1d:T7ec,# Mutation model logic Functions for mutation model logic, e.g. probability of downwards and upwards mutations etc. ```r mutmodel_not_mut(mutmodel, locus, alleles) mutmodel_dw_mut(mutmodel, locus, alleles) mutmodel_up_mut(mutmodel, locus, alleles) approx_stationary_dist(mutmodel, alleles) ``` ## Arguments - `mutmodel`: a `mutmodel` object created with `init_mutmodel`. - `locus`: the locus of interest (integer, remember postfix L). - `alleles`: vector of integers (remember postfix L) of the alleles of interest. ## Returns Mutation probabilities for locus `locus` in mutation model `mutmodel` at alleleles `alleles`. ## Author(s) Mikkel Meyer Andersen and Poul Svante Eriksen ## Examples ```r mutpars.locus1 <- c(0.149, 2.08, 18.3, 0.149, 0.374, 27.4) # DYS19 mutpars.locus2 <- c(0.500, 1.18, 18.0, 0.500, 0.0183, 349) # DYS389I mutpars.locus3 <- c(0.0163, 17.7, 11.1, 0.0163, 0.592, 14.1) # DYS391 mutpars <- matrix(c(mutpars.locus1, mutpars.locus2, mutpars.locus3), ncol = 3) colnames(mutpars) <- c("DYS19", "DYS389I", "DYS391") mutmodel <- init_mutmodel(modeltype = 2L, mutpars = mutpars) mutmodel_not_mut(mutmodel, locus = 1L, alleles = 10L:20L) mutmodel_dw_mut(mutmodel, locus = 1L, alleles = 10L:20L) mutmodel_up_mut(mutmodel, locus = 1L, alleles = 10L:20L) statdists <- approx_stationary_dist(mutmodel, alleles = 5L:20L) bp <- barplot(statdists, beside = TRUE) text(bp, 0.02, round(statdists, 1), cex = 1, pos = 3) text(bp, 0, rep(rownames(statdists), ncol(mutmodel$mutpars)), cex = 1, pos = 3) mutpars <- matrix(c(c(0.003, 0.001), rep(0.004, 2), rep(0.001, 2)), ncol = 3) colnames(mutpars) <- c("DYS19", "DYS389I", "DYS391") mutmodel <- init_mutmodel(modeltype = 1L, mutpars = mutpars) mutmodel statdists <- approx_stationary_dist(mutmodel, alleles = 5L:20L) statdists bp <- barplot(statdists, beside = TRUE) text(bp, 0.02, round(statdists, 1), cex = 1, pos = 3) text(bp, 0, rep(rownames(statdists), ncol(mutmodel$mutpars)), cex = 1, pos = 3) ```

mutmodel function