clonal_sub: Clonal Subrange

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

View source: R/RClone.R

Description

clonal_sub computes the clonal subrange analysis with spatial distance intervals and the corresponding probabilities of clonal identity.

Usage

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clonal_sub(data1, coords = NULL, vecpop = NULL, listMLL = NULL, class1 = FALSE, 
		class2 = FALSE, d = NULL, vecdist = 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.

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.

listMLL

option, a custom list of MLL.

class1

option, if TRUE, computes distance classes of d equidistant classes.

class2

option, if TRUE, computes distance classes of d classes with the same number of units pairs each.

d

numeric, number of distance classes.

vecdist

option, a custom vector distance intervals to construct distance classes.

Details

By default, d = 10 and clonal_sub computes 10 equidistant distance classes for all the ramets pairs.

The function proposes 3 others options:

Value

A list of:

clonal_sub_res

clonal subrange, i.e. maximum distance between two units sharing the same MLG/MLL (Alberto et al., 2005)

clonal_sub_tab

table of results with, per class, the number of units pairs, the min, max and mean distances between pairs and Fr/log(Fr) the fraction of pairs of ramets sharing the same MLG/MLL

For multi-population data1, a list of lists per population.

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

Alberto et al., 2005, Spatial genetic structure, neighbourhood size and clonal subrange in seagrass (Cymodocea nodosa) populations.

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

See Also

autocorrelation, agg_index and edge_effect

Examples

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data(posidonia)
data(coord_posidonia)

distGC <- c(0,10,15,20,30,50,70,76.0411073)

clonal_sub(posidonia, coords = coord_posidonia)
clonal_sub(posidonia, coords = coord_posidonia, vecdist = distGC)

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