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# 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 78 679 rows and 26 columns, containing the following
column names:
*mo*, *fullname*, *status*, *kingdom*, *phylum*, *class*, *order*,
*family*, *genus*, *species*, *subspecies*, *rank*, *ref*,
*oxygen_tolerance*, *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 18 September 2025 12:58:34 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)
(1.8 MB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.txt)
(17.7 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.xlsx)
(8.8 MB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.feather)
(8.4 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.parquet)
(3.8 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.sav)
(28.4 MB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.dta)
(89.5 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 |
|:-----------------:|:----------------------:|
| (unknown kingdom) | 1 |
| Animalia | 1 628 |
| Archaea | 1 419 |
| Bacteria | 39 249 |
| Chromista | 178 |
| Fungi | 28 137 |
First 6 rows when filtering on genus *Escherichia*:
| mo | fullname | status | kingdom | phylum | class | order | family | genus | species | subspecies | rank | ref | oxygen_tolerance | 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 | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | | | genus | Castellani et al., 1919 | facultative anaerobe | LPSN | 515602 | 482 | | | | | | 11158430 | | 1 | 407310004, 407251000, 407281008, … |
| B_ESCHR_ADCR | Escherichia adecarboxylata | synonym | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | adecarboxylata | | species | Leclerc, 1962 | likely facultative anaerobe | LPSN | 776052 | 515602 | 777447 | | | | | | | 1 | |
| B_ESCHR_ALBR | Escherichia albertii | accepted | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | albertii | | species | Huys et al., 2003 | facultative anaerobe | LPSN | 776053 | 515602 | | | | | 5427575 | | | 1 | 419388003 |
| B_ESCHR_BLTT | Escherichia blattae | synonym | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | blattae | | species | Burgess et al., 1973 | likely facultative anaerobe | LPSN | 776056 | 515602 | 788468 | | | | | | | 1 | |
| B_ESCHR_COLI | Escherichia coli | accepted | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | coli | | species | Castellani et al., 1919 | facultative anaerobe | LPSN | 776057 | 515602 | | | | | 11286021 | | | 1 | 1095001000112106, 715307006, 737528008, … |
| B_ESCHR_COLI_COLI | Escherichia coli coli | accepted | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | coli | coli | subspecies | | | GBIF | | 776057 | | | | | 12233256 | 11286021 | | 1 | |
------------------------------------------------------------------------
## `antimicrobials`: Antibiotic and Antifungal Drugs
A data set with 498 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 24 November 2025 10:24:02 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)
(45 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)
(78 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)
(0.1 MB)
- 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 | Beta-lactams/penicillins | 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 | Beta-lactams/penicillins | 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 | Beta-lactams/penicillins | 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/lincosamides | 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 | Beta-lactams/penicillins | 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 40 217 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 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/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)
(88 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt)
(3.7 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.xlsx)
(2.4 MB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.feather)
(1.8 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet)
(0.1 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav)
(6.6 MB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.dta)
(11.1 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 2025 | human | human | DISK | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | 10 mcg | 26.000 | 20.000 | FALSE | FALSE |
| EUCAST 2025 | human | human | MIC | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | | 1.000 | 4.000 | FALSE | FALSE |
| EUCAST 2025 | 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 2025 | human | human | MIC | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans | | 0.125 | 0.125 | FALSE | FALSE |
| EUCAST 2025 | human | human | DISK | | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans | 30/6 mcg | 26.000 | 26.000 | FALSE | FALSE |
| EUCAST 2025 | 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 534 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 26 March 2025 16:19:17 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)
(20 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)
(65 kB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.dta)
(83 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 271 905 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 28 March 2025 10:17:49 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)
(10.1 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.xlsx)
(2.9 MB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.feather)
(2.3 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)
(14.8 MB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.dta)
(22.6 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 | Pirlimycin |
| 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 |
------------------------------------------------------------------------
## `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 15 June 2024 13:33:49 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 6 036 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 4 May 2025 16:50:25 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 | | | |
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