Nothing
## ----installation, eval=FALSE-------------------------------------------------
# vignette("coala-install", package = "coala")
## ----create_model-------------------------------------------------------------
library(coala)
model <- coal_model(sample_size = 3, loci_number = 1)
## ----print_model--------------------------------------------------------------
model
## -----------------------------------------------------------------------------
model <- model + feat_mutation(rate = 1, model = "IFS")
model
## ----echo=FALSE---------------------------------------------------------------
funcs <- ls("package:coala")
funcs[grep("^feat_", funcs)]
## -----------------------------------------------------------------------------
model <- coal_model(sample_size = c(5, 2, 0), loci_number = 1) +
feat_migration(rate = 0.5, symmetric = TRUE) +
feat_pop_merge(0.5, 3, 2) +
feat_pop_merge(0.8, 2, 1)
## -----------------------------------------------------------------------------
model <- coal_model(3, 1) +
feat_mutation(rate = 1) +
sumstat_seg_sites()
model
## ----echo=FALSE---------------------------------------------------------------
funcs[grep("^sumstat_", funcs)]
## -----------------------------------------------------------------------------
sumstats <- simulate(model, seed = 123)
## -----------------------------------------------------------------------------
names(sumstats)
## -----------------------------------------------------------------------------
sumstats$seg_sites[[1]]
## -----------------------------------------------------------------------------
model <- model + locus_single(500)
model
## -----------------------------------------------------------------------------
sumstats <- simulate(model)
sumstats$seg_sites[[1]]
sumstats$seg_sites[[2]]
## -----------------------------------------------------------------------------
model <- model + locus_averaged(2, 750)
sumstats <- simulate(model)
length(sumstats$seg_sites)
## -----------------------------------------------------------------------------
model <- coal_model(5, 1) +
feat_mutation(rate = par_named("theta")) +
sumstat_seg_sites()
sumstats1 <- simulate(model, pars = c(theta = 2.5))
sumstats2 <- simulate(model, pars = c(theta = 4.3))
## ----priors-------------------------------------------------------------------
model <- coal_model(5, 1) +
feat_mutation(rate = par_prior("theta", runif(1, 0, 10))) +
sumstat_seg_sites()
sumstats <- simulate(model)
sumstats$pars
sumstats2 <- simulate(model)
sumstats2$pars
## -----------------------------------------------------------------------------
model <- coal_model(5, 1) +
feat_mutation(rate = par_range("theta", 0.1, 5)) +
sumstat_seg_sites()
## -----------------------------------------------------------------------------
model <- coal_model(4, 2) +
feat_mutation(rate = par_named("theta")) +
feat_recombination(rate = par_expr(theta * 2))
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