SI.gic {RGeostats}

R Documentation

Global Index of Collocation

Description

The global index of collocation looks at how geographically distinct two populations are by comparing the distance between their centers of gravity and the mean distance between individual fish taken at random and independenly from each population.

Usage

SI.gic(db1, db2=NA, name1 = db.getname(db1,"z",1), name2= db.getname(db2,"z",2),
       flag.plot = FALSE, flag.inertia=FALSE, flag.ellipse=FALSE,
       col1 = "black", col2 = "blue", digit = 3, ...)

Arguments

db1	Name of the db-class which contains the first data set
db2	Name of the db-class which contains the second data set. If not defined, the argument 'db2' is set to 'db1'.
name1	Name of the variable used when calculating the center of gravity and the inertia, in the first data set. If not defined, the sample coordinates are used only
name2	Name of the variable used when calculating the center of gravity and the inertia, in the second data set. If not defined, the sample coordinates are used only
flag.plot	When TRUE, both gravity centers and inertiae are represented graphically
flag.inertia	When TRUE, the inertia axes are represented. They correspond to the standard deviation of the projection of the population along these axes. Only valid if flag.plot is TRUE and if Db is defined in 2-D.
flag.ellipse	When TRUE, the inertia ellipse (not its surface) represents the population. This ellipse has the same gravity center, the same inertia and the same anisotropie as the initial population. Only valid if flag.plot is TRUE and if Db is defined in 2-D.
col1	Color used for representing the gravity center and the inertia of the first data set (used when flag.plot=TRUE)
col2	Color used for representing the gravity center and the inertia of the second data set (used when flag.plot=TRUE)
digit	Number of decimal digits for expressing the Inertia
...	Additional parameters passed to the functions SI.cgi and db.plot.

Value

The global Index of collocation

Note

Function originally developped for the EU project Fisboat, DG-Fish, STREP no 502572. Authors: Woillez, M., and Rivoirard, J. (Geosciences/Mines-ParisTech)

Author(s)

Mathieu Woillez, Ifremer, 2013

References

Woillez, M., Poulard, J-C., Rivoirard, J., Petitgas, P., and Bez, N. 2007. Indices for capturing spatial patterns and their evolution in time, with application to European hake (Merluccius merluccius) in the Bay of Biscay. - ICES Journal of Marine Science, 64: 537-550. http://icesjms.oxfordjournals.org/content/64/3/537.abstract

Woillez, M., Rivoirard, J., and Petitgas, P. 2009. Notes on survey-based spatial indicators for monitoring fish populations. - Aquatic Living Resources, 22: 155-164. http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8215490

Examples

# Load data
rg.load(filename="Demo.hake.bob.db.data",objname="db.data")
rg.load(filename="Demo.hake.bob.poly.data",objname="poly.data")
projec.define(projection="mean",db=db.data)

# Global index of collocation (ages A0 & A1)
SI.gic(db1=db.data,db2=db.data,name1="A0",name2="A1",
       flag.plot=TRUE,flag.inertia=TRUE,asp=1,inches=5,title="A0 and A1",
       col1="red",col2="blue")
plot(poly.data,col=8,add=TRUE)

rm(db.data,poly.data)

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