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