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reference/example_isolates.md

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+# Data Set with 2 000 Example Isolates
+
+A data set containing 2 000 microbial isolates with their full
+antibiograms. This data set contains randomised fictitious data, but
+reflects reality and can be used to practise AMR data analysis. For
+examples, please read [the tutorial on our
+website](https://amr-for-r.org/articles/AMR.html).
+
+## Usage
+
+``` r
+example_isolates
+```
+
+## Format
+
+A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 2
+000 observations and 46 variables:
+
+- `date`  
+  Date of receipt at the laboratory
+
+- `patient`  
+  ID of the patient
+
+- `age`  
+  Age of the patient
+
+- `gender`  
+  Gender of the patient, either "F" or "M"
+
+- `ward`  
+  Ward type where the patient was admitted, either "Clinical", "ICU", or
+  "Outpatient"
+
+- `mo`  
+  ID of microorganism created with
+  [`as.mo()`](https://amr-for-r.org/reference/as.mo.md), see also the
+  [microorganisms](https://amr-for-r.org/reference/microorganisms.md)
+  data set
+
+- `PEN:RIF`  
+  40 different antimicrobials with class
+  [`sir`](https://amr-for-r.org/reference/as.sir.md) (see
+  [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)); these column
+  names occur in the
+  [antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
+  data set and can be translated with
+  [`set_ab_names()`](https://amr-for-r.org/reference/ab_property.md) or
+  [`ab_name()`](https://amr-for-r.org/reference/ab_property.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
+#> # A tibble: 2,000 × 46
+#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
+#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
+#>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI   R     NA    NA    NA 
+#>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI   R     NA    NA    NA 
+#>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
+#>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
+#>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
+#>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
+#>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS   R     NA    S     R  
+#>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS   R     NA    S     R  
+#>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR   R     NA    R     NA 
+#> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR   R     NA    S     NA 
+#> # ℹ 1,990 more rows
+#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
+#> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
+#> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
+#> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,
+#> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
+#> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
+```