Skip to contents

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 4 957 observations and 2 variables:

  • code
    Commonly used code of a microorganism

  • 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, SAS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

Examples

microorganisms.codes
#> Error in .Call(Cchin, x, table): NULL value passed as symbol address

# 'ECO' or 'eco' is the WHONET code for E. coli:
microorganisms.codes[microorganisms.codes$code == "ECO", ]
#> Error in .Call(Cchin, x, table): NULL value passed as symbol address

# and therefore, 'eco' will be understood as E. coli in this package:
mo_info("eco")
#> Error in .Call(Cchin, x, table): NULL value passed as symbol address

# works for all AMR functions:
mo_is_intrinsic_resistant("eco", ab = "vancomycin")
#> Error in .Call(Cchin, x, table): NULL value passed as symbol address