Reference

Google Sheet Functions A set of functions for getting data from Google Sheets
get_googlesheet()	get_googlesheet
get_data()	get_data
get_country_urls()	get_country_urls
get_country_url()	get_url_for_country
get_data_type_urls()	get_data_type_urls
get_data_type_url()	get_data_type_url
get_data_for_country()	get_data_for_country
print_data_types_for_country()	print_data_types_for_country
print_data_types()	print_data_types
Microreact metadata manipulation functions A set of functions for making metadata for Microreact
make_microreact_metadata_for_country()	make_microreact_metadata_for_country
make_microreact_metadata_for_all_units()	make_microreact_metadata_for_all_units
make_microreact_metadata()	make_microreact_metadata
clean_data()	clean_data
colour_acquired_amr_data()	colour_acquired_amr_data
colour_point_amr_data()	colour_point_amr_data
colour_dataframe()	colour_dataframe
get_country_colours()	get_country_colours
get_country_locations()	get_country_locations
get_sentinel_site_colours()	get_sentinel_site_colours
fill_missing_epi_data()	fill_missing_epi_data
fill_missing_metadata()	fill_missing_metadata
AMR data functions A set of functions for parsing AMR data
get_ncbi_amr_metadata()	get_ncbi_amr_metadata
get_point_mutation_metadata()	get_point_mutation_metadata
wide_amr_data_to_long()	wide_amr_data_to_long
filter_long_data()	filter_long_data
extract_nucleotide_accession()	extract_nucleotide_accession
annotate_amr_data()	annotate_amr_data
wide_point_amr_data_to_long()	wide_point_amr_data_to_long
get_annotated_point_amr_data()	get_annotated_point_amr_data
replace_ariba_cluster_names()	replace_ariba_cluster_names
WHONET functions A set of functions for obtaining WHONET metadata
whonet_species_map()	whonet_species_map
whonet_drug_codes()	whonet_drug_codes
Plotting functions A set of functions for counting and plotting GHRU data
count_samples_by_sentinel_site()	count_samples_by_sentinel_site
count_sts()	count_sts
count_most_frequent_sts()	count_most_frequent_sts
count_sts_by_sentinel_site()	count_sts_by_sentinel_site
count_most_frequent_sts_per_sentinel_site()	count_most_frequent_sts_per_sentinel_site
count_AMR_subclasses_by_sentinel_site()	count_AMR_subclasses_by_sentinel_site
count_gene_families_by_sentinel_site()	count_gene_families_by_sentinel_site
count_alleles_by_sentinel_site()	count_alleles_by_sentinel_site
plot_sts()	plot_sts
plot_most_frequent_sentinel_site_sts()	plot_most_frequent_sentinel_site_sts
plot_AMR_subclasses_by_sentinel_site()	plot_AMR_subclasses_by_sentinel_site
dot_plot_gene_family_counts_by_sentinel_site()	dot_plot_gene_family_counts_by_sentinel_site
plot_allele_counts_by_sentinel_site()	plot_allele_counts_by_sentinel_site