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