clonal_sub: Clonal Subrange
In RClone: Partially Clonal Populations Analysis

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

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

1 2	clonal_sub(data1, coords = NULL, vecpop = NULL, listMLL = NULL, class1 = FALSE, class2 = FALSE, d = NULL, vecdist = NULL)

`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.

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

The function proposes 3 others options:

class1 fixing d equidistant classes,
class2 fixing d distance classes with the same number of units pairs,
vecdist != NULL allowing the user to give a vector, vecdist of intervals. vecdist must start with 0 and end with max(dist).

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.

Creator/Author: Diane Bailleul <diane.bailleul.pro@gmail.com>
Author: Sophie Arnaud-Haond <sophie.arnaud@ifremer.fr>
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).

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.

autocorrelation, agg_index and edge_effect

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)