With add_custom_antimicrobials()
you can add your own custom antimicrobial drug names and codes.
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 circumvent this and automate the process of adding antimicrobials:
Method 1: Using the package 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 package 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. Note that the definitions will be stored in a user-specific R file, which is a suboptimal workflow. 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.
See also
add_custom_microorganisms()
to add custom microorganisms.
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://atcddd.fhi.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
# }