eco.variogram: Empirical variogram

In EcoGenetics: Management and Exploratory Analysis of Spatial Data in Landscape Genetics

Description

This program computes the empirical variogram of a selected variable. If the coordinates are in decimal degrees, set latlon = TRUE. The program return a table with the mean class distances (d.mean) and the semivariances (obs) for each class.

Usage

eco.variogram(
  Z,
  XY,
  int = NULL,
  smin = 0,
  smax = NULL,
  nclass = NULL,
  seqvec = NULL,
  size = NULL,
  bin = c("sturges", "FD"),
  row.sd = FALSE,
  latlon = FALSE,
  angle = NULL
)

Arguments

Z	Vector for the analysis.
XY	Data frame or matrix with the position of individuals (projected coordinates).
int	Distance interval in the units of XY.
smin	Minimum class distance in the units of XY.
smax	Maximum class distance iin the units of XY.
nclass	Number of classes.
seqvec	Vector with breaks in the units of XY.
size	Number of individuals per class.
bin	Rule for constructing intervals when a partition parameter (int, nclass or size) is not given. Default is Sturge's rule (Sturges, 1926). Other option is Freedman-Diaconis method (Freedman and Diaconis, 1981).
row.sd	Logical. Should be row standardized the matrix? Default FALSE (binary weights).
latlon	Are the coordinates in decimal degrees format? Defalut FALSE. If TRUE, the coordinates must be in a matrix/data frame with the longitude in the first column and latitude in the second. The position is projected onto a plane in meters with the function geoXY.
angle	Direction for computation of a bearing variogram (angle between 0 and 180). Default NULL (omnidirectional).

Value

The program returns an object of class "eco.correlog" with the following slots:

> OUT analysis output

> IN analysis input data

> BEAKS breaks

> CARDINAL number of elements in each class

> DISTMETHOD method used in the construction of breaks

ACCESS TO THE SLOTS The content of the slots can be accessed with the corresponding accessors, using the generic notation of EcoGenetics (<ecoslot.> + <name of the slot> + <name of the object>). See help("EcoGenetics accessors") and the Examples section below

Author(s)

Leandro Roser [e-mail]

References

Borcard D., F. Gillet, and P. Legendre. 2011. Numerical ecology with R. Springer Science & Business Media.

Legendre P., and L. Legendre. 2012. Numerical ecology. Third English edition. Elsevier Science, Amsterdam, Netherlands.

Rosenberg, M. 2000. The bearing correlogram: a new method of analyzing directional spatial autocorrelation. Geographical Analysis, 32: 267-278.

Examples

## Not run: 

data(eco.test)
variog <- eco.variogram(Z = eco[["P"]][, 2],XY =  eco[["XY"]])
eco.plotCorrelog(variog)

# variogram plots support the use of ggplot2 syntax
require(ggplot2)
variogplot <- eco.plotCorrelog(variog) + theme_bw() + theme(legend.position="none")
variogplot

#-----------------------
# ACCESSORS USE EXAMPLE
#-----------------------

# the slots are accessed with the generic format 
# (ecoslot. + name of the slot + name of the object). 
# See help("EcoGenetics accessors")

ecoslot.OUT(variog)        # slot OUT
ecoslot.BREAKS(variog)     # slot BREAKS


## End(Not run)

EcoGenetics documentation built on July 8, 2020, 5:46 p.m.