README.md

In zakrobinson/RLDNe: A Convenient R Interface For NeEstimator V2.1

RLDNe

Description:

An R-package that conveniently interfaces with NeEstimator 2.1 (Do et al. 2014). NeEstimator V2.1 executables are distributed with this package freely, for non-commericial, educational purposes only. Visit http://www.molecularfisherieslaboratory.com.au/neestimator-software/ for more information on NeEstimator V2.1. Currently, this package is set up for the LD-method only.

Install directions:

devtools::install_github(repo="zakrobinson/RLDNe")

Example function sequence for the LD-method in NeEstimator

library(RLDNe)

data("wgp_example")

gp_file<-write_genepop_zlr(loci = wgp_example[,3:ncol(wgp_example)],pops = wgp_example$pop,ind.ids = wgp_example$ind_id,folder = "",filename ="genepop_output.txt",missingVal = NA,ncode = 2,diploid = T)

param_files<- NeV2_LDNe_create(input_file = gp_file$Output_File ,param_file = "Ne_params.txt" ,NE_out_file = "Ne_out.txt")

run_LDNe(LDNe_params = param_files$param_file)

Ne_estimates<-readLDNe_tab(path = param_files$Ne_out_tab)

Example of how to convert from alleles per column format to genotypes per column format

data("wgp_example_2col")

genotype_examp<-alleles2genotypes(df = wgp_example_2col,allele_cols = 3:ncol(wgp_example_2col),allelesAsIntegers = TRUE)

Citation for NeEstimator

Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J. & Ovenden, J. R. (2014). NeEstimator V2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources. 14, 209-214.

zakrobinson/RLDNe documentation built on April 12, 2021, 1:50 p.m.