microorganisms.codes: Data Set with 4 971 Common Microorganism Codes

In msberends/AMR: Antimicrobial Resistance Data Analysis

Data Set with 4 971 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 4 971 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

Details

Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit our website for the download links. The actual files are of course available on 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")

msberends/AMR documentation built on March 5, 2025, 2:28 p.m.