Description Usage Arguments Value Examples
View source: R/calculate_genetree_summary_stat.R
Calculates summary statistics including Colless' statistic, gamma statistic of the locus tree input as an index as part of a list, gamma statistic of gene tree, sackin statistic, cherry statistic, and time to most recent common ancestor
1 2 3 | genetree_summary_stat(lt_obj, lt_indx)
summarize_gt(lt_obj, lt_indx)
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lt_obj |
Locus tree object obtain from 'sim_lt_gt_mlc' |
lt_indx |
Index of locus tree object of interest |
Dataframe with summary statistics for each gene tree
1 2 3 4 5 6 7 8 9 10 11 12 | # first simulate a species tree
mu <- 0.5
lambda <- 1.0
nt <- 6
tr <- sim_stBD(sbr = lambda, sdr = mu, numbsim = 1, n_tips = nt)
# for a locus tree with 100 genes sampled per locus tree
gentrees <- sim_msc(tr[[1]],
ne = 10000,
num_sampled_individuals = 1,
num_genes = 100)
gt_df <- summarize_gt(gentrees, lt_indx = 1)
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