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added taxonomic data from ITIS

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dr. M.S. (Matthijs) Berends
2018-09-17 20:53:32 +02:00
parent 7680e4edd8
commit 5d80cef338
13 changed files with 150 additions and 80 deletions
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12
man/ggplot_rsi.Rd
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@ -62,15 +62,15 @@ Use these functions to create bar plots for antimicrobial resistance analysis. A
At default, the names of antibiotics will be shown on the plots using \code{\link{abname}}. This can be set with the option \code{get_antibiotic_names} (a logical value), so change it e.g. to \code{FALSE} with \code{options(get_antibiotic_names = FALSE)}.
\strong{The functions}\cr
\code{geom_rsi} will take any variable from the data that has an \code{rsi} class (created with \code{\link{as.rsi}}) using \code{fun} (\code{\link{portion_df}} at default, could also be \code{\link{count_df}}) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
\code{geom_rsi} will take any variable from the data that has an \code{rsi} class (created with \code{\link{as.rsi}}) using \code{fun} (\code{\link{count_df}} at default, can also be \code{\link{portion_df}}) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
\code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2]{facet_wrap}}.
\code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_y_continuous}}.
\code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_continuous}}.
\code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R, using \code{\link[ggplot2]{scale_fill_brewer}}.
\code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R, using \code{\link[ggplot2]{scale_colour_brewer}}.
\code{theme_rsi} is a \code{\link[ggplot2]{theme}} with minimal distraction.
\code{theme_rsi} is a \code{ggplot \link[ggplot2]{theme}} with minimal distraction.
\code{labels_rsi_count} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2]{geom_text}}
@ -98,10 +98,10 @@ septic_patients \%>\%
select(amox, nitr, fosf, trim, cipr) \%>\%
ggplot_rsi()
# get counts instead of percentages:
# get only portions and no counts:
septic_patients \%>\%
select(amox, nitr, fosf, trim, cipr) \%>\%
ggplot_rsi(fun = count_df)
ggplot_rsi(fun = portion_df)
# add other ggplot2 parameters as you like:
septic_patients \%>\%

14
man/microorganisms.Rd
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@ -4,20 +4,26 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with human pathogenic microorganisms}
\format{A \code{\link{tibble}} with 2,642 observations and 11 variables:
\format{A \code{\link{tibble}} with 2,642 observations and 14 variables:
\describe{
\item{\code{mo}}{ID of microorganism}
\item{\code{bactsys}}{Bactsyscode of microorganism}
\item{\code{family}}{Family name of microorganism}
\item{\code{genus}}{Genus name of microorganism, like \code{"Echerichia"}}
\item{\code{species}}{Species name of microorganism, like \code{"coli"}}
\item{\code{subspecies}}{Subspecies name of bio-/serovar of microorganism, like \code{"EHEC"}}
\item{\code{fullname}}{Full name, like \code{"Echerichia coli (EHEC)"}}
\item{\code{aerobic}}{Logical whether bacteria is aerobic}
\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
\item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
\item{\code{aerobic}}{Logical whether bacteria is aerobic}
\item{\code{family}}{Taxonomic family of the microorganism as found in ITIS, see Source}
\item{\code{order}}{Taxonomic order of the microorganism as found in ITIS, see Source}
\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{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
\item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
}}
\source{
Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
}
\usage{
microorganisms
}

2
man/microorganisms.umcg.Rd
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@ -3,7 +3,7 @@
\docType{data}
\name{microorganisms.umcg}
\alias{microorganisms.umcg}
\title{Translation table for UMCG with ~1,100 microorganisms}
\title{Translation table for UMCG}
\format{A \code{\link{tibble}} with 1,095 observations and 2 variables:
\describe{
\item{\code{umcg}}{Code of microorganism according to UMCG MMB}

51
man/mo_property.Rd
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@ -2,34 +2,46 @@
% Please edit documentation in R/mo_property.R
\name{mo_property}
\alias{mo_property}
\alias{mo_family}
\alias{mo_genus}
\alias{mo_species}
\alias{mo_subspecies}
\alias{mo_fullname}
\alias{mo_shortname}
\alias{mo_subspecies}
\alias{mo_species}
\alias{mo_genus}
\alias{mo_family}
\alias{mo_order}
\alias{mo_class}
\alias{mo_phylum}
\alias{mo_type}
\alias{mo_gramstain}
\alias{mo_aerobic}
\alias{mo_taxonomy}
\title{Property of a microorganism}
\source{
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
}
\usage{
mo_family(x)
mo_genus(x, language = NULL)
mo_species(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_subspecies(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_fullname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_shortname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_subspecies(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_species(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_genus(x, language = NULL)
mo_family(x)
mo_order(x)
mo_class(x)
mo_phylum(x)
mo_type(x, language = NULL)
mo_gramstain(x, language = NULL)
@ -38,12 +50,12 @@ mo_aerobic(x)
mo_property(x, property = "fullname", Becker = FALSE,
Lancefield = FALSE, language = NULL)
mo_taxonomy(x)
}
\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 the systems language. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).}
\item{Becker}{a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1].
This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
@ -52,16 +64,21 @@ mo_property(x, property = "fullname", Becker = FALSE,
This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
\item{language}{language of the returned text, defaults to the systems language. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).}
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"mo"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
}
\value{
Character or logical (only \code{mo_aerobic})
A logical (in case of \code{mo_aerobic}), a list (in case of \code{mo_taxonomy}), a 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}}.
}
\examples{
# All properties
mo_phylum("E. coli") # "Proteobacteria"
mo_class("E. coli") # "Gammaproteobacteria"
mo_order("E. coli") # "Enterobacteriales"
mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"
@ -132,6 +149,10 @@ mo_fullname("S. pyogenes",
mo_fullname("S. pyogenes",
Lancefield = TRUE,
language = "nl") # "Streptococcus groep A"
# Complete taxonomy up to Phylum, returns a list
mo_taxonomy("E. coli")
}
\seealso{
\code{\link{microorganisms}}