Description Usage Arguments Details Value Author(s) References See Also Examples
This function computes point estimates of Nc and s for a partially clonal population, confidence intervals (using parametric bootstrap) and the coverage rates of the intervals. The parametric bootstrap is also used to propose a bias correction of the point estimates and their confidence intervals.
1 2 |
counts |
2-column matrix whose 1st (resp. 2nd) column gives the counts of strains in sample 1 (resp. 2). |
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. |
start.param |
2-column matrix whose rows give initial values for the effective size (Nc) and the sex rate (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. |
nbBootstrap |
Number (non-negative integer) of bootstrap replications to assess confidence intervals (based on a normal approximation) and to carry out a bias correction. Default to 0 (no bootstrap procedure). |
conf.level |
Confidence level (between 0 and 1) of the marginal confidence intervals for Nc and s. Default to 0.95. Used if |
nbCoverage |
Number of (non-negative integer) iterations to assess the coverage rates of the marginal confidence intervals. Default to 0 (no coverage assessment). Used if |
trace |
Logical indicating if tracing information are displayed ( |
The optimization method that is used is the Nelder and Mead (1965) method implemented in the optim
function (stats
package).
A list whose items are:
bootstrap.estim |
(if |
cover |
(if |
optim.output |
A list consisted of (i) the output of the |
estimates |
A numeric vector providing the estimates of Nc and s (if |
Samuel Soubeyrand
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## Yellow rust data
data(yellowrust)
## Point estimates
ncase(yellowrust,nb1ClonalCycles=17,nb2ClonalCycles=7,
start=expand.grid(c(100,1000),c(0.2,0.8)))
## Point estimates, Parametric bootstrap, Bias correction
## and confidence intervals
ncase(yellowrust,nb1ClonalCycles=17,nb2ClonalCycles=7,
start=expand.grid(c(100,1000),c(0.2,0.8)),
nbBootstrap=5000,conf.level=0.95)
## Point estimates, Parametric bootstrap, Bias correction
## and confidence intervals and their coverage
ncase(yellowrust,nb1ClonalCycles=17,nb2ClonalCycles=7,
start=expand.grid(c(100,1000),c(0.2,0.8)),
nbBootstrap=5000,conf.level=0.95,nbCoverage=100)
|
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