edge_effect: Edge Effect

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/RClone.R

Description

edge_effect tests the occurrence of Edge Effect.

Usage

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edge_effect(data1, coords = NULL, center = NULL, vecpop = NULL, nbrepeat = 1, 
		bar = FALSE, listMLL = NULL)

Arguments

data1

a Rclone table with one allele per column, haploid or diploid data.

coords

a table with coordinates of every units in data1.

center

a vector or a list of vectors, with c(x,y) coordinates of the centre of the sampling area.

vecpop

vector, option, vecpop indicates the population name of each unit of data1, if data1 contains several populations. If data1 contains only one population, leave vecpop = NULL.

nbrepeat

numeric, option, the number of repeats.

bar

logical, option, if TRUE, adds a progression bar.

listMLL

option, a custom list of MLL.

Details

The index of edge effect Ee estimates the effect of sampling (scheme and strategy) on genotypic richness estimation and in particular overestimation due to large clones sampled only once at the edge of the sampling area.

Ee is estimated as Ee=(Du-Da)/Da with Du average geographic distances between unique MLG/MLL and the centre, and Da between all sampling units and the centre.

As for the aggregation index Ac, coordinates of units are randomly permuted nbrepeat times to provide a upper p-value (Monte Carlo).

Value

a list (one population) or list of lists (several populations) with

Author(s)

Creator/Author: Diane Bailleul <[email protected]>
Author: Sophie Arnaud-Haond <[email protected]>
Contributor: Solenn Stoeckel

The R implementation of RClone was written by Diane Bailleul.

The design was inspired by GenClone program described in Arnaud-Haond & Belkhir (2007).

References

Arnaud-Haond et al., 2007, Standardizing methods to address clonality in population studies.

See Also

autocorrelation, clonal_sub and agg_index

Examples

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data(posidonia)
data(coord_posidonia)

center1 <- c(40,10)
#Our sample quadra ranges from 0 to 80 and 0 to 20

edge_effect(posidonia, coords = coord_posidonia, center = center1, nbrepeat = 1000, 
	bar = TRUE)

#But if, for some reasons you don't know where the middle of the sampling 
##area is, you can try some of these:
center <- c(mean(coord_posidonia[,1]), mean(coord_posidonia[,2])) #or
center <- c(mean(c(min(coord_posidonia[,1]), max(coord_posidonia[,1]))), 
mean(c(min(coord_posidonia[,2]), max(coord_posidonia[,2])))) #or
center <- c((max(coord_posidonia[,1])-min(coord_posidonia[,1]))/2, 
(max(coord_posidonia[,2])-min(coord_posidonia[,2]))/2)

dbailleul/RClone documentation built on May 12, 2017, 8:56 p.m.