time

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectBetween

public void selectBetween(long sCutoffTime,
                          long eCutoffTime,
                          boolean fromPrevSelected)
                   throws java.lang.Exception

select all rows with a value greater equal the start time and less or equal the end time

Parameters:

sCutoffTime - the start time

eCutoffTime - the start time

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectAbove

public void selectAbove(double cutoffX,
                        double cutoffY,
                        double cutoffZ,
                        boolean fromPrevSelected)
                 throws java.lang.Exception

select all rows with a value greater than the one provided

Parameters:

cutoffX - lists the comparison value for the x Coordinate

cutoffY - lists the comparison value for the y Coordinate

cutoffZ - lists the comparison value for the z Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectAboveEqual

public void selectAboveEqual(double cutoffX,
                             double cutoffY,
                             double cutoffZ,
                             boolean fromPrevSelected)
                      throws java.lang.Exception

select all rows with a value greater than the one provided

Parameters:

cutoffX - lists the comparison value for the x Coordinate

cutoffY - lists the comparison value for the y Coordinate

cutoffZ - lists the comparison value for the z Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectBelow

public void selectBelow(double cutoffX,
                        double cutoffY,
                        double cutoffZ,
                        boolean fromPrevSelected)
                 throws java.lang.Exception

select all rows with a value less than the one provided

Parameters:

cutoffX - lists the comparison value for the x Coordinate

cutoffY - lists the comparison value for the y Coordinate

cutoffZ - lists the comparison value for the z Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectBelowEqual

public void selectBelowEqual(double cutoffX,
                             double cutoffY,
                             double cutoffZ,
                             boolean fromPrevSelected)
                      throws java.lang.Exception

select all rows with a value less or equal than the one provided

Parameters:

cutoffX - lists the comparison value for the x Coordinate

cutoffY - lists the comparison value for the y Coordinate

cutoffZ - lists the comparison value for the z Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectXBelowEqual

public void selectXBelowEqual(double cutoffX,
                              boolean fromPrevSelected)
                       throws java.lang.Exception

select all rows with an X value less or equal than the one provided

Parameters:

cutoffX - lists the comparison value for the x Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectXBelow

public void selectXBelow(double cutoffX,
                         boolean fromPrevSelected)
                  throws java.lang.Exception

select all rows with an X value less than the one provided

Parameters:

cutoffX - lists the comparison value for the x Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectXAboveEqual

public void selectXAboveEqual(double cutoffX,
                              boolean fromPrevSelected)
                       throws java.lang.Exception

select all rows with an X value greater or equal than the one provided

Parameters:

cutoffX - lists the comparison value for the x Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectXAbove

public void selectXAbove(double cutoffX,
                         boolean fromPrevSelected)
                  throws java.lang.Exception

select all rows with an X value greater than the one provided

Parameters:

cutoffX - lists the comparison value for the x Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectYBelowEqual

public void selectYBelowEqual(double cutoffY,
                              boolean fromPrevSelected)
                       throws java.lang.Exception

select all rows with a Y value less or equal than the one provided

Parameters:

cutoffY - lists the comparison value for the y Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectYBelow

public void selectYBelow(double cutoffY,
                         boolean fromPrevSelected)
                  throws java.lang.Exception

select all rows with a Y value less than the one provided

Parameters:

cutoffY - lists the comparison value for the y Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectYAboveEqual

public void selectYAboveEqual(double cutoffY,
                              boolean fromPrevSelected)
                       throws java.lang.Exception

select all rows with a Y value greater or equal than the one provided

Parameters:

cutoffY - lists the comparison value for the y Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectYAbove

public void selectYAbove(double cutoffY,
                         boolean fromPrevSelected)
                  throws java.lang.Exception

select all rows with a Y value greater than the one provided

Parameters:

cutoffY - lists the comparison value for the y Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectZBelowEqual

public void selectZBelowEqual(double cutoffZ,
                              boolean fromPrevSelected)
                       throws java.lang.Exception

select all rows with a Z value less or equal than the one provided

Parameters:

cutoffZ - lists the comparison value for the z Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectZBelow

public void selectZBelow(double cutoffZ,
                         boolean fromPrevSelected)
                  throws java.lang.Exception

select all rows with a Z value less than the one provided

Parameters:

cutoffZ - lists the comparison value for the z Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectZAboveEqual

public void selectZAboveEqual(double cutoffZ,
                              boolean fromPrevSelected)
                       throws java.lang.Exception

select all rows with a Z value greater or equal than the one provided

Parameters:

cutoffZ - lists the comparison value for the z Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectZAbove

public void selectZAbove(double cutoffZ,
                         boolean fromPrevSelected)
                  throws java.lang.Exception

select all rows with a Z value greater than the one provided

Parameters:

cutoffZ - lists the comparison value for the z Coordinate

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectInArea

public void selectInArea(GridSpace3D a3DBox,
                         boolean fromPrevSelected)
                  throws java.lang.Exception

select all rows with a value locatad within the 3D box

Parameters:

a3DBox - a 3D space

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectBelowSpeed

public void selectBelowSpeed(double speedCutoff,
                             boolean fromPrevSelected)
                      throws java.lang.Exception

select all rows with a value less than the one provided

Parameters:

speedCutoff - lists the maximum speed allowed for selction

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectAboveSpeed

public void selectAboveSpeed(double speedCutoff,
                             boolean fromPrevSelected)
                      throws java.lang.Exception

select all rows with a value less than the one provided

Parameters:

speedCutoff - lists the maximum speed allowed for selection

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectAboveDistance

public void selectAboveDistance(double distanceCutoff,
                                boolean fromPrevSelected)
                         throws java.lang.Exception

select all rows with a value less than the one provided

Parameters:

distanceCutoff - lists the maximum distance allowed for selection

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

selectBelowDistance

public void selectBelowDistance(double distanceCutoff,
                                boolean fromPrevSelected)
                         throws java.lang.Exception

select all rows with a value less than the one provided

Parameters:

distanceCutoff - lists the maximum speed allowed for selection

fromPrevSelected - notes whether the search should only be performed on currently selected rows

Throws:

java.lang.Exception

setExternalMovesDistribution

public void setExternalMovesDistribution(MoveVariable theMoves)

install an external distribution of Moves to sample from

Parameters:

theMoves - a distribution from which to sample random moves and apply them to the current position

setConstraint

public void setConstraint(Constraint aConstraint)
                   throws java.lang.Exception

install a spatial constraint for the variable

Parameters:

aConstraint - a spatial constraint for the CaptureVariable

Throws:

java.lang.Exception

getConstraint

public Constraint getConstraint()
                         throws java.lang.Exception

returns the spatial constraint for the population

Throws:

java.lang.Exception

reMapInConstraint

public SpatialVector reMapInConstraint(SpatialVector aCapture)
                                throws java.lang.Exception

remaps a capture for a given constraint

Parameters:

aCapture - the capture to remap

Throws:

java.lang.Exception

getCapture

public Capture getCapture(int row)

returns the capture stored at a given row of the Vector

Parameters:

row - marks the row in the vector

getXs

public NumberVariable getXs()
                     throws java.lang.Exception

returns the x coordinates as a Vector

Throws:

java.lang.Exception

getYs

public NumberVariable getYs()
                     throws java.lang.Exception

returns the x coordinates as a Vector

Throws:

java.lang.Exception

getZs

public NumberVariable getZs()
                     throws java.lang.Exception

returns the x coordinates as a Vector

Throws:

java.lang.Exception

getSpatialVector

public SpatialVector getSpatialVector(int row)

returns the capture stored at a given row of the Vector

Parameters:

row - marks the row in the vector

applyRandomMoveFromDistribution

public MoveVector applyRandomMoveFromDistribution(Capture StartCapture)
                                           throws java.lang.Exception

generates a single move from a Distribution of Moves

Parameters:

StartCapture - first position at which the animal is captured

Throws:

java.lang.Exception

getStringValue

public java.lang.String getStringValue(int row)

returns the capture stored at a given row of the Vector as a String

Overrides:

getStringValue in class Variable

Parameters:

row - marks the row in the vector

setMinMovingThreshold

public void setMinMovingThreshold(float minMovingThreshold)

sets the threshold for the distance an animal may move to be considered a valid travel

Parameters:

minMovingThreshold - the value to set

setMaxMovingThreshold

public void setMaxMovingThreshold(float maxMovingThreshold)

sets the maximum threshold for the distance an animal may move to be considered a valid travel

Parameters:

maxMovingThreshold - the value to set

getCurrentLocation

public SpatialVector getCurrentLocation()
                                 throws java.lang.Exception

returns the current location for the animal

Throws:

java.lang.Exception

getStartCapture

public Capture getStartCapture()
                        throws java.lang.Exception

returns the start capture for the animal

Throws:

java.lang.Exception

getStartTime

public double getStartTime()
                    throws java.lang.Exception

returns the start time for the animal

Throws:

java.lang.Exception

getEndCapture

public Capture getEndCapture()
                      throws java.lang.Exception

returns the end capture for the animal

Throws:

java.lang.Exception

getEndTime

public double getEndTime()
                  throws java.lang.Exception

returns the start time for the animal

Throws:

java.lang.Exception

getNetTime

public double getNetTime()
                  throws java.lang.Exception

returns the time difference between first and last capture

Throws:

java.lang.Exception

getLatLongAsDistances

public CaptureVariable getLatLongAsDistances()
                                      throws java.lang.Exception

if the Captures are defined in longitude and latitude then this function converts these to distanced measures in meters using Haversines

Throws:

java.lang.Exception

getTimeRefs

public TimeVariable getTimeRefs()
                         throws java.lang.Exception

creates and returns a variable containing the times for these captures

Throws:

java.lang.Exception

getTimes

public IntegerVariable getTimes()
                         throws java.lang.Exception

creates and returns a variable containing the times for these captures

Throws:

java.lang.Exception

getMoves

public MoveVariable getMoves()
                      throws java.lang.Exception

creates and returns a variable containing the series of absolute moves between captures

Throws:

java.lang.Exception

getMoves

public MoveVariable getMoves(boolean relative)
                      throws java.lang.Exception

creates and returns a variable containing the series of absolute moves between captures

Parameters:

relative - are the moves relative to the previous move?

Throws:

java.lang.Exception

getMoveDistances

public NumberVariable getMoveDistances()
                                throws java.lang.Exception

creates and returns a variable containing the series of distances between captures

Throws:

java.lang.Exception

getNetMove

public MoveVector getNetMove()
                      throws java.lang.Exception

returns the time difference between first and last capture

Throws:

java.lang.Exception

getNetDisplacement

public double getNetDisplacement()
                          throws java.lang.Exception

returns the time difference between first and last capture

Throws:

java.lang.Exception

getTinyStepPath

public CaptureVariable getTinyStepPath(int nSteps)
                                throws java.lang.Exception

traces the current selected path in small increments

Parameters:

nSteps - the number of increments in the path

Throws:

java.lang.Exception

getSpeeds

public NumberVariable getSpeeds()
                         throws java.lang.Exception

creates and returns a variable containing the series of speeds between captures

Throws:

java.lang.Exception

getTimeBetweenFrames

public NumberVariable getTimeBetweenFrames()
                                    throws java.lang.Exception

creates and returns a variable containing the series of time distances between captures

Throws:

java.lang.Exception

getSSCP

public SquaresCrossproducts getSSCP()
                             throws java.lang.Exception

returns the sums of squares and crossproducts for the variable

Throws:

java.lang.Exception

getHotellingFResults

public ANOVAResults getHotellingFResults(Variable theXVar)
                                  throws java.lang.Exception

lists the results from an analysis of differences in mean angles for a variable of locations

Parameters:

theXVar - variable that contains grouping information

Throws:

java.lang.Exception

getDistanceMatrix

public DataTable getDistanceMatrix(int DistanceMeasure)
                            throws java.lang.Exception

calculates a matrix of distances between all valid (i.e., selected and non-missing) locations

Parameters:

DistanceMeasure - what type of distance measure should be calculated

Throws:

java.lang.Exception

listDistanceMatrix

public void listDistanceMatrix(int DistanceMeasure)
                        throws java.lang.Exception

lists a matrix of distances between all valid (i.e., selected and non-missing) locations

Parameters:

DistanceMeasure - what type of distance measure should be calculated

Throws:

java.lang.Exception

getMinNeighborDistance

public double getMinNeighborDistance()
                              throws java.lang.Exception

returns the minimum neighbor distance

Throws:

java.lang.Exception

getDistancesToLocation

public NumberVariable getDistancesToLocation(SpatialVector aLocation)
                                      throws java.lang.Exception

returns the distances to one specific location

Parameters:

aLocation - the location to which distances are calculated

Throws:

java.lang.Exception

getAnglesFromCenter

public NumberVariable getAnglesFromCenter()
                                   throws java.lang.Exception

returns the distances to one specific location

Throws:

java.lang.Exception

getCenterLocation

public SpatialVector getCenterLocation()
                                throws java.lang.Exception

returns the average neighbor distance

Throws:

java.lang.Exception

getMeanDistanceToLocation

public double getMeanDistanceToLocation(SpatialVector meanVec)
                                 throws java.lang.Exception

returns the average neighbor distance

Throws:

java.lang.Exception

getHomeRange_MinimumPolygon

public java.awt.Polygon getHomeRange_MinimumPolygon()
                                             throws java.lang.Exception

returns the average neighbor distance

Throws:

java.lang.Exception

resamplePath

public CaptureVariable[] resamplePath(double[] distUnits)
                               throws java.lang.Exception

retraces the path with different step lengths

Parameters:

distUnits - an array of pathlengths

Throws:

java.lang.Exception

estimateD

public double estimateD(double maxPathLength,
                        double stepSize,
                        double pathLength)
                 throws java.lang.Exception

returns the fractal dimension of the coordinates

Throws:

java.lang.Exception

getFractalDimension

public double getFractalDimension()
                           throws java.lang.Exception

returns the fractal dimension of the coordinates

Throws:

java.lang.Exception

getFractalDimension

public double getFractalDimension(double stepSize)
                           throws java.lang.Exception

returns the fractal dimension of the coordinates

Parameters:

stepSize - the original step size of the individual producing the path, use 0 for default

Throws:

java.lang.Exception

listFractalDimension

public void listFractalDimension()
                          throws java.lang.Exception

lists the fractal dimension for the variable using the currently selected set of rows

Throws:

java.lang.Exception

listFractalDimension

public void listFractalDimension(double stepSize)
                          throws java.lang.Exception

lists the fractal dimension for the variable using the currently selected set of rows

Parameters:

stepSize - the original step size of the individual producing the path, use 0 for default

Throws:

java.lang.Exception

makeNewDescriptives

public void makeNewDescriptives()

create a new set of descriptives for the variable the object

Overrides:

makeNewDescriptives in class Variable

fillDescriptives

public void fillDescriptives(java.lang.Double hypVal)
                      throws java.lang.Exception

fills the descriptive statistics for the variable - locations

Overrides:

fillDescriptives in class Variable

Parameters:

hypVal - the value of the a-priori hypothesis mean

Throws:

java.lang.Exception

getSpatialDescriptives

public SpatialDescriptives getSpatialDescriptives()
                                           throws java.lang.Exception

fills the descriptive statistics for the variable and returns the results

Throws:

java.lang.Exception

copySpatialDescriptives

public SpatialDescriptives copySpatialDescriptives()
                                            throws java.lang.Exception

fills the descriptive statistics for the variable and returns the results

Throws:

java.lang.Exception

getGroupDescriptives

public Descriptives[] getGroupDescriptives(Variable theXVar)
                                    throws java.lang.Exception

returns the descriptives for the groups identified by X

Parameters:

theXVar - the independent variable contains information about the experimental group for each case

Throws:

java.lang.Exception

listGroupDescriptives

public void listGroupDescriptives(Variable theXVar)
                           throws java.lang.Exception

lists the descriptives for the groups identified by X

Overrides:

listGroupDescriptives in class Variable

Parameters:

theXVar - the independent variable contains information about the experimental group for each case

Throws:

java.lang.Exception

listMoveDescriptives

public void listMoveDescriptives(boolean relative)
                          throws java.lang.Exception

lists the descriptive statistics for the moves using the currently selected set of rows

Parameters:

relative - are the moves relative to the previous move?

Throws:

java.lang.Exception

listCircularDescriptives

public void listCircularDescriptives(boolean relative)
                              throws java.lang.Exception

lists the descriptive statistics for the angles of the moves using the currently selected set of rows

Parameters:

relative - are the moves relative to the previous move?

Throws:

java.lang.Exception

asSpatialMap

public void asSpatialMap()
                  throws java.lang.Exception

Creates a presenter and plots and connects the locations

Throws:

java.lang.Exception

asSpatialMap

public void asSpatialMap(boolean xDirection,
                         boolean yDirection)
                  throws java.lang.Exception

Creates a presenter and plots the locations

Parameters:

xDirection - do x values increase from left to right?

yDirection - do y values increase from top to bottom?

Throws:

java.lang.Exception

asSpatialMap

public void asSpatialMap(boolean xDirection,
                         boolean yDirection,
                         int view)
                  throws java.lang.Exception

Creates a presenter and plots the locations

Parameters:

xDirection - do x values increase from left to right?

yDirection - do y values increase from top to bottom?

view - 0 - XY, 1 - XZ, 2 - YZ;

Throws:

java.lang.Exception

asSpatialSpeedMap

public void asSpatialSpeedMap()
                       throws java.lang.Exception

Creates a presenter and plots and connects the locations

Throws:

java.lang.Exception

asSpatialSpeedMap

public void asSpatialSpeedMap(boolean xDirection,
                              boolean yDirection)
                       throws java.lang.Exception

Creates a presenter and plots the locations

Parameters:

xDirection - do x values increase from left to right?

yDirection - do y values increase from top to bottom?

Throws:

java.lang.Exception

asCircularGraph

public void asCircularGraph()
                     throws java.lang.Exception

Creates a circular presenter

Throws:

java.lang.Exception

asCircularGraph

public void asCircularGraph(boolean relative)
                     throws java.lang.Exception

Creates a circular presenter

Parameters:

relative - should the direction of the moves be considered relative to the previous direction

Throws:

java.lang.Exception

writeKMLIntro

public void writeKMLIntro(java.io.Writer output)
                   throws java.lang.Exception

export the CaptureVariable's LineStyle into a KML file for display in Google Earth

Throws:

java.lang.Exception

writeKMLLineStyle

public void writeKMLLineStyle(java.io.Writer output)
                       throws java.lang.Exception

export the CaptureVariable's LineStyle into a KML file for display in Google Earth

Throws:

java.lang.Exception

writeKMLLine

public void writeKMLLine(java.io.Writer output)
                  throws java.lang.Exception

export the CaptureVariable's coordinates into a KML file for display in Google Earth

Throws:

java.lang.Exception

writeKMLPoints

public void writeKMLPoints(java.io.Writer output)
                    throws java.lang.Exception

export the CaptureVariable's coordinates into a KML file for display in Google Earth

Throws:

java.lang.Exception

writeKMLOutro

public void writeKMLOutro(java.io.Writer output)
                   throws java.lang.Exception

export the CaptureVariable's LineStyle into a KML file for display in Google Earth

Throws:

java.lang.Exception

writeKMLCoords

public void writeKMLCoords(java.io.Writer output)
                    throws java.lang.Exception

export the CaptureVariable's LineStyle into a KML file for display in Google Earth

Throws:

java.lang.Exception

writeKMLFile

public void writeKMLFile()
                  throws java.lang.Exception

export the coordinates into a KML file for display in Google Earth

Throws:

java.lang.Exception

writeKMLFile

public void writeKMLFile(java.lang.String name)
                  throws java.lang.Exception

export the coordinates into a KML file for display in Google Earth

Throws:

java.lang.Exception