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)smallest minimum allele frequency permitted to include a locus in calculation of Ne.
apply the maf.threshold by strata. If TRUE
then any locus that is below this threshold in any strata will be removed
from the calculation of Ne for every stratum. Otherwise, loci are removed
only if they are below the maf.threshold in the stratum for which
Ne is calculated.
central confidence interval.
a numeric matrix with one row per strata and the following columns:
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