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

`psex`

and `psex_Fis`

compute the probability that repeated
genotypes originate from distinct sexual events (i.e. being different genets
and not ramets of the same MLG), with or without taking account of H-W equilibrium departures.

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`data1` |
a |

`haploid` |
logical, option, |

`vecpop` |
vector, option, |

`genet` |
option, if |

`RR` |
option, if |

`MLGsim` |
option, the method of psex calculation (see details). |

`nbrepeat` |
option, numeric, the population is simulated |

`bar` |
option, if |

We strongly recommand to use `RR = TRUE`

option to compute allelic
frequencies for clonal data.
Otherwise, we let the options to work with frequencies at genet level
(`genet = TRUE`

) or ramet level (`RR = FALSE`

and
`genet = FALSE`

).

if `MLGsim = TRUE`

, `psex`

are computed as probability for two
units to be derived from distinct sexual reproductive event to be `C(N,2)`

(Stenberg et al. 2003).

If `MLGsim = FALSE`

, `psex`

are computed with more conservative
`C(n,1)`

(Parks & Werth 1993) with `n`

, *"number of separated
fragments with identical genotype to some previously encountered ramet"*.

The pvalue method calculation is largely inspired from MLGsim (Stenberg et al., 2003)
and MLGsim2.0 (Ivens et al., 2012), with authors agreements.

For each repeat, a population is simulated with allelic frequencies.

If clones occurred, a simulated `psex`

is computed and kept in memory.

At the end, a distribution of `sim psex`

is constructed and p-value is
computed as upper p-value (Monte Carlo).

`psex`

and `psex_Fis`

could be time consuming with a certain
number of repeats.

Values must differ from MLGsim and MLGsim2.0 because of Round-Robin frequencies
and `Fis`

calculation (see `freq_RR`

and `Fis`

).

For one population:

if

`nbrepeat`

is not provided, a table with psex values,if

`nbrepeat`

is provided, a list of a table with`psex`

values and p-values and a vector of`sim psex`

.

If `data1`

is a multi-population table (`vecpop != NULL`

),
a list of either tables/tables and vectors for each population.

If `sim_psex`

are less than 100, a warning message pops, as
clones are not necessarily generated each simulation.

If no repeated genotype is generated during simulations, a warning message pops as well.

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).

Stenberg et al., 2003, MLGsim: a program for detecting clones using a simulation approach.

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

Ivens, A.B.F., van de Sanden, M. and Bakker, J. MLGsim 2.0: updated software for
detecting clones from micro satellite data using a simulation approach.

In: The Evolutionary Ecology of Mutualism. PhD Thesis, 2012, University of Groningen.
Pg 107-111

http://www.rug.nl/research/institute-evolutionary-life-sciences/tres/downloads
for MLGsim 2.0.

`Fis`

, `freq_RR`

, `pgen`

and `pgen_Fis`

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