vario: Calculate uni- and multi-variate variograms

In mcglinnlab/vario: Community variograms and associated null models

Calculate uni- and multi-variate variograms

Description

This code is largely modified from the 'vegan' function 'mso' by Helene Wagner, also parts of this code were derived from the 'geoR' function 'vairog' by Paulo J. Ribeiro Jr. and Peter J. Diggle. Citations: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens and Helene Wagner (2011). vegan: Community Ecology Package. R package version 2.0-2. http://CRAN.R-project.org/package=vegan Paulo J. Ribeiro Jr & Peter J. Diggle geoR: a package for geostatistical analysis R-NEWS, 1(2):15-18. June, 2001

Usage

vario(
  x,
  coord,
  grain = 1,
  breaks = NA,
  log = FALSE,
  hmin = NA,
  hmax = NA,
  round.int = FALSE,
  pos.neg = FALSE,
  binary = TRUE,
  snap = NA,
  median = FALSE,
  quants = NA,
  direction = "omnidirectional",
  tolerance = pi/8,
  unit.angle = c("radians", "degrees"),
  distance.metric = "euclidean",
  univariate = FALSE
)

Arguments

x	an object of class 'sim' or may be a sitexsp matrix, a vector of values, if x is the later then missing samples should be coded as -999
coord	the spatial coordinates
grain	interval size for distance classes, only used if 'breaks' not supplied
breaks	the spatial breaks that define the spatial lags to be compared
hmax	the maximum spatial lag
pos.neg	if TRUE the positive and negative parts of the covariance matrix are output
binary	if TRUE and x is class sim then abundances are converted to binary 0 1 values
snap	indicates which generation from an object class 'sim' to draw from
median	indicates if in addition to the mean the medians of the distance matrices are calculated
direction	a numerical value for the directional (azimuth) angle. This used to specify directional variograms. Default defines the omnidirectional variogram. The value must be in the interval [0, pi] radians ([0, 180] degrees).
tolerance	numerical value for the tolerance angle, when computing directional variograms. The value must be in the interval [0, pi/2] radians ([0, 90] degrees). Defaults to pi/8.
unit.angle	defines the unit for the specification of angles in the two previous arguments. Options are 'radians' and 'degrees', with default to 'radians'.
distance.metric	can be one of the speices turnover metrics listed by the vegan function vegdist(). This is only appropriate if pos.neg = FALSE. Common options include, 'jaccard' and 'bray'. If computed on pres/abse data then soreson index is computed by 'bray'.
round.up	if TRUE the spatial lags are rounded up to nearest integer
min	minimum value
max	maximum value

Details

Note: that if some areas are unsampled that obs != pos + neg + exp

Examples

x = matrix(runif(100), ncol=10, nrow=10)
coord = cbind(1:10, 1)
vario(x, coord)
## Not run: 
library(vegan)
data(mite)
data(mite.xy)
vario(as.matrix(mite), mite.xy)
vario(as.matrix(mite), mite.xy, pos.neg=T)

## End(Not run)

mcglinnlab/vario documentation built on Feb. 22, 2023, 1:49 p.m.