Create COI dataframe

COI_df_create(
  df,
  groupvars = c("age_bin", "clinical"),
  breaks = c(-0.001, 5, 15, 100.1),
  barcodes = FALSE,
  ibd = FALSE,
  n = Inf,
  reps = 1,
  nl = 24,
  mean_only = TRUE
)

Arguments

df: Output of pop_strains_df
groupvars: Grouping vars for summarySE. Default = c('age_bin','clinical')
breaks: Numberic vector of age breaks. Default = c(-0.001,5,15,100.1)
barcodes: Boolean whether to return tabled barcodes. Default = FALSE
ibd: Boolean for ibd simulations or not. Default = FALSE
n: Number of individuals to sample when creating COI data frame. Default = Inf that means all individuals are included
reps: Numeric for number of population subsamples to make. Default = 1
nl: Number of loci. Default = 24
mean_only: Boolean for whether to just return the mean when summarising vs all summary statistics. Default = TRUE