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reference/index.md
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@@ -116,7 +116,7 @@ from clinical text records, using
[`clear_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md)
: Add Custom Antimicrobials
## Preparing data: antimicrobial results
## Interpreting data: antimicrobial results
With [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and
[`as.disk()`](https://amr-for-r.org/reference/as.disk.md) you can
@@ -125,10 +125,10 @@ transform your raw input to valid MIC or disk diffusion values. Use
data to let it only contain “R”, “I” and “S”, or to interpret MIC or
disk diffusion values as SIR based on the lastest EUCAST and CLSI
guidelines. Afterwards, you can extend antibiotic interpretations by
applying [EUCAST
rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/)
applying interpretive rules, for example [from
EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/)
with
[`eucast_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
[`NA_sir_`](https://amr-for-r.org/reference/as.sir.md)
@@ -153,8 +153,8 @@ with
[`clsi_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
[`eucast_dosage()`](https://amr-for-r.org/reference/interpretive_rules.md)
: Apply Interpretive Rules
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md)
: Define Custom EUCAST Rules
- [`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md)
: Define Custom Interpretive Rules
## Analysing data
@@ -465,8 +465,8 @@ and other utilities. Especially the ‘like’ function can be useful:
## Other: statistical tests
Some statistical tests or methods are not part of base R and were added
to this package for convenience.
Some statistical tests or methods usable for AMR analyses are not part
of base R and were added to this package for convenience.
- [`g.test()`](https://amr-for-r.org/reference/g.test.md) :
@@ -483,6 +483,7 @@ to this package for convenience.
These objects are deprecated, meaning that they will still work but show
a warning that they will be removed in a future version.
- [`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md)
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md)
[`ab_class()`](https://amr-for-r.org/reference/AMR-deprecated.md)
[`ab_selector()`](https://amr-for-r.org/reference/AMR-deprecated.md) :
Deprecated Functions, Arguments, or Datasets