Description Usage Arguments Author(s)
Objective function for the offspring.
1 2 3 | obj_offspring(ocounts, osize, ploidy, prob_geno, bias_val = 1,
seq_error = 0, od_param = 0, outlier = FALSE, out_prop = 0.01,
out_mean = 0.5, out_disp = 1/3)
|
ocounts |
The observed counts of the refernce allele for each individual. |
osize |
The observed number of reads for each individuals. |
ploidy |
An integer. The ploidy of the species. This is assumed to be the same for each individual. |
prob_geno |
The allele frequencies of the genotypes. See |
bias_val |
The bias parameter. A value of 1 means there is no bias toward one allele or the other. A value less than one indicates a bias toward the reference allele. A value greater than one indicates a bias toward the non-reference allele. |
seq_error |
The sequencing error rate. |
od_param |
The overdispersion parameter in the beta-binomial model for the OK counts. When this is zero, this resorts to the binomial model for counts. |
outlier |
A logical. Should we include an outlier model ( |
out_prop |
The proportion of points that are outliers. Defaults
(quite arbitrarily) to |
out_mean |
The mean of beta-binomial for the outlier distribution.
Defaults to |
out_disp |
The overdispersion parameter of the outlier distribution.
Defaults to |
David Gerard
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