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Data Set with Unclean Data

Source: R/data.R
example_isolates_unclean.Rd

A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.

Usage

example_isolates_unclean

Format

A data.frame with 3,000 observations and 8 variables:

  • patient_id
    ID of the patient

  • date
    date of receipt at the laboratory

  • hospital
    ID of the hospital, from A to C

  • bacteria
    info about microorganism that can be transformed with as.mo(), see also microorganisms

  • AMX:GEN
    4 different antibiotics that have to be transformed with as.rsi()

Reference Data Publicly Available

All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.

Examples

head(example_isolates_unclean)
#>   patient_id hospital       date      bacteria AMX AMC CIP GEN
#> 1         J3        A 2012-11-21       E. coli   R   I   S   S
#> 2         R7        A 2018-04-03 K. pneumoniae   R   I   S   S
#> 3         P3        A 2014-09-19       E. coli   R   S   S   S
#> 4        P10        A 2015-12-10       E. coli   S   I   S   S
#> 5         B7        A 2015-03-02       E. coli   S   S   S   S
#> 6         W3        A 2018-03-31     S. aureus   R   S   R   S