simul: Function simulating data sets

In ssoubeyrand/CloNcaSe: Estimation of Effective Size and Sex Rate of a Partially Clonal Population

Description

This function simulates the evolution and the sampling of a partially clonal population.

Usage

simul(start.counts, param, nb1ClonalCycles, nb2ClonalCycles, nb1Sample, nb2Sample, 
	nbPrelCycles)

Arguments

start.counts	Vectors of non-negative integers providing counts of strains used to initialize the simulations.
param	2-component numeric vector with the values of Nc and s used for the simulations.
nb1ClonalCycles	Non-negative integer indicating the number of clonal cycles separating the 1st sample and the mixed (i.e. clonal-sexual) cycle.
nb2ClonalCycles	Non-negative integer indicating the number of clonal cycles separating the mixed (i.e. clonal-sexual) cycle and the 2nd sample.
nb1Sample	Non-negative integer indicating the size of the 1st sample.
nb2Sample	Non-negative integer indicating the size of the 2nd sample.
nbPrelCycles	Number of preliminary series of cycles (one series consists of nb1ClonalCycles clonal cycles, 1 mixed cycle and nb2ClonalCycles clonal cycles) performed before the collection of the 1st sample.

Value

A list consisted of:

population	Counts of strains in the population at the 1st and 2nd sampling dates.
samples	Counts of sampled strains in the population at the 1st and 2nd sampling dates.
statistics	Numeric vector providing the following statistics: the empirical probabilities of sampling two clonemates at the 1st and 2nd sampling dates (1st and 2nd components of the vector), and the empirical probability that two random isolates, the 1st one being collected at the 1st sampling date and the 2nd one being collected at the 2nd sampling date, are clonemates (5th component of the vector). The 3rd and 4th components of the vector can be ignored.

Author(s)

Samuel Soubeyrand

References

Ali S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, de Vallavieille-Pope C and Enjalbert J (2015). CloNcaSe: Estimation of sex frequency and effective population size by clonemate re-sampling in partially clonal organisms. Research Report.

See Also

ncase4simul.

Examples

## count data used to initialize the simulation
counts1=c(20,10,5,1,1,1,1,1)

## simulated data set
simul(start.counts=counts1,param=c(1000,0.8),nb1ClonalCycles=17,nb2ClonalCycles=7,
	nb1Sample=100,nb2Sample=100,nbPrelCycles=5)

ssoubeyrand/CloNcaSe documentation built on May 30, 2019, 8:43 a.m.