Add Custom Microorganisms

With add_custom_microorganisms() you can add your own custom microorganisms, 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 circumvent this and automate the process of adding microorganisms:

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

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.
Set the file location to the package option AMR_custom_mo: 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 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 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: Loading the microorganism 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_microorganisms(
   data.frame(genus = "Enterobacter",
              species = "asburiae/cloacae")
 )

Use clear_custom_microorganisms() to clear the previously added microorganisms.

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_ENTRB_ASB/

# 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")
#> $mo
#> [1] "CUSTOM1_ENTRB_ASB/"
#> 
#> $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"
#> 
#> $oxygen_tolerance
#> [1] NA
#> 
#> $url
#> [1] ""
#> 
#> $ref
#> [1] "Self-added, 2023"
#> 
#> $snomed
#> [1] NA
#> 
#> $lpsn
#> [1] NA
#> 
#> $gbif
#> [1] NA
#> 


# the function tries to be forgiving:
add_custom_microorganisms(
  data.frame(
    GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
    SPECIES = "SPECIES"
  )
)
#> ℹ Added Bacteroides/Parabacteroides to the internal microorganisms data
#>   set.
mo_name("BACTEROIDES / PARABACTEROIDES")
#> [1] "Bacteroides/Parabacteroides"
mo_rank("BACTEROIDES / PARABACTEROIDES")
#> [1] "genus"

# taxonomy still works, although a slashline genus was given as input:
mo_family("Bacteroides/Parabacteroides")
#> [1] "Bacteroidaceae"


# for groups and complexes, set them as species or subspecies:
add_custom_microorganisms(
  data.frame(
    genus = "Citrobacter",
    species = c("freundii", "braakii complex"),
    subspecies = c("complex", "")
  )
)
#> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the
#>   internal microorganisms data set.
mo_name(c("C. freundii complex", "C. braakii complex"))
#> [1] "Citrobacter freundii complex" "Citrobacter braakii complex" 
mo_species(c("C. freundii complex", "C. braakii complex"))
#> [1] "freundii complex" "braakii complex" 
mo_gramstain(c("C. freundii complex", "C. braakii complex"))
#> [1] "Gram-negative" "Gram-negative"
# }

Usage

Arguments

Details

See also

Examples