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Reconnect to an existing tidybreed database

Source: R/restore_pop.R
restore_pop.Rd

Re-opens a .duckdb file and reconstructs the tidybreed_pop R object so that simulation can continue. No metadata is stored on the object; all genome statistics are derived from live DB queries when needed.

This is the intended way to resume a simulation after close_pop(), after a crash, or in a new R session. A common pattern is to call open_pop() once, configure all traits and covariances, then start each replicate with restore_pop() followed by add_founders().

run_dirs are reconstructed from the database location and the tools argument. Set options(tidybreed.tools = ...) before calling restore_pop() to get the same tool dirs back automatically.

Usage

restore_pop(
  db_path,
  pop_name = NULL,
  tools = getOption("tidybreed.tools", NULL)
)

Arguments

db_path

Character. Path to an existing .duckdb file.

pop_name

Character or NULL. Population name to assign to the restored object. When NULL (default) the name is inferred from the filename by stripping a trailing _tidybreed.duckdb or .duckdb suffix.

tools

Character vector or NULL. Tool subdirectory names to reconstruct in pop$run_dirs. Defaults to getOption("tidybreed.tools", NULL).

Value

A fully operational tidybreed_pop object.

Examples

if (FALSE) { # \dontrun{
# One-time setup. db_name is placed inside open_pop()'s layer-2/3 folder
# structure (see ?open_pop), so capture pop$db_path rather than assuming
# the file lives at "cattle_sim.duckdb" in the working directory.
pop <- open_pop(pop_name = "cattle", db_name = "cattle_sim.duckdb") |>
  define_genome(n_loci = 50000, n_chr = 29, chr_len_Mb = 100) |>
  define_founder_haplotypes(n_haplotypes = 100, line_name = "A")
pop <- define_trait(pop, trait_name = "milk", target_add_var = 10)
db_path <- pop$db_path
close_pop(pop)

# Each replicate
pop <- restore_pop(db_path)
pop <- pop |>
  get_table("founder_haplotypes") |>
  add_founders(n_males = 50, n_females = 200, line_name = "A")
} # }