# 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 | | | |