Add Custom Microorganisms to This Package

With add_custom_microorganisms() you can add your own custom microorganisms to the AMR package, such the non-taxonomic outcome of laboratory analysis.

Usage

add_custom_microorganisms(x)

clear_custom_microorganisms()

Arguments

x

a data.frame resembling the microorganisms data set, at least containing column "genus" (case-insensitive)

Details

This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see Examples.

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

There are two ways to automate this process:

Method 1: Save the microorganisms to a local or remote file (can even be the internet). To use this method:

1. Create a data set in the structure of the microorganisms data set (containing at the very least column "genus") and save it with saveRDS() to a location of choice, e.g. "~/my_custom_mo.rds", or any remote location.

2. Set the file location to the AMR_custom_mo R option: options(AMR_custom_mo = "~/my_custom_mo.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 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 microorganism codes:
   options(AMR_custom_mo = "~/my_custom_mo.rds")

   Upon package load, this file will be loaded and run through the add_custom_microorganisms() function.

Method 2: Save the microorganism directly to your .Rprofile file. An important downside is that this requires to load the AMR package at every start-up. To use this method:

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

2. Add a text like below and save the file:

    # Add custom antibiotic drug codes:
    library(AMR)
    add_custom_microorganisms(
      data.frame(genus = "Enterobacter",
                 species = "asburiae/cloacae")
    )

Use clear_custom_microorganisms() to clear the previously added antimicrobials.

See also

add_custom_antimicrobials() to add custom antimicrobials to this package.

Examples

# \donttest{

# a combination of species is not formal taxonomy, so
# this will result in only "Enterobacter asburiae":
mo_name("Enterobacter asburiae/cloacae")
#> [1] "Enterobacter asburiae"

# now add a custom entry - it will be considered by as.mo() and
# all mo_*() functions
add_custom_microorganisms(
  data.frame(genus = "Enterobacter",
             species = "asburiae/cloacae"
  )
)
#> ℹ Added Enterobacter asburiae/cloacae to the internal microorganisms data
#>   set.

# E. asburiae/cloacae is now a new microorganism:
mo_name("Enterobacter asburiae/cloacae")
#> [1] "Enterobacter asburiae/cloacae"

# its code:
as.mo("Enterobacter asburiae/cloacae")
#> Class 'mo'
#> [1] CUSTOM1_ENTRBC_A_C

# all internal algorithms will work as well:
mo_name("Ent asburia cloacae")
#> [1] "Enterobacter asburiae/cloacae"

# and even the taxonomy was added based on the genus!
mo_family("E. asburiae/cloacae")
#> [1] "Enterobacteriaceae"
mo_gramstain("Enterobacter asburiae/cloacae")
#> [1] "Gram-negative"

mo_info("Enterobacter asburiae/cloacae")
#> $identifier
#> Class 'mo'
#> [1] CUSTOM1_ENTRBC_A_C
#> 
#> $kingdom
#> [1] "Bacteria"
#> 
#> $phylum
#> [1] "Pseudomonadota"
#> 
#> $class
#> [1] "Gammaproteobacteria"
#> 
#> $order
#> [1] "Enterobacterales"
#> 
#> $family
#> [1] "Enterobacteriaceae"
#> 
#> $genus
#> [1] "Enterobacter"
#> 
#> $species
#> [1] "asburiae/cloacae"
#> 
#> $subspecies
#> [1] ""
#> 
#> $status
#> [1] "accepted"
#> 
#> $synonyms
#> NULL
#> 
#> $gramstain
#> [1] "Gram-negative"
#> 
#> $url
#> [1] ""
#> 
#> $ref
#> [1] "Self-added, 2023"
#> 
#> $snomed
#> character(0)
#> 


# the function tries to be forgiving:
add_custom_microorganisms(
  data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA",
             SPECIES = "SPECIES"))
#> ℹ Added Escherichia/Klebsiella to the internal microorganisms data set.
mo_name("ESCHERICHIA / KLEBSIELLA")
#> [1] "Escherichia/Klebsiella"
mo_family("Escherichia/Klebsiella")
#> [1] "Enterobacteriaceae"

add_custom_microorganisms(
  data.frame(genus = "Citrobacter", species = "freundii complex"))
#> ℹ Added Citrobacter freundii Complex to the internal microorganisms data
#>   set.
mo_name("C. freundii complex")
#> [1] "Citrobacter freundii Complex"
mo_gramstain("C. freundii complex")
#> [1] "Gram-negative"
# }