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(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'

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dr. M.S. (Matthijs) Berends
2025-01-17 12:09:39 +01:00
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commit 92c4fc0f94
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@ -5,7 +5,7 @@
* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs, disk zones and ECOFFs
* Corrects for duplicate isolates, **calculates** and **predicts** AMR per antibiotic class
* Corrects for duplicate isolates, **calculates** and **predicts** AMR per antimicrobial class
* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI**
* 100% free of costs and dependencies, highly suitable for places with **limited resources**
@ -40,7 +40,7 @@ With the help of contributors from all corners of the world, the `AMR` package i
#### Filtering and selecting data
One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antibiotic columns. This can be done using the so-called [antibiotic class selectors](https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html) that work in base R, `dplyr` and `data.table`:
One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called [antimicrobial class selectors](https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html), which work in base R, `dplyr` and `data.table`:
```r
# AMR works great with dplyr, but it's not required or neccesary
@ -52,7 +52,7 @@ example_isolates %>%
# filtering functions for microorganisms:
filter(mo_is_gram_negative(),
mo_is_intrinsic_resistant(ab = "cefotax")) %>%
# antibiotic selectors:
# antimicrobial selectors:
select(bacteria,
aminoglycosides(),
carbapenems())
@ -162,7 +162,7 @@ example_isolates %>%
|ICU | 0.290 |0.253-0.330 | 0.400 |0.353-0.449 |
|Outpatient | 0.200 |0.131-0.285 | 0.368 |0.254-0.493 |
Or use [antibiotic class selectors](https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html) to select a series of antibiotic columns:
Or use [antimicrobial class selectors](https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html) to select a series of antibiotic columns:
```r
library(AMR)
@ -218,7 +218,7 @@ This package was intended as a comprehensive toolbox for integrated AMR data ana
* Calculating (empirical) susceptibility of both mono therapy and combination therapies ([tutorial](./articles/AMR.html))
* Predicting future antimicrobial resistance using regression models ([tutorial](./articles/resistance_predict.html))
* Getting properties for any microorganism (like Gram stain, species, genus or family) ([manual](./reference/mo_property.html))
* Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) ([manual](./reference/ab_property.html))
* Getting properties for any antimicrobial (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) ([manual](./reference/ab_property.html))
* Plotting antimicrobial resistance ([tutorial](./articles/AMR.html))
* Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
* Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](./reference/mo_property.html))