Estimate Ne from linkage disequilibrium based on Pearson correlation approximation following Waples et al 2016. Adapted from code by R. Waples and W. Larson.
ldNe(
g,
maf.threshold = 0,
by.strata = FALSE,
ci = 0.95,
drop.missing = FALSE,
num.cores = 1
)smallest minimum allele frequency permitted to include a locus in calculation of Ne.
apply the `maf.threshold` by strata. If `TRUE` then loci that are below this threshold in any strata will be removed from the calculation of Ne for all strata. Loci below `maf.threshold` within a stratum are always removed for calculations of Ne for that stratum.
central confidence interval.
drop loci with missing genotypes? If `FALSE`, a slower procedure is used where individuals with missing genotypes are removed in a pairwise fashion.
The number of cores to use to distribute computations over.
If set to NULL, the value will be what is reported
by detectCores - 1.
a data.frame with one row per strata and the following columns:
stratumstratum being summarized
Sharmonic mean of sample size across pairwise comparisons of loci
num.compnumber of pairwise loci comparisons used
mean.rsqmean r^2 over all loci
mean.E.rsqmean expected r^2 over all loci
Neestimated Ne
param.lci, param.uciparametric lower and upper CIs
Waples, R.S. 2006. A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics 7:167-184. Waples RK, Larson WA, and Waples RS. 2016. Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci. Heredity 117:233-240; doi:10.1038/hdy.2016.60