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add oxygen tolerance

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dr. M.S. (Matthijs) Berends
2023-05-11 21:56:27 +02:00
parent bf08d136a0
commit 91fa73dedf
28 changed files with 52310 additions and 52203 deletions
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R/mo.R
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@ -95,13 +95,14 @@
#' 1. Berends MS *et al.* (2022). **AMR: An R Package for Working with Antimicrobial Resistance Data**. *Journal of Statistical Software*, 104(3), 1-31; \doi{10.18637/jss.v104.i03}
#' 2. Becker K *et al.* (2014). **Coagulase-Negative Staphylococci.** *Clin Microbiol Rev.* 27(4): 870-926; \doi{10.1128/CMR.00109-13}
#' 3. Becker K *et al.* (2019). **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** *Clin Microbiol Infect*; \doi{10.1016/j.cmi.2019.02.028}
#' 4. Becker K *et al.* (2020). **Emergence of coagulase-negative staphylococci** *Expert Rev Anti Infect Ther.* 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
#' 5. Lancefield RC (1933). **A serological differentiation of human and other groups of hemolytic streptococci**. *J Exp Med.* 57(4): 571-95; \doi{10.1084/jem.57.4.571}
#' 6. Berends MS *et al.* (2022). **Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019** *Microorganisms* 10(9), 1801; \doi{10.3390/microorganisms10091801}
#' 4. Becker K *et al.* (2020). **Emergence of coagulase-negative staphylococci.** *Expert Rev Anti Infect Ther.* 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
#' 5. Lancefield RC (1933). **A serological differentiation of human and other groups of hemolytic streptococci.** *J Exp Med.* 57(4): 571-95; \doi{10.1084/jem.57.4.571}
#' 6. Berends MS *et al.* (2022). **Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/** *Micro.rganisms* 10(9), 1801; \doi{10.3390/microorganisms10091801}
#' 7. `r TAXONOMY_VERSION$LPSN$citation` Accessed from <`r TAXONOMY_VERSION$LPSN$url`> on `r documentation_date(TAXONOMY_VERSION$LPSN$accessed_date)`.
#' 8. `r TAXONOMY_VERSION$GBIF$citation` Accessed from <`r TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(TAXONOMY_VERSION$GBIF$accessed_date)`.
#' 9. `r TAXONOMY_VERSION$SNOMED$citation` URL: <`r TAXONOMY_VERSION$SNOMED$url`>
#' 10. Bartlett A *et al.* (2022). **A comprehensive list of bacterial pathogens infecting humans** *Microbiology* 168:001269; \doi{10.1099/mic.0.001269}
#' 11. Reimer *et al.* (2022). ***BacDive* in 2022: the knowledge base for standardized bacterial and archaeal data.** *Nucleic Acids Res.* 2022 Jan 7;50(D1):D741-D746; \doi{10.1093/nar/gkab961}
#' @export
#' @return A [character] [vector] with additional class [`mo`]
#' @seealso [microorganisms] for the [data.frame] that is being used to determine ID's.
@ -888,8 +889,6 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
),
collapse = "\n"
),
# Add "Based on {input}" text if it differs from the original input
ifelse(x[i, ]$original_input != x[i, ]$input, paste0(strrep(" ", nchar(x[i, ]$original_input) + 6), "Based on input \"", x[i, ]$input, "\""), ""),
# Add note if result was coerced to accepted taxonomic name
ifelse(x[i, ]$keep_synonyms == FALSE & x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
paste0(