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v0.7.0

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dr. M.S. (Matthijs) Berends
2019-06-03 17:45:22 +02:00
parent 702da574c0
commit 270aa0dd33
87 changed files with 507 additions and 544 deletions
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2
man/AMR.Rd
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@ -32,7 +32,7 @@ This package can be used for:
Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] \cr
[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{https://www.rug.nl} \url{https://www.umcg.nl} \cr
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{https://www.certe.nl}
}
\section{Read more on our website!}{

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man/age.Rd
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@ -11,7 +11,7 @@ age(x, reference = Sys.Date(), exact = FALSE)
\item{reference}{reference date(s) (defaults to today), will be coerced with \code{\link{as.POSIXlt}} and cannot be lower than \code{x}}
\item{exact}{a logical to indicate whether age calculation should be exact, i.e. with decimals}
\item{exact}{a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in a year of \code{reference} (either 365 or 366).}
}
\value{
An integer (no decimals) if \code{exact = FALSE}, a double (with decimals) otherwise

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man/as.mo.Rd
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@ -131,7 +131,7 @@ Group 2 probably contains less microbial pathogens; all other members of phyla t
[3] 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}
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
}
\section{Catalogue of Life}{

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man/microorganisms.Rd
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@ -17,7 +17,7 @@
\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
}}
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link{catalogue_of_life_version}()}).
}

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man/microorganisms.old.Rd
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@ -12,7 +12,7 @@
\item{\code{ref}}{Author(s) and year of concerning scientific publication}
}}
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
}
\usage{
microorganisms.old

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man/mo_property.Rd
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@ -115,7 +115,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
[3] 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}
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
}
\section{Read more on our website!}{