ncase4simul: Function estimating effective size (Nc) and sex rate (s) for...

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, and computes raw point estimates of Nc and s for each simulated data set.

Usage

ncase4simul(param, nb1ClonalCycles, nb2ClonalCycles, nb1Sample, nb2Sample, 
            start.counts, nbPrelCycles, nbSimul, start.param, maxit = 500, trace = TRUE)

Arguments

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.
start.counts	Vectors of non-negative integers providing counts of strains used to initialize the simulations.
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.
nbSimul	Non-negative integer giving the number of simulated data sets that are generated and for which Nc and s are estimated.
start.param	2-column matrix whose rows give initial values for Nc and s that are used in the optimization of the contrast.
maxit	Maximum number (non-negative integer) of iterations in the optimization of the contrast. Default to 500.
trace	Logical indicating if tracing information are displayed (TRUE) or not displayed (FALSE). Default to TRUE.

Details

The optimization method that is used is the Nelder and Mead (1965) method implemented in the optim function (stats package).

Value

A 4-column matrix with true Nc (1st col.), true s (2nd col.), the raw estimate of Nc (3rd col.) and the raw estimate of s (4th col.). The raw estimates are the estimates of Nc and s without bias correction. The matrix contains as many lines as the number of simulations requested by the argument nbSimul.

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.

Nelder J A and Mead R (1965). A simplex algorithm for function minimization. Computer Journal 7: 308-313.

See Also

simul, ncase.

Examples

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

## simulation and raw estimation
ncase4simul(param=c(1000,0.5),nb1ClonalCycles=17,nb2ClonalCycles=7,
            nb1Sample=200,nb2Sample=200,start.counts=counts1,nbPrelCycles=5,
            nbSimul=100,start.param=expand.grid(c(100,1000),c(0.2,0.8)))

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