microorganisms.codes: Data Set with 6 036 Common Microorganism Codes

In AMR: Antimicrobial Resistance Data Analysis

Data Set with 6 036 Common Microorganism Codes

Description

A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions.

Usage

microorganisms.codes

Format

A tibble with 6 036 observations and 2 variables:

• code
  Commonly used code of a microorganism. This is a unique identifier.

• mo
  ID of the microorganism in the microorganisms data set

Download Our Reference Data

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit our website for direct download links, or explore the actual files in our GitHub repository.

See Also

as.mo() microorganisms

Examples

microorganisms.codes

# 'ECO' or 'eco' is the WHONET code for E. coli:
microorganisms.codes[microorganisms.codes$code == "ECO", ]

# and therefore, 'eco' will be understood as E. coli in this package:
mo_info("eco")

# works for all AMR functions:
mo_is_intrinsic_resistant("eco", ab = "vancomycin")

AMR documentation built on June 8, 2025, 10:17 a.m.