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@@ -15,44 +15,44 @@ laboratory information systems.
## `microorganisms`: Full Microbial Taxonomy
A data set with 78 679 rows and 26 columns, containing the following
A data set with 96 982 rows and 28 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*.
*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 18 September 2025 12:58:34 UTC. Find more info
about the contents, (scientific) source, and structure of this [data set
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)
(1.8 MB)
(2.2 MB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.txt)
(17.7 MB)
(23.1 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.xlsx)
(8.8 MB)
(11.4 MB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.feather)
(8.4 MB)
(11 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.parquet)
(3.8 MB)
(4.6 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.sav)
(28.4 MB)
(35.2 MB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.dta)
(89.5 MB)
(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
@@ -69,23 +69,23 @@ 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 |
| | 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 | 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 | |
| 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 | |
------------------------------------------------------------------------
@@ -100,8 +100,8 @@ names:
This data set is in R available as `antimicrobials`, after you load the
`AMR` package.
It was last updated on 2 May 2026 12:56:26 UTC. Find more info about the
contents, (scientific) source, and structure of this [data set
It was last updated on 23 June 2026 12:38:59 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:**
@@ -147,7 +147,7 @@ as comma separated values.
## `clinical_breakpoints`: Interpretation from MIC values & disk diameters to SIR
A data set with 45 730 rows and 14 columns, containing the following
A data set with 45 555 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 2 April 2026 09:42:19 UTC. Find more info about
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/clinical_breakpoints.html).
@@ -176,7 +176,7 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
(2 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet)
(0.2 MB)
(0.1 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav)
(7.5 MB)
@@ -199,14 +199,14 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
## `microorganisms.groups`: Species Groups and Microbiological Complexes
A data set with 534 rows and 4 columns, containing the following column
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 26 March 2025 16:19:17 UTC. Find more info about
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).
@@ -220,7 +220,7 @@ here](https://amr-for-r.org/reference/microorganisms.groups.html).
(50 kB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.xlsx)
(20 kB)
(19 kB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.feather)
(19 kB)
@@ -229,10 +229,10 @@ here](https://amr-for-r.org/reference/microorganisms.groups.html).
(13 kB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.sav)
(65 kB)
(64 kB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.groups.dta)
(83 kB)
(82 kB)
**Example content**
@@ -249,14 +249,14 @@ here](https://amr-for-r.org/reference/microorganisms.groups.html).
## `intrinsic_resistant`: Intrinsic Bacterial Resistance
A data set with 285 928 rows and 2 columns, containing the following
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 April 2026 06:16:44 UTC. Find more info about
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).
@@ -267,10 +267,10 @@ here](https://amr-for-r.org/reference/intrinsic_resistant.html).
(0.1 MB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.txt)
(10.6 MB)
(10.9 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.xlsx)
(3.3 MB)
(3.1 MB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.feather)
(2.5 MB)
@@ -279,10 +279,10 @@ here](https://amr-for-r.org/reference/intrinsic_resistant.html).
(0.3 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.sav)
(15.5 MB)
(16 MB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.dta)
(27.5 MB)
(28.6 MB)
**Example content**
@@ -464,14 +464,14 @@ here](https://amr-for-r.org/reference/example_isolates_unclean.html).
## `microorganisms.codes`: Common Laboratory Codes
A data set with 6 050 rows and 2 columns, containing the following
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 30 March 2026 08:01:49 UTC. Find more info about
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).
@@ -479,7 +479,7 @@ here](https://amr-for-r.org/reference/microorganisms.codes.html).
- Download as [original R Data Structure (RDS)
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.rds)
(28 kB)
(27 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/microorganisms.codes.txt)
(0.1 MB)
@@ -491,7 +491,7 @@ 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)
(69 kB)
(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)