custom_eucast_rules {AMR}R Documentation

Define Custom EUCAST Rules

Description

Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in eucast_rules().

Usage

custom_eucast_rules(...)

Arguments

...

rules in formula notation, see Examples

Details

Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the eucast_rules() function.

Value

A list containing the custom rules

How it works

Basics

If you are familiar with the case_when() function of the dplyr package, you will recognise the input method to set your own rules. Rules must be set using what R considers to be the 'formula notation'. The rule itself is written before the tilde (~) and the consequence of the rule is written after the tilde: 

x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
                         TZP == "R" ~ aminopenicillins == "R")

These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work: 

x
#> A set of custom EUCAST rules:
#>
#>   1. If TZP is "S" then set to  S :
#>      amoxicillin (AMX), ampicillin (AMP)
#>
#>   2. If TZP is "R" then set to  R :
#>      amoxicillin (AMX), ampicillin (AMP)

The rules (the part before the tilde, in above example TZP == "S" and TZP == "R") must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column TZP must exist. We will create a sample data set and test the rules set: 

df <- data.frame(mo = c("Escherichia coli", "Klebsiella pneumoniae"),
                 TZP = as.sir("R"),
                 ampi = as.sir("S"),
                 cipro = as.sir("S"))
df
#>                      mo TZP ampi cipro
#> 1      Escherichia coli   R    S     S
#> 2 Klebsiella pneumoniae   R    S     S

eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE)
#>                      mo TZP ampi cipro
#> 1      Escherichia coli   R    R     S
#> 2 Klebsiella pneumoniae   R    R     S

Using taxonomic properties in rules

There is one exception in columns used for the rules: all column names of the microorganisms data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", and "snomed". Thus, this next example will work as well, despite the fact that the df data set does not contain a column genus: 

y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
                         TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")

eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
#>                      mo TZP ampi cipro
#> 1      Escherichia coli   R    S     S
#> 2 Klebsiella pneumoniae   R    R     S

Usage of antibiotic group names

It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part after the tilde. In above examples, the antibiotic group aminopenicillins is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.

Examples

x <- custom_eucast_rules(
  AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
  AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I"
)
x

# run the custom rule set (verbose = TRUE will return a logbook instead of the data set):
eucast_rules(example_isolates,
  rules = "custom",
  custom_rules = x,
  info = FALSE,
  verbose = TRUE
)

# combine rule sets
x2 <- c(
  x,
  custom_eucast_rules(TZP == "R" ~ carbapenems == "R")
)
x2
[Package AMR version 2.1.1 Index]