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 |
data1 |
a |
coords |
a table with coordinates of every units in |
vecpop |
vector, option, |
nbrepeat |
numeric, the number of repeats. |
bar |
option, if |
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
1 2 3 4 5 | data(posidonia)
data(coord_posidonia)
agg_index(posidonia, coords = coord_posidonia)
#agg_index(posidonia, coords = coord_posidonia, nbrepeat = 1000, bar = TRUE) #takes time
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