# NOTE: THIS DATASET IS NOT BEING USED AT THE MOMENT.
# THE SPECIES TABLE IS TOO BIG TO BE LOADED EACH TIME THE PACKAGE LOADS.
# IN THE FUTURE WE'LL REFACTOR THIS CODE TO SAVE A FRACTION OF THE TABLE.
# Title: Ensembl species.
# Ensembl release version: 97.
# Source: Ensembl's REST API (https://rest.ensembl.org/documentation/info/species) using ensemblr::get_species()
# Last download date: 19 July 2019.
# How to run: just source this file.
# Documentation source: R/data.R
# Output: This script generates a tibble named 'species' of 12 columns:
# - division
# - taxon_id
# - species_name
# - species_display_name
# - species_common_name
# - release
# - genome_assembly_name
# - genbank_assembly_accession
# - strain
# - strain_collection
# - species_aliases
# - groups
#
# The 'species' tibble is saved to 2 files:
# - data/species.rda
# - R/sysdata.rda
library(ensemblr)
species <- get_species()
usethis::use_data(species, compress = "xz", overwrite = TRUE, version = 2)
usethis::use_data(species, internal = TRUE, compress = "xz", overwrite = TRUE, version = 2)
# Having this dataset also exported to R/sysdata.rda so that I can use it inside
# my functions without having R CMD check triggering a Note.
# More about this here:
# - https://stackoverflow.com/questions/48105239/using-datasets-in-an-r-package
# - https://support.bioconductor.org/p/24756/
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