diff --git a/404.html b/404.html index d5b7f7ef6..cb6d714ef 100644 --- a/404.html +++ b/404.html @@ -31,7 +31,7 @@ AMR (for R) - 3.0.1.9018 + 3.0.1.9019 - - - - - -
-
-
-

Apply EUCAST Rules

- Source: R/eucast_rules.R -
eucast_rules.Rd
-
- -
-

Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://www.eucast.org), see Source. Use eucast_dosage() to get a data.frame with advised dosages of a certain bug-drug combination, which is based on the dosage data set.

-

To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.

-
- -
-

Usage

- 
eucast_rules(x, col_mo = NULL, info = interactive(),
-  rules = getOption("AMR_eucastrules", default = c("breakpoints",
-  "expected_phenotypes")), 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_dosage(ab, administration = "iv", version_breakpoints = 15)
-
- -
-

Source

- -

  • EUCAST Expert Rules. Version 2.0, 2012.
    -Leclercq et al. EUCAST expert rules in antimicrobial susceptibility testing. Clin Microbiol Infect. 2013;19(2):141-60; doi:10.1111/j.1469-0691.2011.03703.x

    • -

  • EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. (link)

    • -

  • EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. (link)

    • -

  • EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. (link)

    • -

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. (link)

    • -

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. (link)

    • -

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. (link)

    • -

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. (link)

    • -
-
-

Arguments

- - -
x
-

A data set with antimicrobials columns, such as amox, AMX and AMC.

- - -
col_mo
-

Column name of the names or codes of the microorganisms (see as.mo()) - the default is the first column of class mo. Values will be coerced using as.mo().

- - -
info
-

A logical to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.

- - -
rules
-

A character vector that specifies which rules should be applied. Must be one or more of "breakpoints", "expected_phenotypes", "expert", "other", "custom", "all", and defaults to c("breakpoints", "expected_phenotypes"). The default value can be set to another value using the package option AMR_eucastrules: options(AMR_eucastrules = "all"). If using "custom", be sure to fill in argument custom_rules too. Custom rules can be created with custom_eucast_rules().

- - -
verbose
-

A logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.

- - -
version_breakpoints
-

The version number to use for the EUCAST Clinical Breakpoints guideline. Can be "15.0", "14.0", "13.1", "12.0", "11.0", or "10.0".

- - -
version_expected_phenotypes
-

The version number to use for the EUCAST Expected Phenotypes. Can be "1.2".

- - -
version_expertrules
-

The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".

- - -
ampc_cephalosporin_resistance
-

(only applies when rules contains "expert" or "all") a character value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is NA. Currently only works when version_expertrules is 3.2 and higher; these versions of 'EUCAST Expert Rules on Enterobacterales' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of NA (the default) for this argument will remove results for these three drugs, while e.g. a value of "R" will make the results for these drugs resistant. Use NULL or FALSE to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using TRUE is equal to using "R".
For EUCAST Expert Rules v3.2, this rule applies to: Citrobacter braakii, Citrobacter freundii, Citrobacter gillenii, Citrobacter murliniae, Citrobacter rodenticum, Citrobacter sedlakii, Citrobacter werkmanii, Citrobacter youngae, Enterobacter, Hafnia alvei, Klebsiella aerogenes, Morganella morganii, Providencia, and Serratia.

- - -
only_sir_columns
-

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.

- - -
custom_rules
-

Custom rules to apply, created with custom_eucast_rules().

- - -
overwrite
-

A logical indicating whether to overwrite existing SIR values (default: FALSE). When FALSE, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, this should remain FALSE, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".

- - -
...
-

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.

- - -
ab
-

Any (vector of) text that can be coerced to a valid antimicrobial drug code with as.ab().

- - -
administration
-

Route of administration, either "", "im", "iv", or "oral".

- -
-
-

Value

-

The input of x, possibly with edited values of antimicrobials. Or, if verbose = TRUE, a data.frame with all original and new values of the affected bug-drug combinations.

-
-
-

Details

-

Note: This function does not translate MIC values to SIR values. Use as.sir() for that.
Note: When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.

-

The file containing all EUCAST rules is located here: https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv. Note: Old taxonomic names are replaced with the current taxonomy where applicable. For example, Ochrobactrum anthropi was renamed to Brucella anthropi in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The AMR package contains the full microbial taxonomy updated until June 24th, 2024, see microorganisms.

-

Custom Rules

- - -

Custom rules can be created using custom_eucast_rules(), e.g.:

-

x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
-                         AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
-
-eucast_rules(example_isolates, rules = "custom", custom_rules = x)

-
- -
-

'Other' Rules

- - -

Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:

  1. A drug with enzyme inhibitor will be set to S if the same drug without enzyme inhibitor is S

    2. -

  2. A drug without enzyme inhibitor will be set to R if the same drug with enzyme inhibitor is R

    3. -

Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.

-

Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include "other" to the rules argument, or use eucast_rules(..., rules = "all"). You can also set the package option AMR_eucastrules, i.e. run options(AMR_eucastrules = "all").

-
- -
-
-

Download Our Reference Data

- - -

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

-

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

-

Visit our website for direct download links, or explore the actual files in our GitHub repository.

-
- -
-

Examples

- 
# \donttest{
-a <- data.frame(
-  mo = c(
-    "Staphylococcus aureus",
-    "Enterococcus faecalis",
-    "Escherichia coli",
-    "Klebsiella pneumoniae",
-    "Pseudomonas aeruginosa"
-  ),
-  VAN = "-", # Vancomycin
-  AMX = "-", # Amoxicillin
-  COL = "-", # Colistin
-  CAZ = "-", # Ceftazidime
-  CXM = "-", # Cefuroxime
-  PEN = "S", # Benzylpenicillin
-  FOX = "S", # Cefoxitin
-  stringsAsFactors = FALSE
-)
-
-head(a)
-#>                       mo VAN AMX COL CAZ CXM PEN FOX
-#> 1  Staphylococcus aureus   -   -   -   -   -   S   S
-#> 2  Enterococcus faecalis   -   -   -   -   -   S   S
-#> 3       Escherichia coli   -   -   -   -   -   S   S
-#> 4  Klebsiella pneumoniae   -   -   -   -   -   S   S
-#> 5 Pseudomonas aeruginosa   -   -   -   -   -   S   S
-
-
-# apply EUCAST rules: some results wil be changed
-b <- eucast_rules(a, overwrite = TRUE)
-#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of
-#> class 'sir'. Transform them on beforehand, with e.g.:
-#>   - a %>% as.sir(CXM:AMX)
-#>   - a %>% mutate_if(is_sir_eligible, as.sir)
-#>   - a %>% mutate(across(where(is_sir_eligible), as.sir))
-
-head(b)
-#>                       mo VAN AMX COL CAZ CXM PEN FOX
-#> 1  Staphylococcus aureus   -   S   R   R   S   S   S
-#> 2  Enterococcus faecalis   -   -   R   R   R   S   R
-#> 3       Escherichia coli   R   -   -   -   -   R   S
-#> 4  Klebsiella pneumoniae   R   R   -   -   -   R   S
-#> 5 Pseudomonas aeruginosa   R   R   -   -   R   R   R
-
-
-# do not apply EUCAST rules, but rather get a data.frame
-# containing all details about the transformations:
-c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
-#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of
-#> class 'sir'. Transform them on beforehand, with e.g.:
-#>   - a %>% as.sir(CXM:AMX)
-#>   - a %>% mutate_if(is_sir_eligible, as.sir)
-#>   - a %>% mutate(across(where(is_sir_eligible), as.sir))
-head(c)
-#>   row col           mo_fullname old new rule          rule_group
-#> 1   1 AMX Staphylococcus aureus   -   S              Breakpoints
-#> 2   1 CXM Staphylococcus aureus   -   S              Breakpoints
-#> 3   1 CAZ Staphylococcus aureus   -   R      Expected phenotypes
-#> 4   1 COL Staphylococcus aureus   -   R      Expected phenotypes
-#> 5   2 CAZ Enterococcus faecalis   -   R      Expected phenotypes
-#> 6   2 COL Enterococcus faecalis   -   R      Expected phenotypes
-#>                                                         rule_name
-#> 1                                                  Staphylococcus
-#> 2                                                  Staphylococcus
-#> 3 Table 4: Expected resistant phenotype in gram-positive bacteria
-#> 4 Table 4: Expected resistant phenotype in gram-positive bacteria
-#> 5 Table 4: Expected resistant phenotype in gram-positive bacteria
-#> 6 Table 4: Expected resistant phenotype in gram-positive bacteria
-#>                                         rule_source
-#> 1   'EUCAST Clinical Breakpoint Tables' v15.0, 2025
-#> 2   'EUCAST Clinical Breakpoint Tables' v15.0, 2025
-#> 3 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
-#> 4 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
-#> 5 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
-#> 6 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
-# }
-
-# Dosage guidelines:
-
-eucast_dosage(c("tobra", "genta", "cipro"), "iv")
-#> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint
-#>   Tables' v15.0 (2025). This note will be shown once per session.
-#> # A tibble: 3 × 5
-#>   ab   name          standard_dosage  high_dosage  eucast_version
-#>   <ab> <chr>         <chr>            <chr>                 <dbl>
-#> 1 TOB  Tobramycin    6-7 mg/kg x 1 iv NA                       15
-#> 2 GEN  Gentamicin    6-7 mg/kg x 1 iv NA                       15
-#> 3 CIP  Ciprofloxacin 0.4 g x 2 iv     0.4 g x 3 iv             15
-
-eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
-#> # A tibble: 3 × 5
-#>   ab   name          standard_dosage high_dosage eucast_version
-#>   <ab> <chr>         <chr>           <chr>                <dbl>
-#> 1 TOB  Tobramycin    NA              NA                      NA
-#> 2 GEN  Gentamicin    NA              NA                      NA
-#> 3 CIP  Ciprofloxacin NA              NA                      NA
-
-
-
- - -
- - - - - - + + + + + + + diff --git a/reference/example_isolates.html b/reference/example_isolates.html index 96cc0dbee..059486aa0 100644 --- a/reference/example_isolates.html +++ b/reference/example_isolates.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9018 + 3.0.1.9019 + + + + + +
+
+
+

Apply Interpretive Rules

+ Source: R/interpretive_rules.R +
interpretive_rules.Rd
+
+ +
+

WORK IN PROGRESS

+

The interpretive_rules() function is new, to allow CLSI 'rules' too. The old eucast_rules() function will stay as a wrapper, but we need to generalise more parts of the underlying code to allow more than just EUCAST.

+

Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://www.eucast.org), see Source. Use eucast_dosage() to get a data.frame with advised dosages of a certain bug-drug combination, which is based on the dosage data set.

+

To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see Details.

+
+ +
+

Usage

+ 
interpretive_rules(x, col_mo = NULL, guideline = getOption("AMR_guideline",
+  "EUCAST"), info = interactive(),
+  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
+  "expected_phenotypes")), 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")), ...)
+
+clsi_rules(x, rules = getOption("AMR_interpretive_rules", default =
+  c("breakpoints", "expected_phenotypes")), ...)
+
+eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
+
+ +
+

Source

+ +

  • EUCAST Expert Rules. Version 2.0, 2012.
    +Leclercq et al. EUCAST expert rules in antimicrobial susceptibility testing. Clin Microbiol Infect. 2013;19(2):141-60; doi:10.1111/j.1469-0691.2011.03703.x

    • +

  • EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. (link)

    • +

  • EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. (link)

    • +

  • EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. (link)

    • +

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. (link)

    • +

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. (link)

    • +

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. (link)

    • +

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. (link)

    • +
+
+

Arguments

+ + +
x
+

A data set with antimicrobials columns, such as amox, AMX and AMC.

+ + +
col_mo
+

Column name of the names or codes of the microorganisms (see as.mo()) - the default is the first column of class mo. Values will be coerced using as.mo().

+ + +
guideline
+

A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option AMR_guideline.

+ + +
info
+

A logical to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.

+ + +
rules
+

A character vector that specifies which rules should be applied. Must be one or more of "breakpoints", "expected_phenotypes", "expert", "other", "custom", "all", and defaults to c("breakpoints", "expected_phenotypes"). The default value can be set to another value using the package option AMR_interpretive_rules: options(AMR_interpretive_rules = "all"). If using "custom", be sure to fill in argument custom_rules too. Custom rules can be created with custom_eucast_rules().

+ + +
verbose
+

A logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.

+ + +
version_breakpoints
+

The version number to use for the EUCAST Clinical Breakpoints guideline. Can be "15.0", "14.0", "13.1", "12.0", "11.0", or "10.0".

+ + +
version_expected_phenotypes
+

The version number to use for the EUCAST Expected Phenotypes. Can be "1.2".

+ + +
version_expertrules
+

The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".

+ + +
ampc_cephalosporin_resistance
+

(only applies when rules contains "expert" or "all") a character value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is NA. Currently only works when version_expertrules is 3.2 and higher; these versions of 'EUCAST Expert Rules on Enterobacterales' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of NA (the default) for this argument will remove results for these three drugs, while e.g. a value of "R" will make the results for these drugs resistant. Use NULL or FALSE to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using TRUE is equal to using "R".
For EUCAST Expert Rules v3.2, this rule applies to: Citrobacter braakii, Citrobacter freundii, Citrobacter gillenii, Citrobacter murliniae, Citrobacter rodenticum, Citrobacter sedlakii, Citrobacter werkmanii, Citrobacter youngae, Enterobacter, Hafnia alvei, Klebsiella aerogenes, Morganella morganii, Providencia, and Serratia.

+ + +
only_sir_columns
+

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.

+ + +
custom_rules
+

Custom rules to apply, created with custom_eucast_rules().

+ + +
overwrite
+

A logical indicating whether to overwrite existing SIR values (default: FALSE). When FALSE, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, this should remain FALSE, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".

+ + +
...
+

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.

+ + +
ab
+

Any (vector of) text that can be coerced to a valid antimicrobial drug code with as.ab().

+ + +
administration
+

Route of administration, either "", "im", "iv", "oral", or NA.

+ +
+
+

Value

+

The input of x, possibly with edited values of antimicrobials. Or, if verbose = TRUE, a data.frame with all original and new values of the affected bug-drug combinations.

+
+
+

Details

+

Note: This function does not translate MIC values to SIR values. Use as.sir() for that.
Note: When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.

+

The file containing all EUCAST rules is located here: https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv. Note: Old taxonomic names are replaced with the current taxonomy where applicable. For example, Ochrobactrum anthropi was renamed to Brucella anthropi in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The AMR package contains the full microbial taxonomy updated until June 24th, 2024, see microorganisms.

+

Custom Rules

+ + +

Custom rules can be created using custom_eucast_rules(), e.g.:

+

x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
+                         AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
+
+eucast_rules(example_isolates, rules = "custom", custom_rules = x)

+
+ +
+

'Other' Rules

+ + +

Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:

  1. A drug with enzyme inhibitor will be set to S if the same drug without enzyme inhibitor is S

    2. +

  2. A drug without enzyme inhibitor will be set to R if the same drug with enzyme inhibitor is R

    3. +

Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.

+

Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include "other" to the rules argument, or use eucast_rules(..., rules = "all"). You can also set the package option AMR_interpretive_rules, i.e. run options(AMR_interpretive_rules = "all").

+
+ +
+
+

Download Our Reference Data

+ + +

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

+

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

+

Visit our website for direct download links, or explore the actual files in our GitHub repository.

+
+ +
+

Examples

+ 
# \donttest{
+a <- data.frame(
+  mo = c(
+    "Staphylococcus aureus",
+    "Enterococcus faecalis",
+    "Escherichia coli",
+    "Klebsiella pneumoniae",
+    "Pseudomonas aeruginosa"
+  ),
+  VAN = "-", # Vancomycin
+  AMX = "-", # Amoxicillin
+  COL = "-", # Colistin
+  CAZ = "-", # Ceftazidime
+  CXM = "-", # Cefuroxime
+  PEN = "S", # Benzylpenicillin
+  FOX = "S", # Cefoxitin
+  stringsAsFactors = FALSE
+)
+
+head(a)
+#>                       mo VAN AMX COL CAZ CXM PEN FOX
+#> 1  Staphylococcus aureus   -   -   -   -   -   S   S
+#> 2  Enterococcus faecalis   -   -   -   -   -   S   S
+#> 3       Escherichia coli   -   -   -   -   -   S   S
+#> 4  Klebsiella pneumoniae   -   -   -   -   -   S   S
+#> 5 Pseudomonas aeruginosa   -   -   -   -   -   S   S
+
+
+# apply EUCAST rules: some results wil be changed
+b <- eucast_rules(a, overwrite = TRUE)
+#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of
+#> class 'sir'. Transform them on beforehand, with e.g.:
+#>   - x %>% as.sir(CXM:AMX)
+#>   - x %>% mutate_if(is_sir_eligible, as.sir)
+#>   - x %>% mutate(across(where(is_sir_eligible), as.sir))
+
+head(b)
+#>                       mo VAN AMX COL CAZ CXM PEN FOX
+#> 1  Staphylococcus aureus   -   S   R   R   S   S   S
+#> 2  Enterococcus faecalis   -   -   R   R   R   S   R
+#> 3       Escherichia coli   R   -   -   -   -   R   S
+#> 4  Klebsiella pneumoniae   R   R   -   -   -   R   S
+#> 5 Pseudomonas aeruginosa   R   R   -   -   R   R   R
+
+
+# do not apply EUCAST rules, but rather get a data.frame
+# containing all details about the transformations:
+c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
+#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of
+#> class 'sir'. Transform them on beforehand, with e.g.:
+#>   - x %>% as.sir(CXM:AMX)
+#>   - x %>% mutate_if(is_sir_eligible, as.sir)
+#>   - x %>% mutate(across(where(is_sir_eligible), as.sir))
+head(c)
+#>   row col           mo_fullname old new rule          rule_group
+#> 1   1 AMX Staphylococcus aureus   -   S              Breakpoints
+#> 2   1 CXM Staphylococcus aureus   -   S              Breakpoints
+#> 3   1 CAZ Staphylococcus aureus   -   R      Expected phenotypes
+#> 4   1 COL Staphylococcus aureus   -   R      Expected phenotypes
+#> 5   2 CAZ Enterococcus faecalis   -   R      Expected phenotypes
+#> 6   2 COL Enterococcus faecalis   -   R      Expected phenotypes
+#>                                                         rule_name
+#> 1                                                  Staphylococcus
+#> 2                                                  Staphylococcus
+#> 3 Table 4: Expected resistant phenotype in gram-positive bacteria
+#> 4 Table 4: Expected resistant phenotype in gram-positive bacteria
+#> 5 Table 4: Expected resistant phenotype in gram-positive bacteria
+#> 6 Table 4: Expected resistant phenotype in gram-positive bacteria
+#>                                         rule_source
+#> 1   'EUCAST Clinical Breakpoint Tables' v15.0, 2025
+#> 2   'EUCAST Clinical Breakpoint Tables' v15.0, 2025
+#> 3 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
+#> 4 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
+#> 5 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
+#> 6 'EUCAST Expected Resistant Phenotypes' v1.2, 2023
+# }
+
+# Dosage guidelines:
+
+eucast_dosage(c("tobra", "genta", "cipro"), "iv")
+#> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint
+#>   Tables' v15.0 (2025). This note will be shown once per session.
+#> # A tibble: 3 × 5
+#>   ab   name          standard_dosage  high_dosage  eucast_version
+#>   <ab> <chr>         <chr>            <chr>                 <dbl>
+#> 1 TOB  Tobramycin    6-7 mg/kg x 1 iv NA                       15
+#> 2 GEN  Gentamicin    6-7 mg/kg x 1 iv NA                       15
+#> 3 CIP  Ciprofloxacin 0.4 g x 2 iv     0.4 g x 3 iv             15
+
+eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
+#> # A tibble: 3 × 5
+#>   ab   name          standard_dosage high_dosage eucast_version
+#>   <ab> <chr>         <chr>           <chr>                <dbl>
+#> 1 TOB  Tobramycin    NA              NA                      NA
+#> 2 GEN  Gentamicin    NA              NA                      NA
+#> 3 CIP  Ciprofloxacin NA              NA                      NA
+
+
+
+ + +
+ + + + + + + diff --git a/reference/eucast_rules.md b/reference/interpretive_rules.md similarity index 88% rename from reference/eucast_rules.md rename to reference/interpretive_rules.md index bb3da0f0c..a923697d5 100644 --- a/reference/eucast_rules.md +++ b/reference/interpretive_rules.md @@ -1,26 +1,41 @@ -# Apply EUCAST Rules +# Apply Interpretive Rules + +**WORK IN PROGRESS** + +**The `interpretive_rules()` function is new, to allow CLSI 'rules' too. +The old `eucast_rules()` function will stay as a wrapper, but we need to +generalise more parts of the underlying code to allow more than just +EUCAST.** Apply rules from clinical breakpoints notes and expected resistant -phenotypes as defined by the European Committee on Antimicrobial +phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, ), see *Source*. Use `eucast_dosage()` to get a [data.frame](https://rdrr.io/r/base/data.frame.html) with advised dosages of a certain bug-drug combination, which is based on the [dosage](https://amr-for-r.org/reference/dosage.md) data set. -To improve the interpretation of the antibiogram before EUCAST rules are -applied, some non-EUCAST rules can applied at default, see *Details*. +To improve the interpretation of the antibiogram before CLSI/EUCAST +interpretive rules are applied, some AMR-specific rules can be applied +at default, see *Details*. ## Usage ``` r -eucast_rules(x, col_mo = NULL, info = interactive(), - rules = getOption("AMR_eucastrules", default = c("breakpoints", +interpretive_rules(x, col_mo = NULL, guideline = getOption("AMR_guideline", + "EUCAST"), info = interactive(), + rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")), 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")), ...) + +clsi_rules(x, rules = getOption("AMR_interpretive_rules", default = + c("breakpoints", "expected_phenotypes")), ...) + eucast_dosage(ab, administration = "iv", version_breakpoints = 15) ``` @@ -72,6 +87,12 @@ 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 @@ -86,9 +107,10 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15) `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option - [`AMR_eucastrules`](https://amr-for-r.org/reference/AMR-options.md): - `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to - fill in argument `custom_rules` too. Custom rules can be created with + [`AMR_interpretive_rules`](https://amr-for-r.org/reference/AMR-options.md): + `options(AMR_interpretive_rules = "all")`. If using `"custom"`, be + sure to fill in argument `custom_rules` too. Custom rules can be + created with [`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md). - verbose: @@ -179,7 +201,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15) - administration: - Route of administration, either "", "im", "iv", or "oral". + Route of administration, either "", "im", "iv", "oral", or NA. ## Value @@ -237,8 +259,8 @@ Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option -[`AMR_eucastrules`](https://amr-for-r.org/reference/AMR-options.md), -i.e. run `options(AMR_eucastrules = "all")`. +[`AMR_interpretive_rules`](https://amr-for-r.org/reference/AMR-options.md), +i.e. run `options(AMR_interpretive_rules = "all")`. ## Download Our Reference Data @@ -291,9 +313,9 @@ head(a) b <- eucast_rules(a, overwrite = TRUE) #> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of #> class 'sir'. Transform them on beforehand, with e.g.: -#> - a %>% as.sir(CXM:AMX) -#> - a %>% mutate_if(is_sir_eligible, as.sir) -#> - a %>% mutate(across(where(is_sir_eligible), as.sir)) +#> - x %>% as.sir(CXM:AMX) +#> - x %>% mutate_if(is_sir_eligible, as.sir) +#> - x %>% mutate(across(where(is_sir_eligible), as.sir)) head(b) #> mo VAN AMX COL CAZ CXM PEN FOX @@ -309,9 +331,9 @@ head(b) c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE) #> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of #> class 'sir'. Transform them on beforehand, with e.g.: -#> - a %>% as.sir(CXM:AMX) -#> - a %>% mutate_if(is_sir_eligible, as.sir) -#> - a %>% mutate(across(where(is_sir_eligible), as.sir)) +#> - x %>% as.sir(CXM:AMX) +#> - x %>% mutate_if(is_sir_eligible, as.sir) +#> - x %>% mutate(across(where(is_sir_eligible), as.sir)) head(c) #> row col mo_fullname old new rule rule_group #> 1 1 AMX Staphylococcus aureus - S Breakpoints diff --git a/reference/intrinsic_resistant.html b/reference/intrinsic_resistant.html index 49fbada1b..045207d27 100644 --- a/reference/intrinsic_resistant.html +++ b/reference/intrinsic_resistant.html @@ -7,7 +7,7 @@ AMR (for R) - 3.0.1.9018 + 3.0.1.9019