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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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11
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`

17
man/microorganisms.Rd
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@ -3,11 +3,11 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~20,000 microorganisms}
\format{A \code{\link{data.frame}} with 19,456 observations and 15 variables:
\title{Data set with ~60,000 microorganisms}
\format{A \code{\link{data.frame}} with 56,659 observations and 15 variables:
\describe{
\item{\code{mo}}{ID of microorganism}
\item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{col_id}}{Catalogue of Life ID}
\item{\code{genus}}{Taxonomic genus of the microorganism as found in ITIS, see Source}
\item{\code{species}}{Taxonomic species of the microorganism as found in ITIS, see Source}
\item{\code{subspecies}}{Taxonomic subspecies of the microorganism as found in ITIS, see Source}
@ -29,20 +29,15 @@ Integrated Taxonomic Information System (ITIS) public online database, \url{http
microorganisms
}
\description{
A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using \code{\link{as.mo}}.
A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
}
\details{
Manually added were:
\itemize{
\item{605 species of Aspergillus (as Aspergillus misses from ITIS, list from https://en.wikipedia.org/wiki/List_of_Aspergillus_species on 2019-02-05)}
\item{23 species of Trichophyton (as Trichophyton misses from ITIS, list from https://en.wikipedia.org/wiki/Trichophyton on 2019-02-05)}
\item{9 species of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{2 species of Straphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{1 species of Candida (C. glabrata)}
\item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{2 species of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{2 other undefined (unknown Gram negatives and unknown Gram positives)}
}
These manual entries have no Taxonomic Serial Number (TSN), so can be looked up with \code{filter(microorganisms, is.na(tsn)}.
}
\section{ITIS}{

10
man/microorganisms.old.Rd
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@ -4,12 +4,12 @@
\name{microorganisms.old}
\alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names}
\format{A \code{\link{data.frame}} with 2,383 observations and 4 variables:
\format{A \code{\link{data.frame}} with 14,506 observations and 4 variables:
\describe{
\item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
\item{\code{tsn_new}}{New Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
\item{\code{col_id}}{Catalogue of Life ID}
\item{\code{tsn_new}}{New Catalogue of Life ID}
\item{\code{fullname}}{Old taxonomic name of the microorganism as found in the CoL, see Source}
\item{\code{ref}}{Author(s) and year of concerning publication as found in the CoL, see Source}
}}
\source{
[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.

6
man/mo_property.Rd
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@ -15,7 +15,6 @@
\alias{mo_kingdom}
\alias{mo_type}
\alias{mo_gramstain}
\alias{mo_TSN}
\alias{mo_ref}
\alias{mo_authors}
\alias{mo_year}
@ -48,8 +47,6 @@ mo_type(x, language = get_locale(), ...)
mo_gramstain(x, language = get_locale(), ...)
mo_TSN(x, ...)
mo_ref(x, ...)
mo_authors(x, ...)
@ -71,7 +68,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
}
\value{
\itemize{
\item{An \code{integer} in case of \code{mo_TSN} and \code{mo_year}}
\item{An \code{integer} in case of \code{mo_year}}
\item{A \code{list} in case of \code{mo_taxonomy}}
\item{A \code{character} in all other cases}
}
@ -129,7 +126,6 @@ mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"
mo_subspecies("E. coli") # NA
mo_TSN("E. coli") # 285 (Taxonomic Serial Number)
## colloquial properties
mo_fullname("E. coli") # "Escherichia coli"

30
man/supplementary_data.Rd
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@ -1,30 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{supplementary_data}
\alias{supplementary_data}
\alias{microorganismsDT}
\alias{microorganisms.prevDT}
\alias{microorganisms.unprevDT}
\alias{microorganisms.oldDT}
\title{Supplementary Data}
\format{An object of class \code{data.table} (inherits from \code{data.frame}) with 19456 rows and 15 columns.}
\usage{
microorganismsDT
microorganisms.prevDT
microorganisms.unprevDT
microorganisms.oldDT
}
\description{
These \code{\link{data.table}s} are transformed from the \code{\link{microorganisms}} and \code{\link{microorganisms}} data sets to improve speed of \code{\link{as.mo}}. They are meant for internal use only, and are only mentioned here for reference.
}
\section{Read more on our website!}{
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\keyword{datasets}