Description Usage Arguments Details Value
Internal simulation function to generate a matrix to weight the genotypes when estimating d and stickbreaking coefficients
1 | generate.geno.weight.matrix(geno.matrix, fit.matrix, wts = c(2, 1))
|
geno.matrix |
Genotype matrix generated in |
fit.matrix |
Fitness matrix generated in |
wts |
Vector of weights to be applied of form c(singletons, multiples). Default |
To calculate the likelihood of the data under the stickbreaking model for a given value of d,
we need to estimate the stickbreaking coefficients. The issue is whether all genotypes in the network provide equally good information
about the coefficients. The default assumption is that the wild type fitness
is know without error while all other genotypes have the same error structure. Coefficient estimates are based
on comparing pairs of genotypes: with and without the mutation. Therefore, estimates based on comparing wild type to
the single mutations (singletons) are expected to have half the variance of all other comparisons (i.e. multiples). This
function generates the weights matrix that reflects this. To change this assumption, change the wts
parameter. For example,
if the wild type has the same error as all other genotypes, wts = c(1,1)
would be appropriate.
weight.matrix
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