net.talvi.puffinplot.data

Class Site

java.lang.Object

net.talvi.puffinplot.data.Site

All Implemented Interfaces:

SampleGroup

public class Site
extends java.lang.Object
implements SampleGroup

A site is a grouping of samples within a suite. In practice, it usually corresponds to a group of samples from a small physical area. In a discrete study, it usually corresponds to a physical field site within a section. In a long core study, it usually corresponds to a narrow ‘slice’ of the core between two defined depths.

Constructor Summary

Constructors

Constructor and Description
Site(java.lang.String name) Creates a site containing no samples.
Site(java.lang.String name, java.util.List<Sample> samples) Creates a site containing the specified samples.

Method Summary

Modifier and Type	Method and Description
void	calculateFisherStats(Correction correction) Calculate Fisherian statistics on the PCA directions of samples within this site.
void	calculateGreatCirclesDirection(Correction correction, java.lang.String validityCondition) Calculate a mean direction for the site using best-fit great circles.
void	calculateVgp() Calculates a virtual geomagnetic pole for the site, if possible.
void	clearFisherStats() Clears the stored Fisher statistics, if any.
void	clearGcFit() Clears the stored great-circle fit parameters, if any
void	fromString(java.lang.String string) Sets site data from information in a string.
FisherParams	getFisherParams() Returns the Fisherian parameters of the site mean direction, as calculated by Fisher statistics or great-circle analysis.
FisherValues	getFisherValues() Returns the Fisher statistics (if any) calculated for this site.
static java.util.List<java.lang.String>	getGreatCircleLimitHeader() Returns headers for information on the treatment steps used for the great-circle analysis.
java.util.List<java.lang.String>	getGreatCircleLimitStrings() Returns information on the treatment steps used for the great-circle analysis.
GreatCircles	getGreatCircles() Returns the great-circle parameters (if any) calculated for this site.
Location	getLocation()
Vec3	getMeanDirection() Returns the site mean direction.
java.lang.String	getName()
java.util.List<Sample>	getSamples() Returns the samples in this site
VGP	getVgp()
boolean	isEmpty() Reports whether there are any samples in this site.
void	setLocation(Location location) Sets the location of this site.
java.lang.String	toString() Returns the name of this site.
java.util.List<java.lang.String>	toStrings() Returns a list of strings giving information about this site.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Site

public Site(java.lang.String name,
            java.util.List<Sample> samples)

Creates a site containing the specified samples.

Parameters:

name - the name of the site

samples - the samples contained in the site

Site

public Site(java.lang.String name)

Creates a site containing no samples.

Parameters:

name - the name of the site

Method Detail

calculateFisherStats

public void calculateFisherStats(Correction correction)

Calculate Fisherian statistics on the PCA directions of samples within this site. The PCA directions will be automatically calculated (or recalculated) before the Fisher statistics are calculated, if sufficient points have been selected for the operation. If no PCA direction is available, the sample Fisher mean (if any) and the imported sample direction (if any) are used in turn as fallbacks. The results are stored within the site. If the site has a location set, the VGP will also be calculated and stored. If no sample directions exist for this site, the site's current Fisherian statistics (if any) will be cleared.

Parameters:

correction - the correction to apply to the magnetic moment data when performing the PCA calculations

clearFisherStats

public void clearFisherStats()

Clears the stored Fisher statistics, if any.

calculateGreatCirclesDirection

public void calculateGreatCirclesDirection(Correction correction,
                                           java.lang.String validityCondition)

Calculate a mean direction for the site using best-fit great circles. For each sample at the site, the great circle is incorporated into a calculation of the mean direction. If no great circle has been fitted for a site, the PCA direction (if any) is used. Mean direction estimate is by the method of McFadden and McElhinny (1988). If the site has a location set, the VGP will also be calculated and stored.

The syntax of the validity condition is detailed at GreatCircles.instance(java.util.List, java.util.List, java.lang.String).

Parameters:

correction - the correction to apply to the magnetic moment data when fitting the great circles.

validityCondition - a Javascript expression to determine the validity of great-circle fits

See Also:

GreatCircles

toString

public java.lang.String toString()

Returns the name of this site.

Overrides:

toString in class java.lang.Object

Returns:

the name of this site

getSamples

public java.util.List<Sample> getSamples()

Returns the samples in this site

Specified by:

getSamples in interface SampleGroup

Returns:

the samples in this site

getFisherValues

public FisherValues getFisherValues()

Returns the Fisher statistics (if any) calculated for this site.

Returns:

the Fisher statistics (if any) calculated for this site

getGreatCircles

public GreatCircles getGreatCircles()

Returns the great-circle parameters (if any) calculated for this site.

Returns:

the great-circle parameters (if any) calculated for this site

getFisherParams

public FisherParams getFisherParams()

Returns the Fisherian parameters of the site mean direction, as calculated by Fisher statistics or great-circle analysis. If a great-circle mean has been calculated, its parameters will be returned. If there is no great-circle mean but a Fisher mean has been calculated, the Fisher mean will be returned. If neither type of mean has been calculated, a null value will be returned.

Returns:

the Fisherian parameters of the site mean direction

getGreatCircleLimitHeader

public static java.util.List<java.lang.String> getGreatCircleLimitHeader()

Returns headers for information on the treatment steps used for the great-circle analysis. See the PuffinPlot user manual for details of their interpretation.

Returns:

headers for information on the treatment steps used for the great-circle analyses

getGreatCircleLimitStrings

public java.util.List<java.lang.String> getGreatCircleLimitStrings()

Returns information on the treatment steps used for the great-circle analysis. The list consists of: minFirstGc, maxFirstGc, minLastGc, MaxLastGc. Where minFirstGc is the minimum (among samples in this site) first treatment step value for any great-circle fit, and so forth. Temperatures are given in degrees Celsius, and AF field strengths as equivalent inductions in millitesla.

Returns:

information on the treatment steps used for the great-circle analysis

clearGcFit

public void clearGcFit()

Clears the stored great-circle fit parameters, if any

getName

public java.lang.String getName()

Returns:

the name of this site

isEmpty

public boolean isEmpty()

Reports whether there are any samples in this site.

Returns:

true if there are no samples in this site

toStrings

public java.util.List<java.lang.String> toStrings()

Returns a list of strings giving information about this site.

Returns:

a list of strings giving information about this site

fromString

public void fromString(java.lang.String string)

Sets site data from information in a string. The format is the same as that exported from toStrings().

Parameters:

string - a string containing site data

getLocation

public Location getLocation()

Returns:

the location of this site

setLocation

public void setLocation(Location location)

Sets the location of this site.

Parameters:

location - the location to set

getMeanDirection

public Vec3 getMeanDirection()

Returns the site mean direction. See getFisherParams() for details of how the mean direction is chosen.

Returns:

the site mean direction, or null if none exists

calculateVgp

public void calculateVgp()

Calculates a virtual geomagnetic pole for the site, if possible. A site mean and location are necessary to calculate a VGP.

getVgp

public VGP getVgp()

Returns:

the site VGP (virtual geomagnetic pole)