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dr. M.S. (Matthijs) Berends committed 2026-10-11 22:32:15 +02:00
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DESCRIPTION
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Package: AMR
Version: 3.0.1.9117
Version: 3.0.1.9118
Date: 2026-10-11
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
NEWS.md
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# AMR 3.0.1.9117
# AMR 3.0.1.9118
Planned as v3.1.0, mid October 2026.
R/sir_combine.R
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# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Combine SIR Results of Multiple Antimicrobials
#'
#' @description Combine the SIR results of two or more antimicrobials into one SIR result per isolate, e.g. to create a variable `TZP_GEN` for the combination therapy of piperacillin/tazobactam with gentamicin. The result is the best result of the antimicrobials, as a combination therapy covers the isolate if any of its antimicrobials is active. See *Combination Therapy* below for the exact rules.
#' @description Combine the SIR results of two or more antimicrobials into one SIR result per isolate, e.g. to create a variable for the combination therapy of piperacillin/tazobactam with gentamicin. The result is the best result of the antimicrobials, as a combination therapy covers the isolate if any of its antimicrobials is active. See *Combination Therapy* below for the exact rules.
#'
#' The same rules are used by [antibiogram()] and [wisca()] for combination antibiograms, and by the [`count_*()`][count()] and [`proportion_*()`][proportion()] functions when more than one variable is used, so the result of [sir_combine()] can be used in any further analysis.
#' @param ... Two or more vectors (or columns) with antimicrobial interpretations, or a data frame with such columns. They will be transformed internally with [as.sir()] if needed. All vectors must be of the same length.
#' @param only_all_tested A [logical] to indicate that isolates must be tested for all antimicrobials. If `TRUE`, the result is `NA` for isolates with a missing result for any of the antimicrobials. If `FALSE` (default), a missing result only leads to `NA` if a result for the missing antimicrobial could have changed the result of the combination, see *Combination Therapy* below.
#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`, to determine whether the 'I' category is considered susceptible. This only affects isolates with a missing result for any of the antimicrobials when `only_all_tested = FALSE`, see *Combination Therapy* below. The default can be changed with the `AMR_guideline` option, see [AMR-options].
#' @section Combination Therapy:
#' A combination of antimicrobials is considered as good as its most active antimicrobial. Results are ranked as follows, from best to worst:
#' A combination of antimicrobials is considered as good as its most active antimicrobial: `"S"` is preferred over `"WT"`, and `"R"` over `"NWT"` and `"NS"`. The value `"NI"` (non-interpretable) is considered a missing result.
#'
#' 1. `"S"` and `"WT"`
#' 2. `"SDD"`
#' 3. `"I"`
#' 4. `"R"`, `"NWT"`, and `"NS"`
#' A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the `only_all_tested` argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (*susceptible, increased exposure*), and under CLSI, it is not.
#'
#' The result of the combination is the best result of the antimicrobials, i.e., the result keeps its original category instead of being reduced to only S or R. If antimicrobials have an equally ranked result, `"S"` is preferred over `"WT"`, and `"R"` over `"NWT"` and `"NS"`. The value `"NI"` (non-interpretable) is considered a missing result.
#'
#' A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the `only_all_tested` argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (*susceptible, increased exposure*), and under CLSI, it is not. This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
#' This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
#'
#' ```
#' -------------------------------------------------------------------------
@@ -86,6 +80,7 @@
#' if (require("dplyr")) {
#' # create a new variable for piperacillin/tazobactam + gentamicin
#' example_isolates %>%
#' filter(!is.na(TZP)) %>%
#' mutate(TZP_GEN = sir_combine(TZP, GEN)) %>%
#' select(mo, TZP, GEN, TZP_GEN)
#' }
@@ -102,7 +97,10 @@
#' group_by(ward) %>%
#' summarise(
#' TZP = susceptibility(TZP),
#' TZP_GEN = susceptibility(TZP_GEN)
#' GEN = susceptibility(GEN),
#' TZP_GEN = susceptibility(TZP_GEN),
#' # or directly, without combining first:
#' TZP_GEN2 = susceptibility(TZP, GEN)
#' )
#' }
#' }
index.md
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#> ℹ Using column mo as input for `mo_fullname()`
#> ℹ Using column mo as input for `mo_is_gram_negative()`
#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
#> This note will be shown once per session.
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
#> (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
#> Resistant Phenotypes' v1.2 (2023). This note will be shown
#> once per session.
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
#> (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -251,7 +253,8 @@ for tracking resistance per species over time:
antibiogram(example_isolates,
mo_transform = "gramstain",
antimicrobials = c("AMC", carbapenems(), "TZP"))
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
#> (meropenem)
```
| Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
@@ -366,15 +369,16 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
#> (kanamycin)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
#> ℹ For `polymyxins()` using column COL (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()),
#> resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =
#> 30`).
#> ! Introducing NA: only 23 results available for KAN in group:
#> ward = "Outpatient" (whilst `minimum = 30`).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL
man/antibiogram.Rd
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\section{Combination Therapy}{
A combination of antimicrobials is considered as good as its most active antimicrobial. Results are ranked as follows, from best to worst:
\enumerate{
\item \code{"S"} and \code{"WT"}
\item \code{"SDD"}
\item \code{"I"}
\item \code{"R"}, \code{"NWT"}, and \code{"NS"}
}
A combination of antimicrobials is considered as good as its most active antimicrobial: \code{"S"} is preferred over \code{"WT"}, and \code{"R"} over \code{"NWT"} and \code{"NS"}. The value \code{"NI"} (non-interpretable) is considered a missing result.
The result of the combination is the best result of the antimicrobials, i.e., the result keeps its original category instead of being reduced to only S or R. If antimicrobials have an equally ranked result, \code{"S"} is preferred over \code{"WT"}, and \code{"R"} over \code{"NWT"} and \code{"NS"}. The value \code{"NI"} (non-interpretable) is considered a missing result.
A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the \code{only_all_tested} argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (\emph{susceptible, increased exposure}), and under CLSI, it is not.
A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the \code{only_all_tested} argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (\emph{susceptible, increased exposure}), and under CLSI, it is not. This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
\if{html}{\out{<div class="sourceCode">}}\preformatted{-------------------------------------------------------------------------
Result of the combination
man/count.Rd
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\section{Combination Therapy}{
A combination of antimicrobials is considered as good as its most active antimicrobial. Results are ranked as follows, from best to worst:
\enumerate{
\item \code{"S"} and \code{"WT"}
\item \code{"SDD"}
\item \code{"I"}
\item \code{"R"}, \code{"NWT"}, and \code{"NS"}
}
A combination of antimicrobials is considered as good as its most active antimicrobial: \code{"S"} is preferred over \code{"WT"}, and \code{"R"} over \code{"NWT"} and \code{"NS"}. The value \code{"NI"} (non-interpretable) is considered a missing result.
The result of the combination is the best result of the antimicrobials, i.e., the result keeps its original category instead of being reduced to only S or R. If antimicrobials have an equally ranked result, \code{"S"} is preferred over \code{"WT"}, and \code{"R"} over \code{"NWT"} and \code{"NS"}. The value \code{"NI"} (non-interpretable) is considered a missing result.
A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the \code{only_all_tested} argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (\emph{susceptible, increased exposure}), and under CLSI, it is not.
A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the \code{only_all_tested} argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (\emph{susceptible, increased exposure}), and under CLSI, it is not. This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
\if{html}{\out{<div class="sourceCode">}}\preformatted{-------------------------------------------------------------------------
Result of the combination
man/proportion.Rd
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@@ -135,17 +135,11 @@ This AMR package follows insight; use \code{\link[=susceptibility]{susceptibilit
\section{Combination Therapy}{
A combination of antimicrobials is considered as good as its most active antimicrobial. Results are ranked as follows, from best to worst:
\enumerate{
\item \code{"S"} and \code{"WT"}
\item \code{"SDD"}
\item \code{"I"}
\item \code{"R"}, \code{"NWT"}, and \code{"NS"}
}
A combination of antimicrobials is considered as good as its most active antimicrobial: \code{"S"} is preferred over \code{"WT"}, and \code{"R"} over \code{"NWT"} and \code{"NS"}. The value \code{"NI"} (non-interpretable) is considered a missing result.
The result of the combination is the best result of the antimicrobials, i.e., the result keeps its original category instead of being reduced to only S or R. If antimicrobials have an equally ranked result, \code{"S"} is preferred over \code{"WT"}, and \code{"R"} over \code{"NWT"} and \code{"NS"}. The value \code{"NI"} (non-interpretable) is considered a missing result.
A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the \code{only_all_tested} argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (\emph{susceptible, increased exposure}), and under CLSI, it is not.
A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the \code{only_all_tested} argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (\emph{susceptible, increased exposure}), and under CLSI, it is not. This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
\if{html}{\out{<div class="sourceCode">}}\preformatted{-------------------------------------------------------------------------
Result of the combination
man/sir_combine.Rd
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@@ -21,23 +21,17 @@ sir_combine(
A \code{\link{sir}} vector with the same length as the input.
}
\description{
Combine the SIR results of two or more antimicrobials into one SIR result per isolate, e.g. to create a variable \code{TZP_GEN} for the combination therapy of piperacillin/tazobactam with gentamicin. The result is the best result of the antimicrobials, as a combination therapy covers the isolate if any of its antimicrobials is active. See \emph{Combination Therapy} below for the exact rules.
Combine the SIR results of two or more antimicrobials into one SIR result per isolate, e.g. to create a variable for the combination therapy of piperacillin/tazobactam with gentamicin. The result is the best result of the antimicrobials, as a combination therapy covers the isolate if any of its antimicrobials is active. See \emph{Combination Therapy} below for the exact rules.
The same rules are used by \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}} for combination antibiograms, and by the \code{\link[=count]{count_*()}} and \code{\link[=proportion]{proportion_*()}} functions when more than one variable is used, so the result of \code{\link[=sir_combine]{sir_combine()}} can be used in any further analysis.
}
\section{Combination Therapy}{
A combination of antimicrobials is considered as good as its most active antimicrobial. Results are ranked as follows, from best to worst:
\enumerate{
\item \code{"S"} and \code{"WT"}
\item \code{"SDD"}
\item \code{"I"}
\item \code{"R"}, \code{"NWT"}, and \code{"NS"}
}
A combination of antimicrobials is considered as good as its most active antimicrobial: \code{"S"} is preferred over \code{"WT"}, and \code{"R"} over \code{"NWT"} and \code{"NS"}. The value \code{"NI"} (non-interpretable) is considered a missing result.
The result of the combination is the best result of the antimicrobials, i.e., the result keeps its original category instead of being reduced to only S or R. If antimicrobials have an equally ranked result, \code{"S"} is preferred over \code{"WT"}, and \code{"R"} over \code{"NWT"} and \code{"NS"}. The value \code{"NI"} (non-interpretable) is considered a missing result.
A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the \code{only_all_tested} argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (\emph{susceptible, increased exposure}), and under CLSI, it is not.
A missing result can only be ignored if the result of the combination is susceptible regardless of the missing result, which depends on the \code{only_all_tested} argument and on the guideline: under EUCAST, the 'I' category is considered susceptible (\emph{susceptible, increased exposure}), and under CLSI, it is not. This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
This is an example for two antimicrobials, Drug A and Drug B (the order of the antimicrobials does not matter):
\if{html}{\out{<div class="sourceCode">}}\preformatted{-------------------------------------------------------------------------
Result of the combination
@@ -75,6 +69,7 @@ susceptibility(sir_combine(drug_a, drug_b), minimum = 0)
if (require("dplyr")) {
# create a new variable for piperacillin/tazobactam + gentamicin
example_isolates \%>\%
filter(!is.na(TZP)) \%>\%
mutate(TZP_GEN = sir_combine(TZP, GEN)) \%>\%
select(mo, TZP, GEN, TZP_GEN)
}
@@ -91,7 +86,10 @@ if (require("dplyr")) {
group_by(ward) \%>\%
summarise(
TZP = susceptibility(TZP),
TZP_GEN = susceptibility(TZP_GEN)
GEN = susceptibility(GEN),
TZP_GEN = susceptibility(TZP_GEN),
# or directly, without combining first:
TZP_GEN2 = susceptibility(TZP, GEN)
)
}
}