proportion_SI()
our_data_1st %>% resistance(AMX) +#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I' +#> category susceptible. Set the `guideline` argument or the `AMR_guideline` +#> option to either "CLSI" or "EUCAST", see `?AMR-options`. +#> ℹ This message will be shown once per session. #> [1] 0.4294272
Or can be used in conjunction with group_by() and summarise(), both from the dplyr package:
group_by()
summarise()
dplyr
# our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example -data %>% freq(AMC_ND2)
Frequency table
Class: factor > ordered > sir (numeric) Length: 500 diff --git a/articles/WHONET.md b/articles/WHONET.md index 0f07eabf7..21b8030f4 100644 --- a/articles/WHONET.md +++ b/articles/WHONET.md @@ -101,6 +101,10 @@ Longest: 40 # our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example data %>% freq(AMC_ND2) +#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the +#> 'I' category susceptible. Set the `guideline` argument or the +#> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`. +#> ℹ This message will be shown once per session. ``` **Frequency table** diff --git a/articles/WISCA.html b/articles/WISCA.html index 7c560e4f7..b9277f717 100644 --- a/articles/WISCA.html +++ b/articles/WISCA.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/articles/datasets.html b/articles/datasets.html index c042f62cf..d9fe441a1 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -30,7 +30,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 @@ -80,7 +80,7 @@ Download data sets for download / own use - 09 February 2026 + 12 February 2026 Source: vignettes/datasets.Rmd datasets.Rmd diff --git a/articles/index.html b/articles/index.html index db5661530..f51b0be64 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/authors.html b/authors.html index ed22aa49d..6745f62fe 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/index.html b/index.html index ba7f3c3b8..4bd215260 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/news/index.html b/news/index.html index 22bdf3f7a..6007ca31a 100644 --- a/news/index.html +++ b/news/index.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 @@ -49,9 +49,9 @@ -AMR 3.0.1.9020 +AMR 3.0.1.9021 -New +New Integration with the tidymodels framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via recipes step_mic_log2() to transform <mic> columns with log2, and step_sir_numeric() to convert <sir> columns to numeric @@ -83,17 +83,19 @@ -Fixes +Fixes Fixed a bug in antibiogram() for when no antimicrobials are set -Fixed a bug in as.sir() where for numeric input the arguments S, i, and R would not be considered (#244) +Fixed a bug in as.sir() where for numeric input the arguments S, I, and R would not be considered (#244) Fixed some foreign translations of antimicrobial drugs Fixed a bug for printing column names to the console when using mutate_at(vars(...), as.mic) (#249) Fixed a bug to disregard NI for susceptibility proportion functions Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256) -Updates +Updates +susceptibility() and resistance() gained the argument guideline, which defaults to EUCAST, for interpreting the ‘I’ category correctly. + as.mic() and rescale_mic() gained the argument round_to_next_log2, which can be set to TRUE to round all values up to the nearest next log2 level (#255) antimicrobials$group is now a list instead of a character, to contain any group the drug is in (#246) diff --git a/news/index.md b/news/index.md index 71368577a..b75f2580f 100644 --- a/news/index.md +++ b/news/index.md @@ -1,6 +1,6 @@ # Changelog -## AMR 3.0.1.9020 +## AMR 3.0.1.9021 #### New @@ -45,7 +45,7 @@ [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) for when no antimicrobials are set - Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) - where for numeric input the arguments `S`, `i`, and `R` would not be + where for numeric input the arguments `S`, `I`, and `R` would not be considered ([\#244](https://github.com/msberends/AMR/issues/244)) - Fixed some foreign translations of antimicrobial drugs - Fixed a bug for printing column names to the console when using @@ -58,6 +58,10 @@ #### Updates +- [`susceptibility()`](https://amr-for-r.org/reference/proportion.md) + and [`resistance()`](https://amr-for-r.org/reference/proportion.md) + gained the argument `guideline`, which defaults to EUCAST, for + interpreting the ‘I’ category correctly. - [`as.mic()`](https://amr-for-r.org/reference/as.mic.md) and [`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md) gained the argument `round_to_next_log2`, which can be set to `TRUE` to round diff --git a/pkgdown.yml b/pkgdown.yml index e30d0b1e8..49fb6eaf4 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -10,7 +10,7 @@ articles: PCA: PCA.html WHONET: WHONET.html WISCA: WISCA.html -last_built: 2026-02-09T12:49Z +last_built: 2026-02-12T19:40Z urls: reference: https://amr-for-r.org/reference article: https://amr-for-r.org/articles diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html index 5464c08e8..c9c3fc4a8 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 05f0b6321..60a14d25b 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -1,5 +1,7 @@ -Options for the AMR package — AMR-options • AMR (for R) +Options for the AMR package — AMR-options • AMR (for R) Skip to contents @@ -7,7 +9,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 @@ -50,12 +52,13 @@ - This is an overview of all the package-specific options() you can set in the AMR package. + This is an overview of all the package-specific options you can set in the AMR package. Set them using the options() function, e.g.: +options(AMR_guideline = "CLSI") - Options + Options (alphabetical order) AMR_antibiogram_formatting_type A numeric (1-22) to use in antibiogram(), to indicate which formatting type to use. @@ -65,6 +68,11 @@ AMR_custom_ab A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in add_custom_antimicrobials(). AMR_custom_mo A file location to an RDS file, to use custom microorganisms with this package. This is explained in add_custom_microorganisms(). AMR_eucastrules A character to set the default types of rules for eucast_rules() function, must be one or more of: "breakpoints", "expert", "other", "custom", "all", and defaults to c("breakpoints", "expert"). +AMR_guideline A character to set the default guideline used throughout the AMR package wherever a guideline argument is available. This option is used as the default in e.g. as.sir(), resistance(), susceptibility(), interpretive_rules() and many plotting functions. While unset, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).For as.sir(), this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., "CLSI" or "EUCAST") or the name including a year (e.g., "CLSI 2019"). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025. +For resistance() and susceptibility(), this setting determines how the "I" (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, "I" is considered resistant in susceptibility calculations; under EUCAST, "I" is considered susceptible in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates. +For interpretive_rules(), this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI. +For many plotting functions (e.g., for MIC or disk diffusion values), supplying mo and ab enables automatic SIR-based interpretative colouring. These colours are derived from as.sir() in the background and therefore depend on the active guideline setting, which again uses EUCAST 2025 if not set explicitly. + AMR_guideline A character to set the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default to the latest implemented EUCAST guideline, currently "EUCAST 2025". Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025). AMR_ignore_pattern A regular expression to ignore (i.e., make NA) any match given in as.mo() and all mo_* functions. AMR_include_PKPD A logical to use in as.sir(), to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is TRUE. @@ -87,7 +95,7 @@ Share Options Within Team -For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings. +For a more collaborative approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings. For each user, open the .Rprofile file using utils::file.edit("~/.Rprofile") and put in there: source("X:/team_folder/R_options.R") Reload R/RStudio and check the settings with getOption(), e.g. getOption("AMR_locale") if you have set that value. diff --git a/reference/AMR-options.md b/reference/AMR-options.md index fefe51e94..6b20bfefb 100644 --- a/reference/AMR-options.md +++ b/reference/AMR-options.md @@ -1,10 +1,12 @@ # Options for the AMR package -This is an overview of all the package-specific -[`options()`](https://rdrr.io/r/base/options.html) you can set in the -`AMR` package. +This is an overview of all the package-specific options you can set in +the `AMR` package. Set them using the +[`options()`](https://rdrr.io/r/base/options.html) function, e.g.: -## Options +`options(AMR_guideline = "CLSI")` + +## Options (alphabetical order) - `AMR_antibiogram_formatting_type` A [numeric](https://rdrr.io/r/base/numeric.html) (1-22) to use in @@ -52,6 +54,46 @@ This is an overview of all the package-specific `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. +- `AMR_guideline` + A [character](https://rdrr.io/r/base/character.html) to set the + default guideline used throughout the `AMR` package wherever a + `guideline` argument is available. This option is used as the default + in e.g. [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), + [`resistance()`](https://amr-for-r.org/reference/proportion.md), + [`susceptibility()`](https://amr-for-r.org/reference/proportion.md), + [`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md) + and many plotting functions. **While unset**, the AMR package uses the + latest implemented EUCAST guideline (currently EUCAST 2025). + + - For [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), this + determines which clinical breakpoint guideline is used to interpret + MIC values and disk diffusion diameters. It can be either the + guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including + a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST 2011 + to 2025, and CLSI 2011 to 2025. + + - For [`resistance()`](https://amr-for-r.org/reference/proportion.md) + and + [`susceptibility()`](https://amr-for-r.org/reference/proportion.md), + this setting determines how the `"I"` (Intermediate / Increased + exposure) category is handled in calculations. Under CLSI, `"I"` is + considered *resistant* in susceptibility calculations; under EUCAST, + `"I"` is considered *susceptible* in susceptibility calculations. + Explicitly setting this option ensures reproducible AMR proportion + estimates. + + - For + [`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md), + this determines which guideline-specific interpretive (expert) rules + are applied to antimicrobial test results, either EUCAST or CLSI. + + - For many plotting functions (e.g., for MIC or disk diffusion + values), supplying `mo` and `ab` enables automatic SIR-based + interpretative colouring. These colours are derived from + [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the + background and therefore depend on the active `guideline` setting, + which again uses EUCAST 2025 if not set explicitly. + - `AMR_guideline` A [character](https://rdrr.io/r/base/character.html) to set the default guideline for interpreting MIC values and disk diffusion @@ -132,10 +174,10 @@ rules when interpreting MIC values with ### Share Options Within Team -For a more global approach, e.g. within a (data) team, save an options -file to a remote file location, such as a shared network drive, and have -each user read in this file automatically at start-up. This would work -in this way: +For a more collaborative approach, e.g. within a (data) team, save an +options file to a remote file location, such as a shared network drive, +and have each user read in this file automatically at start-up. This +would work in this way: 1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings. diff --git a/reference/AMR.html b/reference/AMR.html index ba06b276f..c73acdad1 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/reference/WHOCC.html b/reference/WHOCC.html index cc0c461a3..3bd4c3d61 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/reference/WHONET.html b/reference/WHONET.html index 27a8bce29..c209b41ba 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index b05d13c54..2f87cb109 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/reference/ab_property.html b/reference/ab_property.html index c2968a82b..f8b8e8919 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 911da88d8..34265352c 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html index d4d05e5a5..d445256c8 100644 --- a/reference/add_custom_microorganisms.html +++ b/reference/add_custom_microorganisms.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 diff --git a/reference/age.html b/reference/age.html index 84846c011..a6670075c 100644 --- a/reference/age.html +++ b/reference/age.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9020 + 3.0.1.9021 @@ -112,16 +112,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1980-02-27 45 45.95068 19 -#> 2 1953-07-26 72 72.54247 46 -#> 3 1949-09-02 76 76.43836 50 -#> 4 1986-08-03 39 39.52055 13 -#> 5 1932-11-19 93 93.22466 67 -#> 6 1949-03-30 76 76.86575 50 -#> 7 1996-06-23 29 29.63288 3 -#> 8 1963-09-16 62 62.40000 36 -#> 9 1952-05-16 73 73.73699 47 -#> 10 1952-11-14 73 73.23836 47 +#> 1 1980-02-27 45 45.95890 19 +#> 2 1953-07-26 72 72.55068 46 +#> 3 1949-09-02 76 76.44658 50 +#> 4 1986-08-03 39 39.52877 13 +#> 5 1932-11-19 93 93.23288 67 +#> 6 1949-03-30 76 76.87397 50 +#> 7 1996-06-23 29 29.64110 3 +#> 8 1963-09-16 62 62.40822 36 +#> 9 1952-05-16 73 73.74521 47 +#> 10 1952-11-14 73 73.24658 47
vignettes/datasets.Rmd
datasets.Rmd
recipes
step_mic_log2()
<mic>
step_sir_numeric()
<sir>
antibiogram()
as.sir()
S
i
R
I
mutate_at(vars(...), as.mic)
NI
susceptibility()
resistance()
guideline
as.mic()
rescale_mic()
round_to_next_log2
TRUE
antimicrobials$group
list
character
This is an overview of all the package-specific options() you can set in the AMR package.
options()
AMR
This is an overview of all the package-specific options you can set in the AMR package. Set them using the options() function, e.g.:
options(AMR_guideline = "CLSI")
AMR_antibiogram_formatting_type A numeric (1-22) to use in antibiogram(), to indicate which formatting type to use.
AMR_antibiogram_formatting_type
AMR_custom_ab A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in add_custom_antimicrobials().
AMR_custom_ab
add_custom_antimicrobials()
AMR_custom_mo A file location to an RDS file, to use custom microorganisms with this package. This is explained in add_custom_microorganisms().
AMR_custom_mo
add_custom_microorganisms()
AMR_eucastrules A character to set the default types of rules for eucast_rules() function, must be one or more of: "breakpoints", "expert", "other", "custom", "all", and defaults to c("breakpoints", "expert").
AMR_eucastrules
eucast_rules()
"breakpoints"
"expert"
"other"
"custom"
"all"
c("breakpoints", "expert")
AMR_guideline A character to set the default guideline used throughout the AMR package wherever a guideline argument is available. This option is used as the default in e.g. as.sir(), resistance(), susceptibility(), interpretive_rules() and many plotting functions. While unset, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).
AMR_guideline
interpretive_rules()
For as.sir(), this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., "CLSI" or "EUCAST") or the name including a year (e.g., "CLSI 2019"). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025.
"CLSI"
"EUCAST"
"CLSI 2019"
For resistance() and susceptibility(), this setting determines how the "I" (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, "I" is considered resistant in susceptibility calculations; under EUCAST, "I" is considered susceptible in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
"I"
For interpretive_rules(), this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.
For many plotting functions (e.g., for MIC or disk diffusion values), supplying mo and ab enables automatic SIR-based interpretative colouring. These colours are derived from as.sir() in the background and therefore depend on the active guideline setting, which again uses EUCAST 2025 if not set explicitly.
mo
ab
AMR_guideline A character to set the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default to the latest implemented EUCAST guideline, currently "EUCAST 2025". Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).
"EUCAST 2025"
AMR_ignore_pattern A regular expression to ignore (i.e., make NA) any match given in as.mo() and all mo_* functions.
AMR_ignore_pattern
NA
as.mo()
mo_*
AMR_include_PKPD A logical to use in as.sir(), to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is TRUE.
AMR_include_PKPD
For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
For a more collaborative approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
For each user, open the .Rprofile file using utils::file.edit("~/.Rprofile") and put in there:
.Rprofile
utils::file.edit("~/.Rprofile")
source("X:/team_folder/R_options.R")
Reload R/RStudio and check the settings with getOption(), e.g. getOption("AMR_locale") if you have set that value.
getOption()
getOption("AMR_locale")