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reference/example_isolates_unclean.md

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+# Data Set with Unclean Data
+
+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
+
+``` r
+example_isolates_unclean
+```
+
+## Format
+
+A [tibble](https://tibble.tidyverse.org/reference/tibble.html) 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()`](https://amr-for-r.org/reference/as.mo.md), see also
+  [microorganisms](https://amr-for-r.org/reference/microorganisms.md)
+
+- `AMX:GEN`  
+  4 different antimicrobials that have to be transformed with
+  [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
+
+## 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](https://amr-for-r.org/articles/datasets.html), or explore the
+actual files in [our GitHub
+repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
+
+## Examples
+
+``` r
+example_isolates_unclean
+#> # A tibble: 3,000 × 8
+#>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN  
+#>    <chr>      <chr>    <date>     <chr>         <chr> <chr> <chr> <chr>
+#>  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    
+#>  7 J8         A        2016-06-14 E. coli       R     S     S     S    
+#>  8 M3         A        2015-10-25 E. coli       R     S     S     S    
+#>  9 J3         A        2019-06-19 E. coli       S     S     S     S    
+#> 10 G6         A        2015-04-27 S. aureus     S     S     S     S    
+#> # ℹ 2,990 more rows
+```