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Catalogue of Life, replaces ITIS

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dr. M.S. (Matthijs) Berends
2019-02-18 02:33:37 +01:00
parent 9209787a53
commit 54f8258f8c
88 changed files with 607 additions and 590 deletions
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man/as.mo.Rd
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@ -54,7 +54,8 @@ A microbial ID from this package (class: \code{mo}) typically looks like these e
| | | ----> subspecies, a 3-4 letter acronym
| | ----> species, a 3-4 letter acronym
| ----> genus, a 5-7 letter acronym, mostly without vowels
----> taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
----> taxonomic kingdom: A (Archaea), B (Bacteria), C (Chromista),
F (Fungi), P (Protozoa) or V (Viruses)
}
Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
@ -88,7 +89,7 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
Examples:
\itemize{
\item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPTC_GRB}) needs review.}
\item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPT_GRB}) needs review.}
\item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
\item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
\item{\code{"Fluoroquinolone-resistant Neisseria gonorrhoeae"}. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result \emph{Neisseria gonorrhoeae} (\code{B_NESSR_GON}) needs review.}
@ -137,8 +138,6 @@ as.mo("Staphylococcus aureus (MRSA)")
as.mo("MRSA") # Methicillin Resistant S. aureus
as.mo("VISA") # Vancomycin Intermediate S. aureus
as.mo("VRSA") # Vancomycin Resistant S. aureus
as.mo(369) # Search on TSN (Taxonomic Serial Number), a unique identifier
# for the Integrated Taxonomic Information System (ITIS)
as.mo("Streptococcus group A")
as.mo("GAS") # Group A Streptococci
@ -147,8 +146,8 @@ as.mo("GBS") # Group B Streptococci
as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
as.mo("S. pyogenes") # will remain species: B_STRPT_PYO
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRA
# Use mo_* functions to get a specific property based on `mo`
Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`