P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-02-10 03:52:56 +01:00
Code Releases Activity

Built site for AMR@3.0.1.9020: 499c830

Browse Source
This commit is contained in:
github-actions
2026-02-09 12:53:52 +00:00
parent 8b71d0eb99
commit c149bb1f65
92 changed files with 154 additions and 22838 deletions
Download Patch File Download Diff File Expand all files Collapse all files

28
reference/interpretive_rules.md
View File

@@ -22,19 +22,21 @@ at default, see *Details*.
## Usage
``` r
interpretive_rules(x, col_mo = NULL, guideline = getOption("AMR_guideline",
"EUCAST"), info = interactive(),
interpretive_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), verbose = FALSE, version_breakpoints = 15,
"expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"),
verbose = FALSE, version_breakpoints = 15,
version_expected_phenotypes = 1.2, version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
custom_rules = NULL, overwrite = FALSE, ...)
eucast_rules(x, rules = getOption("AMR_interpretive_rules", default =
c("breakpoints", "expected_phenotypes")), ...)
eucast_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
clsi_rules(x, rules = getOption("AMR_interpretive_rules", default =
c("breakpoints", "expected_phenotypes")), ...)
clsi_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
```
@@ -87,12 +89,6 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
[`mo`](https://amr-for-r.org/reference/as.mo.md). Values will be
coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md).
- guideline:
A guideline name, either "EUCAST" (default) or "CLSI". This can be set
with the package option
[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
- info:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
@@ -113,6 +109,12 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
created with
[`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md).
- guideline:
A guideline name, either "EUCAST" (default) or "CLSI". This can be set
with the package option
[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
- verbose:
A [logical](https://rdrr.io/r/base/logical.html) to turn Verbose mode