# Download data sets for download / own use

All reference data (about microorganisms, antimicrobials, SIR
interpretation, EUCAST rules, etc.) in this `AMR` package are reliable,
up-to-date and freely available. We continually export our data sets to
formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS,
and Stata. We also provide tab-separated text files that are
machine-readable and suitable for input in any software program, such as
laboratory information systems.

> If you are working in Python, be sure to use our [AMR for
> Python](https://amr-for-r.org/articles/AMR_for_Python.html) package.
> It allows all relevant AMR data sets to be natively available in
> Python.

## `microorganisms`: Full Microbial Taxonomy

A data set with 96 982 rows and 28 columns, containing the following
column names:  
*mo*, *fullname*, *status*, *domain*, *kingdom*, *phylum*, *class*,
*order*, *family*, *genus*, *species*, *subspecies*, *rank*, *ref*,
*oxygen_tolerance*, *morphology*, *source*, *lpsn*, *lpsn_parent*,
*lpsn_renamed_to*, *mycobank*, *mycobank_parent*, *mycobank_renamed_to*,
*gbif*, *gbif_parent*, *gbif_renamed_to*, *prevalence*, and *snomed*.

This data set is in R available as `microorganisms`, after you load the
`AMR` package.

It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/microorganisms.html).

**Direct download links:**

- Download as [original R Data Structure (RDS)
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.rds)
  (2.2 MB)  
- Download as [tab-separated text
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.txt)
  (23.1 MB)  
- Download as [Microsoft Excel
  workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.xlsx)
  (11.4 MB)  
- Download as [Apache Feather
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.feather)
  (11 MB)  
- Download as [Apache Parquet
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.parquet)
  (4.6 MB)  
- Download as [IBM SPSS Statistics data
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.sav)
  (35.2 MB)  
- Download as [Stata DTA
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.dta)
  (96.6 MB)

**NOTE: The exported files for SPSS and Stata contain only the first 50
SNOMED codes per record, as their file size would otherwise exceed 100
MB; the file size limit of GitHub.** Their file structures and
compression techniques are very inefficient. Advice? Use R instead. It’s
free and much better in many ways.

The tab-separated text file and Microsoft Excel workbook both contain
all SNOMED codes as comma separated values.

**Example content**

Included (sub)species per taxonomic kingdom:

|      Kingdom      | Number of (sub)species |
|:-----------------:|:----------------------:|
|                   |           20           |
| (unknown kingdom) |           8            |
|     Animalia      |         2 015          |
|      Archaea      |          150           |
|     Bacillati     |         24 200         |
|     Bacteria      |           2            |

First 6 rows when filtering on genus *Escherichia*:

| mo | fullname | status | domain | kingdom | phylum | class | order | family | genus | species | subspecies | rank | ref | oxygen_tolerance | morphology | source | lpsn | lpsn_parent | lpsn_renamed_to | mycobank | mycobank_parent | mycobank_renamed_to | gbif | gbif_parent | gbif_renamed_to | prevalence | snomed |
|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|
| B_ESCHR | Escherichia | accepted | Bacteria | Pseudomonadati | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia |  |  | genus | Castellani et al., 1919 | facultative anaerobe | rods | LPSN | 515602 | 482 |  |  |  |  | CS33H | CRYWR |  | 1 | 407310004, 407251000, 407281008, … |
| B_ESCHR_ADCR | Escherichia adecarboxylata | synonym | Bacteria | Pseudomonadati | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | adecarboxylata |  | species | Leclerc, 1962 | likely facultative anaerobe | rods | LPSN | 776052 | 515602 | 777447 |  |  |  | CS33J | CS33H | 3SVX6 | 1 |  |
| B_ESCHR_ALBR | Escherichia albertii | accepted | Bacteria | Pseudomonadati | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | albertii |  | species | Huys et al., 2003 | facultative anaerobe | rods | LPSN | 776053 | 515602 |  |  |  |  | 3BGTB | CS33H |  | 1 | 419388003 |
| B_ESCHR_BLTT | Escherichia blattae | synonym | Bacteria | Pseudomonadati | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | blattae |  | species | Burgess et al., 1973 | likely facultative anaerobe | rods | LPSN | 776056 | 515602 | 788468 |  |  |  | CS33K | CS33H | 4X4P7 | 1 |  |
| B_ESCHR_COLI | Escherichia coli | accepted | Bacteria | Pseudomonadati | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | coli |  | species | Castellani et al., 1919 | facultative anaerobe | rods | LPSN | 776057 | 515602 |  |  |  |  | NT3L7 | CS33H |  | 1 | 1095001000112106, 715307006, 737528008, … |
| B_ESCHR_COLI_COLI | Escherichia coli coli | accepted | Bacteria | Pseudomonadati | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | coli | coli | subspecies |  |  |  | GBIF |  | 776057 |  |  |  |  | 12233256 | NT3L7 |  | 1 |  |

------------------------------------------------------------------------

## `antimicrobials`: Antibiotic and Antifungal Drugs

A data set with 505 rows and 14 columns, containing the following column
names:  
*ab*, *cid*, *name*, *group*, *atc*, *atc_group1*, *atc_group2*,
*abbreviations*, *synonyms*, *oral_ddd*, *oral_units*, *iv_ddd*,
*iv_units*, and *loinc*.

This data set is in R available as `antimicrobials`, after you load the
`AMR` package.

It was last updated on 13 August 2026 09:12:12 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html).

**Direct download links:**

- Download as [original R Data Structure (RDS)
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds)
  (44 kB)  
- Download as [tab-separated text
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt)
  (0.1 MB)  
- Download as [Microsoft Excel
  workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.xlsx)
  (79 kB)  
- Download as [Apache Feather
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.feather)
  (0.1 MB)  
- Download as [Apache Parquet
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.parquet)
  (94 kB)  
- Download as [IBM SPSS Statistics data
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.sav)
  (0.4 MB)  
- Download as [Stata DTA
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.dta)
  (10 kB)

The tab-separated text, Microsoft Excel, SPSS, and Stata files all
contain the ATC codes, common abbreviations, trade names and LOINC codes
as comma separated values.

**Example content**

| ab | cid | name | group | atc | atc_group1 | atc_group2 | abbreviations | synonyms | oral_ddd | oral_units | iv_ddd | iv_units | loinc |
|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|
| AMK | 37768 | Amikacin | Aminoglycosides | D06AX12, J01GB06, QD06AX12, … | Aminoglycoside antibacterials | Other aminoglycosides | ak, ami, amik, … | amikacillin, amikacina, amikacine, … |  |  | 1.0 | g | 101493-5, 11-7, 12-5, … |
| AMX | 33613 | Amoxicillin | Aminopenicillins, Penicillins, Beta-lactams | J01CA04, QG51AA03, QJ01CA04 | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | ac, amox, amoxic, … | acuotricina, alfamox, alfida, … | 1.5 | g | 3.0 | g | 101498-4, 15-8, 16-6, … |
| AMC | 23665637 | Amoxicillin/clavulanic acid | Aminopenicillins, Penicillins, Beta-lactams, … | J01CR02, QJ01CR02 | Beta-lactam antibacterials, penicillins | Combinations of penicillins, incl. beta-lactamase inhibitors | a/c, amcl, aml, … | amocla, amoclan, amoclav, … | 1.5 | g | 3.0 | g |  |
| AMP | 6249 | Ampicillin | Aminopenicillins, Penicillins, Beta-lactams | J01CA01, QJ01CA01, QJ51CA01, … | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | am, amp, amp100, … | adobacillin, alpen, amblosin, … | 2.0 | g | 6.0 | g | 101477-8, 101478-6, 18864-9, … |
| AZM | 447043 | Azithromycin | Macrolides | J01FA10, QJ01FA10, QS01AA26, … | Macrolides, lincosamides and streptogramins | Macrolides | az, azi, azit, … | aritromicina, aruzilina, azasite, … | 0.3 | g | 0.5 | g | 100043-9, 16420-2, 16421-0, … |
| PEN | 5904 | Benzylpenicillin | Penicillins, Beta-lactams | J01CE01, QJ01CE01, QJ51CE01, … | Combinations of antibacterials | Combinations of antibacterials | bepe, pen, peni, … | bencilpenicilina, benzopenicillin, benzylpenicilline, … |  |  | 3.6 | g |  |

------------------------------------------------------------------------

## `clinical_breakpoints`: Interpretation from MIC values & disk diameters to SIR

A data set with 45 735 rows and 14 columns, containing the following
column names:  
*guideline*, *type*, *host*, *method*, *site*, *mo*, *rank_index*, *ab*,
*ref_tbl*, *disk_dose*, *breakpoint_S*, *breakpoint_R*, *uti*, and
*is_SDD*.

This data set is in R available as `clinical_breakpoints`, after you
load the `AMR` package.

It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/clinical_breakpoints.html).

**Direct download links:**

- Download as [original R Data Structure (RDS)
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.rds)
  (93 kB)  
- Download as [tab-separated text
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt)
  (4.2 MB)  
- Download as [Microsoft Excel
  workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.xlsx)
  (2.7 MB)  
- Download as [Apache Feather
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.feather)
  (2 MB)  
- Download as [Apache Parquet
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet)
  (0.2 MB)  
- Download as [IBM SPSS Statistics data
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav)
  (7.5 MB)  
- Download as [Stata DTA
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.dta)
  (12.6 MB)

**Example content**

| guideline | type | host | method | site | mo | mo_name | rank_index | ab | ab_name | ref_tbl | disk_dose | breakpoint_S | breakpoint_R | uti | is_SDD |
|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|
| EUCAST 2026 | human | human | DISK |  | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | 10 mcg | 26.000 | 20.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | MIC |  | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans |  | 1.000 | 4.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | DISK |  | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans | 1.25/23.75 mcg | 26.000 | 26.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | MIC |  | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans |  | 0.125 | 0.125 | FALSE | FALSE |
| EUCAST 2026 | human | human | DISK |  | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans | 30/6 mcg | 26.000 | 26.000 | FALSE | FALSE |
| EUCAST 2026 | human | human | MIC |  | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans |  | 4.000 | 4.000 | FALSE | FALSE |

------------------------------------------------------------------------

## `microorganisms.groups`: Species Groups and Microbiological Complexes

A data set with 530 rows and 4 columns, containing the following column
names:  
*mo_group*, *mo*, *mo_group_name*, and *mo_name*.

This data set is in R available as `microorganisms.groups`, after you
load the `AMR` package.

It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/microorganisms.groups.html).

**Direct download links:**

- Download as [original R Data Structure (RDS)
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.rds)
  (6 kB)  
- Download as [tab-separated text
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.txt)
  (50 kB)  
- Download as [Microsoft Excel
  workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.xlsx)
  (19 kB)  
- Download as [Apache Feather
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.feather)
  (19 kB)  
- Download as [Apache Parquet
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.parquet)
  (13 kB)  
- Download as [IBM SPSS Statistics data
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.sav)
  (64 kB)  
- Download as [Stata DTA
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.dta)
  (82 kB)

**Example content**

| mo_group | mo | mo_group_name | mo_name |
|:--:|:--:|:--:|:--:|
| B_ACNTB_BMNN-C | B_ACNTB_BMNN | Acinetobacter baumannii complex | Acinetobacter baumannii |
| B_ACNTB_BMNN-C | B_ACNTB_CLCC | Acinetobacter baumannii complex | Acinetobacter calcoaceticus |
| B_ACNTB_BMNN-C | B_ACNTB_LCTC | Acinetobacter baumannii complex | Acinetobacter dijkshoorniae |
| B_ACNTB_BMNN-C | B_ACNTB_NSCM | Acinetobacter baumannii complex | Acinetobacter nosocomialis |
| B_ACNTB_BMNN-C | B_ACNTB_PITT | Acinetobacter baumannii complex | Acinetobacter pittii |
| B_ACNTB_BMNN-C | B_ACNTB_SFRT | Acinetobacter baumannii complex | Acinetobacter seifertii |

------------------------------------------------------------------------

## `intrinsic_resistant`: Intrinsic Bacterial Resistance

A data set with 294 079 rows and 2 columns, containing the following
column names:  
*mo* and *ab*.

This data set is in R available as `intrinsic_resistant`, after you load
the `AMR` package.

It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/intrinsic_resistant.html).

**Direct download links:**

- Download as [original R Data Structure (RDS)
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.rds)
  (0.1 MB)  
- Download as [tab-separated text
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.txt)
  (10.9 MB)  
- Download as [Microsoft Excel
  workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.xlsx)
  (3.1 MB)  
- Download as [Apache Feather
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.feather)
  (2.5 MB)  
- Download as [Apache Parquet
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.parquet)
  (0.3 MB)  
- Download as [IBM SPSS Statistics data
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.sav)
  (16 MB)  
- Download as [Stata DTA
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.dta)
  (28.6 MB)

**Example content**

Example rows when filtering on *Enterobacter cloacae*:

|    microorganism     |         antibiotic          |
|:--------------------:|:---------------------------:|
| Enterobacter cloacae |      Acetylmidecamycin      |
| Enterobacter cloacae |      Acetylspiramycin       |
| Enterobacter cloacae |         Amoxicillin         |
| Enterobacter cloacae | Amoxicillin/clavulanic acid |
| Enterobacter cloacae |         Ampicillin          |
| Enterobacter cloacae |    Ampicillin/sulbactam     |
| Enterobacter cloacae |          Avoparcin          |
| Enterobacter cloacae |        Azithromycin         |
| Enterobacter cloacae |      Benzylpenicillin       |
| Enterobacter cloacae |          Bleomycin          |
| Enterobacter cloacae |          Cadazolid          |
| Enterobacter cloacae |         Cefadroxil          |
| Enterobacter cloacae |          Cefalexin          |
| Enterobacter cloacae |          Cefalotin          |
| Enterobacter cloacae |          Cefazolin          |
| Enterobacter cloacae |          Cefoxitin          |
| Enterobacter cloacae |       Clarithromycin        |
| Enterobacter cloacae |         Clindamycin         |
| Enterobacter cloacae |         Cycloserine         |
| Enterobacter cloacae |         Dalbavancin         |
| Enterobacter cloacae |        Dirithromycin        |
| Enterobacter cloacae |        Erythromycin         |
| Enterobacter cloacae |       Flurithromycin        |
| Enterobacter cloacae |        Fusidic acid         |
| Enterobacter cloacae |        Gamithromycin        |
| Enterobacter cloacae |          Josamycin          |
| Enterobacter cloacae |         Kitasamycin         |
| Enterobacter cloacae |         Lincomycin          |
| Enterobacter cloacae |          Linezolid          |
| Enterobacter cloacae |         Meleumycin          |
| Enterobacter cloacae |         Midecamycin         |
| Enterobacter cloacae |         Miocamycin          |
| Enterobacter cloacae |        Nafithromycin        |
| Enterobacter cloacae |        Norvancomycin        |
| Enterobacter cloacae |        Oleandomycin         |
| Enterobacter cloacae |         Oritavancin         |
| Enterobacter cloacae |        Ostreogrycin         |
| Enterobacter cloacae |         Pirlimycin          |
| Enterobacter cloacae |          Primycin           |
| Enterobacter cloacae |        Pristinamycin        |
| Enterobacter cloacae |  Quinupristin/dalfopristin  |
| Enterobacter cloacae |         Ramoplanin          |
| Enterobacter cloacae |         Rifampicin          |
| Enterobacter cloacae |         Rokitamycin         |
| Enterobacter cloacae |        Roxithromycin        |
| Enterobacter cloacae |        Solithromycin        |
| Enterobacter cloacae |         Spiramycin          |
| Enterobacter cloacae |          Tedizolid          |
| Enterobacter cloacae |         Teicoplanin         |
| Enterobacter cloacae |         Telavancin          |
| Enterobacter cloacae |        Telithromycin        |
| Enterobacter cloacae |        Thiacetazone         |
| Enterobacter cloacae |        Tildipirosin         |
| Enterobacter cloacae |         Tilmicosin          |
| Enterobacter cloacae |       Troleandomycin        |
| Enterobacter cloacae |        Tulathromycin        |
| Enterobacter cloacae |           Tylosin           |
| Enterobacter cloacae |         Tylvalosin          |
| Enterobacter cloacae |         Vancomycin          |
| Enterobacter cloacae |       Virginiamycine        |
| Enterobacter cloacae |         Zorbamycin          |

------------------------------------------------------------------------

## `dosage`: Dosage Guidelines from EUCAST

A data set with 759 rows and 9 columns, containing the following column
names:  
*ab*, *name*, *type*, *dose*, *dose_times*, *administration*, *notes*,
*original_txt*, and *eucast_version*.

This data set is in R available as `dosage`, after you load the `AMR`
package.

It was last updated on 20 April 2025 10:55:31 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/dosage.html).

**Direct download links:**

- Download as [original R Data Structure (RDS)
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.rds)
  (4 kB)  
- Download as [tab-separated text
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.txt)
  (66 kB)  
- Download as [Microsoft Excel
  workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.xlsx)
  (37 kB)  
- Download as [Apache Feather
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.feather)
  (28 kB)  
- Download as [Apache Parquet
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.parquet)
  (9 kB)  
- Download as [IBM SPSS Statistics data
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.sav)
  (97 kB)  
- Download as [Stata DTA
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/dosage.dta)
  (0.2 MB)

**Example content**

| ab | name | type | dose | dose_times | administration | notes | original_txt | eucast_version |
|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|
| AMK | Amikacin | standard_dosage | 25-30 mg/kg | 1 | iv |  | 25-30 mg/kg x 1 iv | 15 |
| AMX | Amoxicillin | high_dosage | 2 g | 6 | iv |  | 2 g x 6 iv | 15 |
| AMX | Amoxicillin | standard_dosage | 1 g | 3 | iv |  | 1 g x 3-4 iv | 15 |
| AMX | Amoxicillin | high_dosage | 0.75-1 g | 3 | oral |  | 0.75-1 g x 3 oral | 15 |
| AMX | Amoxicillin | standard_dosage | 0.5 g | 3 | oral |  | 0.5 g x 3 oral | 15 |
| AMX | Amoxicillin | uncomplicated_uti | 0.5 g | 3 | oral |  | 0.5 g x 3 oral | 15 |

------------------------------------------------------------------------

## `example_isolates`: Example Data for Practice

A data set with 2 000 rows and 46 columns, containing the following
column names:  
*date*, *patient*, *age*, *gender*, *ward*, *mo*, *PEN*, *OXA*, *FLC*,
*AMX*, *AMC*, *AMP*, *TZP*, *CZO*, *FEP*, *CXM*, *FOX*, *CTX*, *CAZ*,
*CRO*, *GEN*, *TOB*, *AMK*, *KAN*, *TMP*, *SXT*, *NIT*, *FOS*, *LNZ*,
*CIP*, *MFX*, *VAN*, *TEC*, *TCY*, *TGC*, *DOX*, *ERY*, *CLI*, *AZM*,
*IPM*, *MEM*, *MTR*, *CHL*, *COL*, *MUP*, and *RIF*.

This data set is in R available as `example_isolates`, after you load
the `AMR` package.

It was last updated on 24 June 2026 16:36:47 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/example_isolates.html).

**Example content**

| date | patient | age | gender | ward | mo | PEN | OXA | FLC | AMX | AMC | AMP | TZP | CZO | FEP | CXM | FOX | CTX | CAZ | CRO | GEN | TOB | AMK | KAN | TMP | SXT | NIT | FOS | LNZ | CIP | MFX | VAN | TEC | TCY | TGC | DOX | ERY | CLI | AZM | IPM | MEM | MTR | CHL | COL | MUP | RIF |
|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|
| 2002-01-02 | A77334 | 65 | F | Clinical | B_ESCHR_COLI | R |  |  |  | I |  |  |  |  | I |  |  |  |  |  |  |  |  | R | R |  |  | R |  |  | R | R | R |  |  | R | R | R |  |  |  |  |  |  | R |
| 2002-01-03 | A77334 | 65 | F | Clinical | B_ESCHR_COLI | R |  |  |  | I |  |  |  |  | I |  |  |  |  |  |  |  |  | R | R |  |  | R |  |  | R | R | R |  |  | R | R | R |  |  |  |  |  |  | R |
| 2002-01-07 | 067927 | 45 | F | ICU | B_STPHY_EPDR | R |  | R |  |  |  |  |  |  | R |  |  | R |  |  |  |  |  | S | S |  |  |  |  |  | S |  | S | S | S | R |  | R |  |  |  |  | R |  |  |
| 2002-01-07 | 067927 | 45 | F | ICU | B_STPHY_EPDR | R |  | R |  |  |  |  |  |  | R |  |  | R |  |  |  |  |  | S | S |  |  |  |  |  | S |  | S | S | S | R |  | R |  |  |  |  | R |  |  |
| 2002-01-13 | 067927 | 45 | F | ICU | B_STPHY_EPDR | R |  | R |  |  |  |  |  |  | R |  |  | R |  |  |  |  |  | R |  |  |  |  |  |  | S |  | S | S | S | R |  | R |  |  |  |  | R |  |  |
| 2002-01-13 | 067927 | 45 | F | ICU | B_STPHY_EPDR | R |  | R |  |  |  |  |  |  | R |  |  | R |  |  |  |  |  | R |  |  |  |  |  |  | S |  | S | S | S | R | R | R |  |  |  |  | R |  |  |

------------------------------------------------------------------------

## `example_isolates_unclean`: Example Data for Practice

A data set with 3 000 rows and 8 columns, containing the following
column names:  
*patient_id*, *hospital*, *date*, *bacteria*, *AMX*, *AMC*, *CIP*, and
*GEN*.

This data set is in R available as `example_isolates_unclean`, after you
load the `AMR` package.

It was last updated on 27 August 2022 18:49:37 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/example_isolates_unclean.html).

**Example content**

| patient_id | hospital |    date    |   bacteria    | AMX | AMC | CIP | GEN |
|:----------:|:--------:|:----------:|:-------------:|:---:|:---:|:---:|:---:|
|     J3     |    A     | 2012-11-21 |    E. coli    |  R  |  I  |  S  |  S  |
|     R7     |    A     | 2018-04-03 | K. pneumoniae |  R  |  I  |  S  |  S  |
|     P3     |    A     | 2014-09-19 |    E. coli    |  R  |  S  |  S  |  S  |
|    P10     |    A     | 2015-12-10 |    E. coli    |  S  |  I  |  S  |  S  |
|     B7     |    A     | 2015-03-02 |    E. coli    |  S  |  S  |  S  |  S  |
|     W3     |    A     | 2018-03-31 |   S. aureus   |  R  |  S  |  R  |  S  |

------------------------------------------------------------------------

## `microorganisms.codes`: Common Laboratory Codes

A data set with 6 029 rows and 2 columns, containing the following
column names:  
*code* and *mo*.

This data set is in R available as `microorganisms.codes`, after you
load the `AMR` package.

It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/microorganisms.codes.html).

**Direct download links:**

- Download as [original R Data Structure (RDS)
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.rds)
  (27 kB)  
- Download as [tab-separated text
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.txt)
  (0.1 MB)  
- Download as [Microsoft Excel
  workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.xlsx)
  (98 kB)  
- Download as [Apache Feather
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.feather)
  (0.1 MB)  
- Download as [Apache Parquet
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.parquet)
  (68 kB)  
- Download as [IBM SPSS Statistics data
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.sav)
  (0.2 MB)  
- Download as [Stata DTA
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.dta)
  (0.2 MB)

**Example content**

| code |      mo      |
|:----:|:------------:|
| 1011 |   B_GRAMP    |
| 1012 |   B_GRAMP    |
| 1013 |   B_GRAMN    |
| 1014 |   B_GRAMN    |
| 1015 |   F_YEAST    |
| 103  | B_ESCHR_COLI |

------------------------------------------------------------------------

## `antivirals`: Antiviral Drugs

A data set with 120 rows and 11 columns, containing the following column
names:  
*av*, *name*, *atc*, *cid*, *atc_group*, *synonyms*, *oral_ddd*,
*oral_units*, *iv_ddd*, *iv_units*, and *loinc*.

This data set is in R available as `antivirals`, after you load the
`AMR` package.

It was last updated on 20 October 2023 12:51:48 UTC. Find more info
about the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html).

**Direct download links:**

- Download as [original R Data Structure (RDS)
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.rds)
  (6 kB)  
- Download as [tab-separated text
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.txt)
  (17 kB)  
- Download as [Microsoft Excel
  workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.xlsx)
  (16 kB)  
- Download as [Apache Feather
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.feather)
  (16 kB)  
- Download as [Apache Parquet
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.parquet)
  (13 kB)  
- Download as [IBM SPSS Statistics data
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.sav)
  (32 kB)  
- Download as [Stata DTA
  file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antivirals.dta)
  (78 kB)

The tab-separated text, Microsoft Excel, SPSS, and Stata files all
contain the trade names and LOINC codes as comma separated values.

**Example content**

| av | name | atc | cid | atc_group | synonyms | oral_ddd | oral_units | iv_ddd | iv_units | loinc |
|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|:--:|
| ABA | Abacavir | J05AF06 | 441300 | Nucleoside and nucleotide reverse transcriptase inhibitors | abacavir sulfate, avacavir, ziagen | 0.6 | g |  |  | 29113-8, 30273-7, 30287-7, … |
| ACI | Aciclovir | J05AB01 | 135398513 | Nucleosides and nucleotides excl. reverse transcriptase inhibitors | acicloftal, aciclovier, aciclovirum, … | 4.0 | g | 4 | g |  |
| ADD | Adefovir dipivoxil | J05AF08 | 60871 | Nucleoside and nucleotide reverse transcriptase inhibitors | adefovir di, adefovir di ester, adefovir dipivoxyl, … | 10.0 | mg |  |  |  |
| AME | Amenamevir | J05AX26 | 11397521 | Other antivirals | amenalief | 0.4 | g |  |  |  |
| AMP | Amprenavir | J05AE05 | 65016 | Protease inhibitors | agenerase, carbamate, prozei | 1.2 | g |  |  | 29114-6, 30296-8, 30297-6, … |
| ASU | Asunaprevir | J05AP06 | 16076883 | Antivirals for treatment of HCV infections | sunvepra, sunvepratrade | 0.2 | g |  |  |  |
