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 automate this process:

Method 1: Using the 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 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. 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_microorganisms(
   data.frame(genus = "Enterobacter",
              species = "asburiae/cloacae")
 )

Use clear_custom_microorganisms() to clear the previously added antimicrobials.

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")
#> $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
#> [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