P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 14:01:55 +02:00
Code Releases Activity

new kingdom

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-09 13:11:54 +01:00
parent 9be5e0318b
commit 6b0f4ffbd4
17 changed files with 193 additions and 82 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
man/as.mo.Rd
View File

@ -76,9 +76,9 @@ This means that looking up human pathogenic microorganisms takes less time than
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

6
man/microorganisms.Rd
View File

@ -17,8 +17,8 @@
\item{\code{class}}{Taxonomic class of the microorganism as found in ITIS, see Source}
\item{\code{phylum}}{Taxonomic phylum of the microorganism as found in ITIS, see Source}
\item{\code{subkingdom}}{Taxonomic subkingdom of the microorganism as found in ITIS, see Source}
\item{\code{kingdom}}{Taxonomic kingdom of the microorganism as found in ITIS, see Source}
\item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
\item{\code{prevalence}}{An integer based on estimated prevalence of the microorganism in humans. Used internally by \code{\link{as.mo}}, otherwise quite meaningless. It has a value of 25 for manually added items and a value of 1000 for all unprevalent microorganisms whose genus was somewhere in the top 250 (with another species).}
\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
}}
@ -34,9 +34,9 @@ A data set containing the complete microbial taxonomy of the kingdoms Bacteria,
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

4
man/microorganisms.old.Rd
View File

@ -23,9 +23,9 @@ A data set containing old (previously valid or accepted) taxonomic names accordi
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

69
man/mo_property.Rd
View File

@ -12,10 +12,13 @@
\alias{mo_class}
\alias{mo_phylum}
\alias{mo_subkingdom}
\alias{mo_ref}
\alias{mo_kingdom}
\alias{mo_type}
\alias{mo_TSN}
\alias{mo_gramstain}
\alias{mo_TSN}
\alias{mo_ref}
\alias{mo_authors}
\alias{mo_year}
\alias{mo_taxonomy}
\title{Property of a microorganism}
\usage{
@ -39,33 +42,51 @@ mo_phylum(x, ...)
mo_subkingdom(x, ...)
mo_ref(x, ...)
mo_kingdom(x, ...)
mo_type(x, language = get_locale(), ...)
mo_TSN(x, ...)
mo_gramstain(x, language = get_locale(), ...)
mo_property(x, property = "fullname", language = get_locale(), ...)
mo_TSN(x, ...)
mo_ref(x, ...)
mo_authors(x, ...)
mo_year(x, ...)
mo_taxonomy(x, ...)
mo_property(x, property = "fullname", language = get_locale(), ...)
}
\arguments{
\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}}
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}.}
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{...}{other parameters passed on to \code{\link{as.mo}}}
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}}
}
\value{
A \code{list} (in case of \code{mo_taxonomy}) or a \code{character} otherwise
\itemize{
\item{An \code{integer} in case of \code{mo_TSN} and \code{mo_year}}
\item{A \code{list} in case of \code{mo_taxonomy}}
\item{A \code{character} in all other cases}
}
}
\description{
Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
}
\details{
All functions will return the most recently known taxonomic property according to ITIS, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
\itemize{
\item{\code{mo_fullname("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)}
\item{\code{mo_ref("Chlamydia psittaci")} will return \code{"Page, 1968"} (with a warning about the renaming)}
\item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
}
}
\section{Supported languages}{
Supported languages are \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish), \code{"it"} (Italian), \code{"fr"} (French), and \code{"pt"} (Portuguese).
@ -74,9 +95,9 @@ Supported languages are \code{"en"} (English), \code{"de"} (German), \code{"nl"}
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}
@ -92,6 +113,8 @@ ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic spec
\examples{
# All properties of Escherichia coli
## taxonomic properties
mo_kingdom("E. coli") # "Bacteria"
mo_subkingdom("E. coli") # "Negibacteria"
mo_phylum("E. coli") # "Proteobacteria"
mo_class("E. coli") # "Gammaproteobacteria"
@ -100,12 +123,20 @@ 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"
mo_shortname("E. coli") # "E. coli"
## other properties
mo_gramstain("E. coli") # "Gram negative"
mo_TSN("E. coli") # 285
mo_type("E. coli") # "Bacteria"
mo_type("E. coli") # "Bacteria" (equal to kingdom)
## scientific reference
mo_ref("E. coli") # "Castellani and Chalmers, 1919"
mo_authors("E. coli") # "Castellani and Chalmers"
mo_year("E. coli") # 1919
# Abbreviations known in the field
@ -137,17 +168,19 @@ mo_shortname("S. epi", Becker = TRUE) # "CoNS"
mo_fullname("S. pyo") # "Streptococcus pyogenes"
mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
mo_shortname("S. pyo") # "S. pyogenes"
mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"
mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" ('Group A streptococci')
# Language support for German, Dutch, Spanish and Portuguese
mo_type("E. coli", language = "de") # "Bakterium"
mo_type("E. coli", language = "nl") # "Bacterie"
mo_type("E. coli", language = "es") # "Bakteria"
# Language support for German, Dutch, Spanish, Portuguese, Italian and French
mo_gramstain("E. coli", language = "de") # "Gramnegativ"
mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
mo_gramstain("E. coli", language = "es") # "Gram negativo"
# mo_type is equal to mo_kingdom, but mo_kingdom will remain official
mo_kingdom("E. coli") # "Bacteria" on a German system
mo_type("E. coli") # "Bakterien" on a German system
mo_type("E. coli") # "Bacteria" on an English system
mo_fullname("S. pyogenes",
Lancefield = TRUE,
language = "de") # "Streptococcus Gruppe A"
@ -156,7 +189,7 @@ mo_fullname("S. pyogenes",
language = "nl") # "Streptococcus groep A"
# Complete taxonomy up to Subkingdom, returns a list
# Get a list with the complete taxonomy (subkingdom to subspecies)
mo_taxonomy("E. coli")
}
\seealso{