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mirror of https://github.com/msberends/AMR.git synced 2025-07-10 20:21:52 +02:00

use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

This commit is contained in:
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions

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@ -78,6 +78,9 @@ navbar:
- text: "Conduct AMR Analysis"
icon: "fa-directions"
href: "articles/AMR.html"
- text: "Generate Antibiogram (Trad./Syndromic/WISCA)"
icon: "fa-file-prescription"
href: "reference/antibiogram.html" # reference instead of an article
- text: "Predict Antimicrobial Resistance"
icon: "fa-dice"
href: "articles/resistance_predict.html"
@ -161,9 +164,12 @@ reference:
- title: "Analysing data: antimicrobial resistance"
desc: >
Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column.
With `antibiogram()`, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination
antibiogram(WISCA). This function also comes with support for R Markdown and Quarto.
Be sure to first select the isolates that are appropiate for analysis, by using `first_isolate()` or `is_new_episode()`.
You can also filter your data on certain resistance in certain antibiotic classes (`carbapenems()`, `aminoglycosides()`), or determine multi-drug resistant microorganisms (MDRO, `mdro()`).
contents:
- "`antibiogram`"
- "`proportion`"
- "`count`"
- "`is_new_episode`"