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 columns "genus" and "species"

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 columns "genus" and "species") 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 one record 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] CUSTOM_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")
#> $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] NA
#> 
#> $snomed
#> character(0)
#> 
# }