mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
- verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
+ verbose = FALSE, only_sir_columns = any(is.sir(x)),
+ infer_from_combinations = TRUE, ...)
brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
@@ -82,7 +83,7 @@
guideline
-A specific guideline to follow, see sections Supported international / national guidelines and Using Custom Guidelines below. When left empty, the publication by Magiorakos et al. (see below) will be followed.
+A specific guideline to follow, see sections Supported International / National Guidelines and Using Custom Guidelines below. When left empty, the publication by Magiorakos et al. (see below) will be followed.
col_mo
@@ -133,6 +134,10 @@
A logical to indicate whether only antimicrobial columns must be included that were transformed to class sir on beforehand. Defaults to FALSE if no columns of x have a class sir.
+infer_from_combinations
+A logical to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does not imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to TRUE.
+
+
...
Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; guess_ab_col() will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. AMX = "amoxicillin". To skip a specific antimicrobial, set it to NULL, e.g. TIC = NULL to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.
diff --git a/reference/mdro.md b/reference/mdro.md
index 871d9e516..3e7433502 100644
--- a/reference/mdro.md
+++ b/reference/mdro.md
@@ -9,7 +9,8 @@ according to international, national, or custom guidelines.
mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
- verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
+ verbose = FALSE, only_sir_columns = any(is.sir(x)),
+ infer_from_combinations = TRUE, ...)
brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
@@ -34,8 +35,8 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
- guideline:
- A specific guideline to follow, see sections *Supported international
- / national guidelines* and *Using Custom Guidelines* below. When left
+ A specific guideline to follow, see sections *Supported International
+ / National Guidelines* and *Using Custom Guidelines* below. When left
empty, the publication by Magiorakos *et al.* (see below) will be
followed.
@@ -125,6 +126,18 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
Defaults to `FALSE` if no columns of `x` have a class
[sir](https://amr-for-r.org/reference/as.sir.md).
+- infer_from_combinations:
+
+ A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
+ resistance for a missing base beta-lactam drug should be inferred from
+ an available drug+inhibitor combination (e.g., piperacillin from
+ piperacillin/tazobactam). The clinical basis is that resistance in a
+ combination always implies resistance in the base drug, since the
+ enzyme inhibitor provides no benefit when the organism is truly
+ resistant. Only resistance is inferred; susceptibility in a
+ combination does **not** imply susceptibility in the base drug (the
+ inhibitor may be responsible). Defaults to `TRUE`.
+
- ...:
Column names of antimicrobials. To automatically detect antimicrobial
diff --git a/reference/mean_amr_distance.html b/reference/mean_amr_distance.html
index be9b8357c..2de600dd5 100644
--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@@ -7,7 +7,7 @@
AMR (for R)
- 3.0.1.9030
+ 3.0.1.9031