NORM-VET DATABASE R PACKAGE

Description

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.

Usage

The noRmvet package has a suite of functions for different purposes. All functions have specific usage descriptions in R, accessible with ?.

Fetching data from the database

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.

Datasets

Two datasets are stored within the package, namely am_groups and cutoff_data. The am_groups dataset holds the antimicrobial substance names and their respective antimicrobial group names and codes from the internal system. The dataset cutoff_data contains all 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.

Functions for updating the database

All functions that start with the name update are used to update data in the NORM-VET database whenever this is needed. The name of these functions are listed below. All of the update functions are structured in the same way and are used in a similar manner. The functions provide an output that makes it possible to compare existing data in the database to the updated data generated by the function. Users should check this and verify the differences before updating the database. Check the function descriptions with ? for detailed usage.

- update_analyte_sens_group
- update_bacterial_category
- update_bacterial_group
- update_cutoff
- update_material_group
- update_plate_grouping
- update_report_year
- update_species_groups