get_genome_id_from_phenotype_id {avidaR}

R Documentation

Get genome from phenotype

Description

Get the genome of a digital organism that encodes a specific phenotype for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_genome_id_from_phenotype_id(
  phenotype_id,
  seed_id = sample(1:1000, 1),
  genome_seq = FALSE,
  triplestore
)

Arguments

phenotype_id	Integer or a list of integer values.
seed_id	Integer (from 1 to 1000) or a vector of integer values. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If seed_id value is not specified, it returns data for a single randomly chosen seed_id value (between 1 and 1000).
genome_seq	Logical value (TRUE/FALSE) to show/hide this column ("FALSE" by default).
triplestore	Object of class triplestore_access which manages database access.

Value

Data frame. Columns: "seed_id" (optional), "phenotype_id", "genome_seq" (optional).

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

# Single phenotype
get_genome_id_from_phenotype_id(phenotype_id = 1, triplestore = avidaDB)

# More than one phenotype
get_genome_id_from_phenotype_id(
  phenotype_id = c(1, 2),
  genome_seq = TRUE,
  triplestore = avidaDB
)

# At seeds_4 and seed_5
get_genome_id_from_phenotype_id(
  phenotype_id = c(1, 2),
  seed_id = c(4, 5),
  triplestore = avidaDB
)

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