The noRmvet package contains functions and data frames used to analyse and
visualize NORM-VET data from the NORM-VET database. The package also contains
functions that are used to update the database when needed.
The noRmvet package has a suite of functions for different purposes. All
functions have specific usage descriptions in R, accessible with ?.
The functions fetch_nv_data and fetch_nv_mic_data are used to extract
the main data from the database. To generate phenotypes from the mic-values,
the function create_mic_and_phenotype can be used. To generate gene data from
the main data, create_gene_data can be used.
Several datasets are stored within the package, namely am_groups,
panel_ranges and cutoff_data, to name a few. The am_groups dataset holds
the antimicrobial substance names and their respective antimicrobial group
names and codes from the internal system. The dataset panel_ranges contains
information on which panels were used for each bacterium for each year, and
holds the minimum and maximum concentrations per substance in each panel. The
dataset cutoff_data containsall the cut-off values used for each substance
and bacterial species group. NOTE: This table holds all the cut-off values,
even older values, in contrast to the table in the NORM-VET database that only
holds the actual cut-off values relevant for the current year.
the noRmvet package have several functions for generating data for EFSA
reporting, such as generate_efsa_data, generate_efsa_gene_data, and
generate_efsa_neg_data. Several other functions are used to detect erroneous
or missing data, calculate synergies, and write EFSA-compatible XML files.