agg_index: Aggregation of clones
In RClone: Partially Clonal Populations Analysis

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

agg_index computes Ac (aggregation of clonal lineages) assessed by comparing the probability of clonal identity between nearest units pairs.

1 2	agg_index(data1, coords = NULL, vecpop = NULL, nbrepeat = 1, bar = FALSE, listMLL = 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`.
`nbrepeat`	numeric, the number of repeats.
`bar`	option, if `TRUE`, adds a progression bar.
`listMLL`	option, a custom list of MLL.

The probability of clonal identity is set as 0 if ramets belong to the same MLG/MLL and 1 otherwise.

Ac is computed as Ac=(Psg-Psp)/Psg with Psg the average probability of clonal identity of all pairs and Psp among pairwise nearest neighbours.

Coordinates of units are randomly permuted nbrepeat times to provide a upper pvalue for Ac (Monte Carlo).

a list (one population) or a list of lists (multi-populations) of:

results a table with Ac value, pvalue and the number of permutations.
simulations a vector of nbrepeat values of sim-Ac.

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).

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

autocorrelation, clonal_sub and edge_effect

data(posidonia)
data(coord_posidonia)

agg_index(posidonia, coords = coord_posidonia)
#agg_index(posidonia, coords = coord_posidonia, nbrepeat = 1000, bar = TRUE) #takes time