costantinicarlo/ckmrsim

efficient sampling for close-kin mark recapture power estimation

CKMRsim

This package implements Monte Carlo methods (including efficient importance sampling approaches) for assessing the false positive and false negative rates expected when using a particular set of genetic markers for pairwise relationship inference. It also provides functions implemented in C++ for computing likelihood ratios for different relationships between all pairs of individuals in a data set.

CKMRsim can be installed with devtools. It requires that development tools be installed on your system to allow compilation of C++ via RCpp.

devtools::install_github("eriqande/CKMRsim", build_vignettes = TRUE)

After this, the various vignettes can be accessed and read like this:

vignette("CKMRsim-example-1")

vignette("CKMRsim-example-2-microsatellites")

vignette("CKMRsim-simulating-linked-markers")

vignette("CKMRsim-writing-geno-error-funcs")

In order to pursue simulations in the face of physical linkage, you must download and install the external dependency, Mendel version 16. For Windows and Mac OS X, CKMRsim will look for the Mendel binary in its default install location. So download it from http://software.genetics.ucla.edu/mendel and do a default install. Note that you need to register with your email in order to download Mendel.