## ----include = FALSE----------------------------------------------------------
env_present <- slendr:::is_slendr_env_present()

knitr::opts_chunk$set(
  collapse = FALSE,
  comment = "#>",
  eval = env_present,
  fig.width = 6,
  fig.height = 4,
  dpi = 70
)

## -----------------------------------------------------------------------------
library(slendr)

init_env()

# African ancestral population
afr <- population("AFR", time = 100000, N = 3000)

# first migrants out of Africa
ooa <- population("OOA", parent = afr, time = 60000, N = 500, remove = 23000) %>%
  resize(N = 2000, time = 40000, how = "step")

# Eastern hunter-gatherers
ehg <- population("EHG", parent = ooa, time = 28000, N = 1000, remove = 6000)

# European population
eur <- population("EUR", parent = ehg, time = 25000, N = 2000) %>%
  resize(N = 10000, how = "exponential", time = 5000, end = 0)

# Anatolian farmers
ana <- population("ANA", time = 28000, N = 3000, parent = ooa, remove = 4000)

# Yamnaya steppe population
yam <- population("YAM", time = 7000, N = 500, parent = ehg, remove = 2500)

## -----------------------------------------------------------------------------
gf <- list(
  gene_flow(from = ana, to = yam, rate = 0.5, start = 6500, end = 6400),
  gene_flow(from = ana, to = eur, rate = 0.5, start = 8000, end = 6000),
  gene_flow(from = yam, to = eur, rate = 0.75, start = 4000, end = 3000)
)

## -----------------------------------------------------------------------------
model <- compile_model(
  populations = list(afr, ooa, ehg, eur, ana, yam),
  gene_flow = gf, generation_time = 30,
  time_units = "years before present"
)

## -----------------------------------------------------------------------------
samples <- schedule_sampling(
  model,
  times = c(0, 5000, 12000, 20000, 35000, 39000, 43000),
  list(eur, 3), list(ehg, 1), list(yam, 1), list(ana, 3), list(ooa, 1), list(afr, 1)
)

## ----non-spatial-graph_sampling, fig.width=6, fig.height=4--------------------
plot_model(model, samples = samples)

## ----eval = FALSE-------------------------------------------------------------
#  ts_slim <- slim(model, sequence_length = 100000, recombination_rate = 0)

## -----------------------------------------------------------------------------
ts_msprime <- msprime(model, sequence_length = 100000, recombination_rate = 0)

## -----------------------------------------------------------------------------
extract_parameters(ts_msprime)

## -----------------------------------------------------------------------------
introgression_model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

extract_parameters(introgression_model)