Description Usage Arguments Details Value Author(s) References Examples
Estimating g2 from microsatellite data
1 2  g2_microsats(genotypes, nperm = 0, nboot = 0, boot_over = "inds",
CI = 0.95, verbose = TRUE)

genotypes 

nperm 
Number of permutations for testing the hypothesis that the empirical g2value is higher than the g2 for random associations between individuals and genotypes. 
nboot 
Number of bootstraps for estimating a confidence interval 
boot_over 
Bootstrap over individuals by specifying "inds" and over loci with "loci". Defaults to "ind". 
CI 
Confidence interval (default to 0.95) 
verbose 
If FALSE, nothing will be printed to show the status of bootstraps and permutations. 
Calculates g2 from smaller datasets. The underlying formula is compationally expensive due to double summations over all paits of loci (see David et al. 2007). Use convert_raw to convert raw genotypes (with 2 columns per locus) into the required format.
g2_microsats returns an object of class "inbreed". The functions 'print' and 'plot' are used to print a summary and to plot the distribution of bootstrapped g2 values and CI.
An 'inbreed' object from g2_microsats
is a list containing the following components:
call 
function call. 
g2 
g2 value 
p_val 
p value from permutation test 
g2_permut 
g2 values from permuted genotypes 
g2_boot 
g2 values from bootstrap samples 
CI_boot 
confidence interval from bootstraps 
se_boot 
standard error of g2 from bootstraps 
nobs 
number of observations 
nloc 
number of markers 
Martin A. Stoffel (martin.adam.stoffel@gmail.com) & Mareike Esser (messer@techfak.unibielefeld.de)
David, P., Pujol, B., Viard, F., Castella, V. and Goudet, J. (2007), Reliable selfing rate estimates from imperfect population genetic data. Molecular Ecology, 16: 2474
1 2 3 4  data(mouse_msats)
# tranform raw genotypes into 0/1 format
genotypes < convert_raw(mouse_msats)
(g2_mouse < g2_microsats(genotypes, nperm = 1000, nboot = 100, boot_over = "inds", CI = 0.95))

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