fgm: Floating Grid Method

In FGM: Floating Grid Method

Description

The Floating Grid Method is a spatially restricted permutation technique. Please read the reference mentioned below before using this function. This particular function can be used to perform permutation tests which make use of the Floating Grid permutation technique

Usage

fgm(xy, group=1, marks, iter=999, ratio=1, scale.seq=seq(from=0, to=max(dist(xy)), length.out=21)[2:21], bootstrap=FALSE, correlate=FALSE)

Arguments

xy	Geographical locations of observations.
group	Group membership for the observations. group is optional.
marks	Should be a vector containing all observations, a two-column matrix containing two paired observations or a squared matrix containing relationships or distances between all observations (such as genetic relatedness or distance).The latter is a way to perform multivariate analyses. Note that the squared matrix does not need to be symmetrical: for instance, the genetic relatedness between paired individuals can be investigated by using males as columns and females as rows. NAs are allowed.
iter	Number of iterations for every grid cell size. Default is 999, though it is adviseable to perform 9999 interations for the final results.
ratio	The ratio between the sides of the grid cells. Default is 1.
scale.seq	Sequence of all grid cell sizes that will be tested. The number, order and values of this sequence are completely free, as long as they are numeric. Default is 20 equaly spaced out grid cell sizes from slightly larger than 0 to the maximum distance between any two individuals. Use the explore.fgm function to make a informed decision on the right sequence of grid cell sizes.
bootstrap	TRUE if observations should to be drawn with replacement, FALSE if not. Default is FALSE.
correlate	If one wants to compare two paired observations correlate should be the method of correlation with the FGM should use as available in cor.test; so "pearson", "kendall" or "spearman". If marks is not a two-column matrix correlate should be FALSE. Default is FALSE.

Value

fgm returns an object of class "fgm", which can be accessed with the functions summary and plot.

Author(s)

Reinder Radersma

References

Reinder Radersma & Ben C. Sheldon, 2014. A new permutation test to explore and control for spatial autocorrelation in point pattern data. Manuscript submitted to MEE

See Also

cor.test

Examples

## Produce 20 geographical locations.
loc.x <- 1:20
loc.y <- runif(20,0,5)

## Produce 2 x 20 phenotypes.
type1 <- 11:30+runif(20,0,5)
type2 <- 11:30+runif(20,0,5)

fg <- fgm(xy=cbind(loc.x,loc.y), marks=cbind(type1,type2), iter=99, correlate="pearson")
summary(fg)
plot(fg)
  

FGM documentation built on May 2, 2019, 4:51 p.m.