README.md

In eriqande/afblue: Best Linear Unbiased Erediction of Allele Frequencies Given Pairwise Kinship

afblue

17 January, 2017

• Installing the package
• Reproducing the simulations of Waples and Anderson
  • Main paper simulations
  • Coho salmon population investigations

This is an R-package that makes it easy to compute the BLUE for estimating allele frequency amongst the founders given the pedigree connecting a sample.

It also provides an algorithm for determining optimal sibling removal schemes and it makes it easy to compute effective sample sizes.

Installing the package

You can get the package thus:

devtools::install_github("eriqande/afblue")

Because devtools::install_github might not recursively install dependencies you might need or want to also do this:

install.packages(c("dplyr", "kinship2", "magrittr", "stringr", "tidyr"))

Reproducing the simulations of Waples and Anderson

If you want to see how the package was used in the paper "Purging putative siblings from population genetic datasets: A cautionary view" by Robin S. Waples and Eric C. Anderson in Molecular Ecology then, after you have done the above line, you should get the whole repository which includes the scripts. Do it like this on your command line.

git clone https://github.com/eriqande/afblue

Or just get the package from Dryad.

Then open up the Rstudio project (afblue.Rproj) in that repository.

Main paper simulations

In order to rerun the simulations done in the paper you must run the code in the files R-Robin/ESS.R and R-Robin/Sims.R. The top part of these files, e.g., the lines:

NLoci = 100
Ne = 100
S = 40
NGens = 10
NReps = 200
MaxSib = seq(1:NReps)
MaxFamily = 9
Familysize = seq(1:MaxFamily)
ProbFamily = 0.5 ## Only used with Mixed mating model
Sibcheck = 0 ## 0 removes FS+HS; 1 removes FS only
Mating = 1  ## 1 = random; 2 = monogamy; 3 = mixed
     if (Mating==3) {Familysize = seq(2:MaxFamily)+1}

provide a place for the user to change the simulation parameters as needed or desired.

Coho salmon population investigations

In order to rerun the analyses on the coho salmon populations you may need to install some more packages if you do not already have them:

install.packages(c("readr", "ggplot2", "grid", "gridExtra", "forcats"))

Then, armed with those packages, you must run the code in ./R-main/coho-afblue-analysis.R with the working directory being the top level of the repository/Rstudio project.

Running that script will produce a directory called outputs and will fill it with the following output files:

as-if-true-pedigrees.pdf
coho_summ_table-related.csv
coho_summ_table-unrelated.csv
ess_fig_a.pdf
ess_fig_b.pdf
full_blue_results.csv
unrelateds-with-spuriously-inferred-pedigrees.pdf

which are various plots and outputs that appear in the paper.

eriqande/afblue documentation built on May 16, 2019, 8:44 a.m.