Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
mo_name("Staph schlei coa")
#> ℹ Assuming the Dutch language (Nederlands) for the AMR package. See set_AMR_locale() to change this or to silence this once-per-session note.
#> ℹ Microorganism translation was uncertain for "Staph schlei coa" (assumed Staphylococcus schleiferi coagulans). Run mo_uncertainties() to
#> review this, or use add_custom_microorganisms() to add custom entries.
#> ℹ The following microorganism was taxonomically renamed (use keep_synonyms = TRUE to leave uncorrected):
#> • Staphylococcus schleiferi coagulans (Igimi et al., 1990) -> Staphylococcus coagulans (Madhaiyan et al., 2020)
#> [1] "Staphylococcus coagulans"
as.mo("Staph schlei coa")
#> ℹ Returning previously coerced value for "Staph schlei coa". Run mo_reset_session() to reset this. This note will be shown once per session
#> for this input.
#> ℹ The following microorganism was taxonomically renamed (use keep_synonyms = TRUE to leave uncorrected):
#> • Staphylococcus schleiferi coagulans (Igimi et al., 1990) -> Staphylococcus coagulans (Madhaiyan et al., 2020)
#> Class 'mo'
#> [1] B_STPHY_CGLN
as.mo("Staph schlei coa", keep_synonyms = TRUE)
#> Class 'mo'
#> [1] B_STPHY_SCHL_CGLN
#> Warning message:
#> Function as.mo() returned one old taxonomic name. Use as.mo(..., keep_synonyms = FALSE) to clean the input to currently accepted taxonomic
#> names, or set the R option AMR_keep_synonyms to FALSE. This warning will be shown once per session.
mo_name("B_STPHY_SCHL_CGLN")
#> [1] "Staphylococcus schleiferi coagulans"
mo_name("B_STPHY_SCHL_CGLN", keep_synonyms = T)
#> [1] "Staphylococcus schleiferi coagulans"
mo_name("B_STPHY_SCHL_CGLN", keep_synonyms = F)
#> [1] "Staphylococcus schleiferi coagulans"
After renaming, this should not be happening: