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speed improvement for as.mo, more old taxonomic names

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dr. M.S. (Matthijs) Berends
2018-09-27 23:23:48 +02:00
parent 450992baea
commit 2b0080995e
18 changed files with 481 additions and 441 deletions
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2
man/as.mo.Rd
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@ -65,7 +65,7 @@ This means that looking up human non-pathogenic microorganisms takes a longer ti
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
}
\section{Source}{

2
man/microorganisms.Rd
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@ -34,7 +34,7 @@ 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 \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
}
\seealso{

21
man/microorganisms.certe.Rd Normal file
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@ -0,0 +1,21 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{microorganisms.certe}
\alias{microorganisms.certe}
\title{Translation table for Certe}
\format{A \code{\link{tibble}} with 2,664 observations and 2 variables:
\describe{
\item{\code{certe}}{Code of microorganism according to Certe MMB}
\item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
}}
\usage{
microorganisms.certe
}
\description{
A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
}
\seealso{
\code{\link{as.mo}} \code{\link{microorganisms}}
}
\keyword{datasets}

6
man/microorganisms.old.Rd
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@ -4,7 +4,7 @@
\name{microorganisms.old}
\alias{microorganisms.old}
\title{Data set with old taxonomic data from ITIS}
\format{A \code{\link{data.frame}} with 1,682 observations and 5 variables:
\format{A \code{\link{data.frame}} with 2,384 observations and 5 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}
@ -19,12 +19,12 @@
microorganisms.old
}
\description{
A data set containing old, previously valid, taxonomic names. This data set is used internally by \code{\link{as.mo}}.
A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by \code{\link{as.mo}}.
}
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
}
\seealso{

4
man/microorganisms.umcg.Rd
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@ -7,7 +7,7 @@
\format{A \code{\link{tibble}} with 1,095 observations and 2 variables:
\describe{
\item{\code{umcg}}{Code of microorganism according to UMCG MMB}
\item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
\item{\code{certe}}{Code of microorganism according to Certe MMB}
}}
\usage{
microorganisms.umcg
@ -16,6 +16,6 @@ microorganisms.umcg
A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
}
\seealso{
\code{\link{as.mo}} \code{\link{microorganisms}}
\code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
}
\keyword{datasets}

6
man/mo_property.Rd
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@ -65,7 +65,7 @@ mo_taxonomy(x)
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}}
}
\value{
A logical (in case of \code{mo_aerobic}), a list (in case of \code{mo_taxonomy}), a character otherwise
A \code{list} (in case of \code{mo_taxonomy}) or a \code{character} otherwise
}
\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}}.
@ -73,7 +73,7 @@ Use these functions to return a specific property of a microorganism from the \c
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
}
\section{Source}{
@ -94,7 +94,7 @@ mo_order("E. coli") # "Enterobacteriales"
mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"
mo_subspecies("E. coli") # ""
mo_subspecies("E. coli") # NA
mo_fullname("E. coli") # "Escherichia coli"
mo_shortname("E. coli") # "E. coli"
mo_gramstain("E. coli") # "Gram negative"