mirror of
https://github.com/msberends/AMR.git
synced 2025-12-16 08:40:26 +01:00
Built site for AMR@3.0.1.9003: ba30b08
This commit is contained in:
github-actions
151
reference/WHONET.md
Normal file
151
reference/WHONET.md
Normal file
@@ -0,0 +1,151 @@
|
||||
# Data Set with 500 Isolates - WHONET Example
|
||||
|
||||
This example data set has the exact same structure as an export file
|
||||
from WHONET. Such files can be used with this package, as this example
|
||||
data set shows. The antimicrobial results are from our
|
||||
[example_isolates](https://amr-for-r.org/reference/example_isolates.md)
|
||||
data set. All patient names were created using online surname generators
|
||||
and are only in place for practice purposes.
|
||||
|
||||
## Usage
|
||||
|
||||
``` r
|
||||
WHONET
|
||||
```
|
||||
|
||||
## Format
|
||||
|
||||
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 500
|
||||
observations and 53 variables:
|
||||
|
||||
- `Identification number`
|
||||
ID of the sample
|
||||
|
||||
- `Specimen number`
|
||||
ID of the specimen
|
||||
|
||||
- `Organism`
|
||||
Name of the microorganism. Before analysis, you should transform this
|
||||
to a valid microbial class, using
|
||||
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md).
|
||||
|
||||
- `Country`
|
||||
Country of origin
|
||||
|
||||
- `Laboratory`
|
||||
Name of laboratory
|
||||
|
||||
- `Last name`
|
||||
Fictitious last name of patient
|
||||
|
||||
- `First name`
|
||||
Fictitious initial of patient
|
||||
|
||||
- `Sex`
|
||||
Fictitious gender of patient
|
||||
|
||||
- `Age`
|
||||
Fictitious age of patient
|
||||
|
||||
- `Age category`
|
||||
Age group, can also be looked up using
|
||||
[`age_groups()`](https://amr-for-r.org/reference/age_groups.md)
|
||||
|
||||
- `Date of admission`
|
||||
[Date](https://rdrr.io/r/base/Dates.html) of hospital admission
|
||||
|
||||
- `Specimen date`
|
||||
[Date](https://rdrr.io/r/base/Dates.html) when specimen was received
|
||||
at laboratory
|
||||
|
||||
- `Specimen type`
|
||||
Specimen type or group
|
||||
|
||||
- `Specimen type (Numeric)`
|
||||
Translation of `"Specimen type"`
|
||||
|
||||
- `Reason`
|
||||
Reason of request with Differential Diagnosis
|
||||
|
||||
- `Isolate number`
|
||||
ID of isolate
|
||||
|
||||
- `Organism type`
|
||||
Type of microorganism, can also be looked up using
|
||||
[`mo_type()`](https://amr-for-r.org/reference/mo_property.md)
|
||||
|
||||
- `Serotype`
|
||||
Serotype of microorganism
|
||||
|
||||
- `Beta-lactamase`
|
||||
Microorganism produces beta-lactamase?
|
||||
|
||||
- `ESBL`
|
||||
Microorganism produces extended spectrum beta-lactamase?
|
||||
|
||||
- `Carbapenemase`
|
||||
Microorganism produces carbapenemase?
|
||||
|
||||
- `MRSA screening test`
|
||||
Microorganism is possible MRSA?
|
||||
|
||||
- `Inducible clindamycin resistance`
|
||||
Clindamycin can be induced?
|
||||
|
||||
- `Comment`
|
||||
Other comments
|
||||
|
||||
- `Date of data entry`
|
||||
[Date](https://rdrr.io/r/base/Dates.html) this data was entered in
|
||||
WHONET
|
||||
|
||||
- `AMP_ND10:CIP_EE`
|
||||
28 different antimicrobials. You can lookup the abbreviations in the
|
||||
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
|
||||
data set, or use e.g.
|
||||
[`ab_name("AMP")`](https://amr-for-r.org/reference/ab_property.md) to
|
||||
get the official name immediately. Before analysis, you should
|
||||
transform this to a valid antimicrobial class, using
|
||||
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md).
|
||||
|
||||
## Download Our Reference Data
|
||||
|
||||
All reference data sets in the AMR package - including information on
|
||||
microorganisms, antimicrobials, and clinical breakpoints - are freely
|
||||
available for download in multiple formats: R, MS Excel, Apache Feather,
|
||||
Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable,
|
||||
tab-separated plain text files suitable for use in any software,
|
||||
including laboratory information systems.
|
||||
|
||||
Visit [our website for direct download
|
||||
links](https://amr-for-r.org/articles/datasets.html), or explore the
|
||||
actual files in [our GitHub
|
||||
repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
|
||||
|
||||
## Examples
|
||||
|
||||
``` r
|
||||
WHONET
|
||||
#> # A tibble: 500 × 53
|
||||
#> `Identification number` `Specimen number` Organism Country Laboratory
|
||||
#> <chr> <int> <chr> <chr> <chr>
|
||||
#> 1 fe41d7bafa 1748 SPN Belgium National …
|
||||
#> 2 91f175ec37 1767 eco The Netherlands National …
|
||||
#> 3 cc4015056e 1343 eco The Netherlands National …
|
||||
#> 4 e864b692f5 1894 MAP Denmark National …
|
||||
#> 5 3d051fe345 1739 PVU Belgium National …
|
||||
#> 6 c80762a08d 1846 103 The Netherlands National …
|
||||
#> 7 8022d3727c 1628 103 Denmark National …
|
||||
#> 8 f3dc5f553d 1493 eco The Netherlands National …
|
||||
#> 9 15add38f6c 1847 eco France National …
|
||||
#> 10 fd41248def 1458 eco Germany National …
|
||||
#> # ℹ 490 more rows
|
||||
#> # ℹ 48 more variables: `Last name` <chr>, `First name` <chr>, Sex <chr>,
|
||||
#> # Age <dbl>, `Age category` <chr>, `Date of admission` <date>,
|
||||
#> # `Specimen date` <date>, `Specimen type` <chr>,
|
||||
#> # `Specimen type (Numeric)` <dbl>, Reason <chr>, `Isolate number` <int>,
|
||||
#> # `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>,
|
||||
#> # Carbapenemase <lgl>, `MRSA screening test` <lgl>, …
|
||||
```
|
||||
Reference in New Issue
Block a user