Add Custom Antimicrobials

With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes.

Usage

add_custom_antimicrobials(x)

clear_custom_antimicrobials()

Arguments

x: a data.frame resembling the antibiotics data set, at least containing columns "ab" and "name"

Details

Important: Due to how R works, the add_custom_antimicrobials() function has to be run in every R session - added antimicrobials are not stored between sessions and are thus lost when R is exited.

There are two ways to automate this process:

Method 1: Using the option AMR_custom_ab, which is the preferred method. To use this method:

Create a data set in the structure of the antibiotics data set (containing at the very least columns "ab" and "name") and save it with saveRDS() to a location of choice, e.g. "~/my_custom_ab.rds", or any remote location.
Set the file location to the option AMR_custom_ab: options(AMR_custom_ab = "~/my_custom_ab.rds"). This can even be a remote file location, such as an https URL. Since options are not saved between R sessions, it is best to save this option to the .Rprofile file so that it will be loaded on start-up of R. To do this, open the .Rprofile file using e.g. utils::file.edit("~/.Rprofile"), add this text and save the file:
```
# Add custom antimicrobial codes:
options(AMR_custom_ab = "~/my_custom_ab.rds")
```
Upon package load, this file will be loaded and run through the add_custom_antimicrobials() function.

Method 2: Loading the antimicrobial additions directly from your .Rprofile file. An important downside is that this requires the AMR package to be installed or else this method will fail. To use this method:

Edit the .Rprofile file using e.g. utils::file.edit("~/.Rprofile").

Add a text like below and save the file:

 # Add custom antibiotic drug codes:
 AMR::add_custom_antimicrobials(
   data.frame(ab = "TESTAB",
              name = "Test Antibiotic",
              group = "Test Group")
 )

Use clear_custom_antimicrobials() to clear the previously added antimicrobials.

Examples

# \donttest{

# returns NA and throws a warning (which is suppressed here):
suppressWarnings(
  as.ab("testab")
)
#> Class 'ab'
#> [1] <NA>

# now add a custom entry - it will be considered by as.ab() and
# all ab_*() functions
add_custom_antimicrobials(
  data.frame(
    ab = "TESTAB",
    name = "Test Antibiotic",
    # you can add any property present in the
    # 'antibiotics' data set, such as 'group':
    group = "Test Group"
  )
)
#> ℹ Added one record to the internal antibiotics data set.

# "testab" is now a new antibiotic:
as.ab("testab")
#> Class 'ab'
#> [1] TESTAB
ab_name("testab")
#> [1] "Test Antibiotic"
ab_group("testab")
#> [1] "Test Group"

ab_info("testab")
#> $ab
#> [1] "TESTAB"
#> 
#> $cid
#> [1] NA
#> 
#> $name
#> [1] "Test Antibiotic"
#> 
#> $group
#> [1] "Test Group"
#> 
#> $atc
#> [1] NA
#> 
#> $atc_group1
#> [1] NA
#> 
#> $atc_group2
#> [1] NA
#> 
#> $tradenames
#> [1] NA
#> 
#> $loinc
#> [1] NA
#> 
#> $ddd
#> $ddd$oral
#> $ddd$oral$amount
#> [1] NA
#> 
#> $ddd$oral$units
#> [1] NA
#> 
#> 
#> $ddd$iv
#> $ddd$iv$amount
#> [1] NA
#> 
#> $ddd$iv$units
#> [1] NA
#> 
#> 
#> 


# Add Co-fluampicil, which is one of the many J01CR50 codes, see
# https://www.whocc.no/ddd/list_of_ddds_combined_products/
add_custom_antimicrobials(
  data.frame(
    ab = "COFLU",
    name = "Co-fluampicil",
    atc = "J01CR50",
    group = "Beta-lactams/penicillins"
  )
)
#> ℹ Added one record to the internal antibiotics data set.
ab_atc("Co-fluampicil")
#> [1] "J01CR50"
ab_name("J01CR50")
#> [1] "Co-fluampicil"

# even antibiotic selectors work
x <- data.frame(
  random_column = "some value",
  coflu = as.sir("S"),
  ampicillin = as.sir("R")
)
x
#>   random_column coflu ampicillin
#> 1    some value     S          R
x[, betalactams()]
#> ℹ For betalactams() using columns 'coflu' (co-fluampicil) and
#>   'ampicillin'
#>   coflu ampicillin
#> 1     S          R
# }

Usage

Arguments

Details

See also

Examples