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71 lines
2.4 KiB
Markdown
71 lines
2.4 KiB
Markdown
# Data Set with Unclean Data
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A data set containing 3 000 microbial isolates that are not cleaned up
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and consequently not ready for AMR data analysis. This data set can be
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used for practice.
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## Usage
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``` r
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example_isolates_unclean
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```
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## Format
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A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 3
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000 observations and 8 variables:
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- `patient_id`
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ID of the patient
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- `date`
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date of receipt at the laboratory
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- `hospital`
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ID of the hospital, from A to C
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- `bacteria`
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info about microorganism that can be transformed with
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md), see also
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[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
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- `AMX:GEN`
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4 different antimicrobials that have to be transformed with
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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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example_isolates_unclean
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#> # A tibble: 3,000 × 8
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#> patient_id hospital date bacteria AMX AMC CIP GEN
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#> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr>
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#> 1 J3 A 2012-11-21 E. coli R I S S
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#> 2 R7 A 2018-04-03 K. pneumoniae R I S S
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#> 3 P3 A 2014-09-19 E. coli R S S S
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#> 4 P10 A 2015-12-10 E. coli S I S S
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#> 5 B7 A 2015-03-02 E. coli S S S S
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#> 6 W3 A 2018-03-31 S. aureus R S R S
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#> 7 J8 A 2016-06-14 E. coli R S S S
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#> 8 M3 A 2015-10-25 E. coli R S S S
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#> 9 J3 A 2019-06-19 E. coli S S S S
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#> 10 G6 A 2015-04-27 S. aureus S S S S
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#> # ℹ 2,990 more rows
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```
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