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@@ -147,7 +147,7 @@ as comma separated values.
## `clinical_breakpoints`: Interpretation from MIC values & disk diameters to SIR
A data set with 40 217 rows and 14 columns, containing the following
A data set with 45 797 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
@@ -156,7 +156,7 @@ column names:
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
It was last updated on 30 March 2026 08:01:49 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).
@@ -164,36 +164,36 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
- Download as [original R Data Structure (RDS)
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.rds)
(88 kB)
(92 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt)
(3.7 MB)
(4.2 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.xlsx)
(2.4 MB)
(2.7 MB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.feather)
(1.8 MB)
(2 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)
(7.5 MB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.dta)
(11.1 MB)
(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 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 |
| 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 |
------------------------------------------------------------------------
@@ -460,22 +460,22 @@ here](https://amr-for-r.org/reference/example_isolates_unclean.html).
## `microorganisms.codes`: Common Laboratory Codes
A data set with 6 036 rows and 2 columns, containing the following
A data set with 6 050 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
It was last updated on 30 March 2026 08:01:49 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)
(28 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.txt)
(0.1 MB)
@@ -487,7 +487,7 @@ here](https://amr-for-r.org/reference/microorganisms.codes.html).
(0.1 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.parquet)
(68 kB)
(69 kB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.sav)
(0.2 MB)