coala-data-import.R
In coala: A Framework for Coalescent Simulation

## ----import_data, results="hide", eval=FALSE----------------------------------
#  suppressPackageStartupMessages(library(PopGenome))
#  fasta <- system.file("example_fasta_files", package = "coala")
#  data_pg <- readData(fasta, progress_bar_switch = FALSE)
#  data_pg <- set.outgroup(data_pg, c("Individual_Out-1", "Individual_Out-2"))
#  individuals <- list(paste0("Individual_1-", 1:5), paste0("Individual_2-", 1:5))
#  data_pg <- set.populations(data_pg, individuals)

## ----eval=FALSE---------------------------------------------------------------
#  library(coala)
#  segsites <- as.segsites(data_pg)

## ----calc_sumstats_1, eval=FALSE----------------------------------------------
#  model <- coal_model(c(5, 5, 2), 1, 25) +
#    feat_mutation(5) +
#    feat_outgroup(3) +
#    sumstat_sfs(population = 1)
#  stats <- calc_sumstats_from_data(model, segsites)
#  stats$sfs

## ----calc_sumstats_2, eval=FALSE----------------------------------------------
#  stats <- calc_sumstats_from_data(model, data_pg)
#  stats$sfs