count_AMR_subclasses_by_sentinel_site — count_AMR_subclasses_by_sentinel

A function to count specified AMR subclasses by sentinel_site

count_AMR_subclasses_by_sentinel_site(
  long_acquired_gene_amr_data,
  samples_per_sentinel_site,
  drug_subclasses = NULL
)

Arguments

long_acquired_gene_amr_data	The acquired gene data in long format as obtained by the annotate_amr_data function
samples_per_sentinel_site	Counts of the total number of samples per country obtained by the count_samples_by_sentinel_site function
drug_subclasses	The desired drug subclasses to count (specifying none will count all but this may not be desired)

Value

subclass_counts_by_csentinel_site Counts of each subclass by sentinel site # A tibble: 6 x 4 Country subclass count proportion <chr> <fct> <int> <dbl> 1 Colombia BETA-LACTAM 406 0.822 2 Colombia CARBAPENEM 422 0.854 3 Colombia CEPHALOSPORIN 367 0.743 4 India BETA-LACTAM 292 0.951 5 India CARBAPENEM 250 0.814 6 India CEPHALOSPORIN 291 0.948