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(v0.7.1.9055) algorithm improvements

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dr. M.S. (Matthijs) Berends
2019-08-13 16:15:08 +02:00
parent 6c4822164c
commit 7108454ba5
77 changed files with 644 additions and 582 deletions
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12
man/as.mo.Rd
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@ -31,7 +31,7 @@ mo_renamed()
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{allow_uncertain}{a logical (\code{TRUE} or \code{FALSE}) or a value between 0 and 3 to indicate whether the input should be checked for less possible results, see Details}
\item{allow_uncertain}{a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less possible results, see Details}
\item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
@ -58,8 +58,7 @@ A microbial ID from this package (class: \code{mo}) typically looks like these e
| | ----> species, a 3-4 letter acronym
| ----> genus, a 5-7 letter acronym, mostly without vowels
----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa) or
PL (Plantae)
C (Chromista), F (Fungi), P (Protozoa)
}
Values that cannot be coered will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
@ -134,9 +133,9 @@ Group 2 probably contains less microbial pathogens; all other members of phyla t
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{
@ -179,7 +178,8 @@ as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRA
# All mo_* functions use as.mo() internally too (see ?mo_property):
mo_genus("E. coli") # returns "Escherichia"
mo_gramstain("E. coli") # returns "Gram negative"#'
mo_gramstain("E. coli") # returns "Gram negative"
}
\dontrun{
df$mo <- as.mo(df$microorganism_name)

6
man/catalogue_of_life.Rd
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@ -9,9 +9,9 @@ This package contains the complete taxonomic tree of almost all microorganisms f
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Included taxa}{
@ -26,7 +26,7 @@ Included are:
\item{The responsible author(s) and year of scientific publication}
}
The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
}

4
man/catalogue_of_life_version.Rd
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@ -18,9 +18,9 @@ For DSMZ, see \code{?microorganisms}.
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{

12
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~70,000 microorganisms}
\format{A \code{\link{data.frame}} with 69,854 observations and 16 variables:
\format{A \code{\link{data.frame}} with 69,855 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
@ -13,7 +13,7 @@
\item{\code{rank}}{Text of the taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}}
\item{\code{ref}}{Author(s) and year of concerning scientific publication}
\item{\code{species_id}}{ID of the species as used by the Catalogue of Life}
\item{\code{source}}{Either \code{"CoL"}, \code{"DSMZ"} (see source) or "manually added"}
\item{\code{source}}{Either "CoL", "DSMZ" (see Source) or "manually added"}
\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
}}
\source{
@ -30,9 +30,9 @@ A data set containing the microbial taxonomy of six kingdoms from the Catalogue
\details{
Manually added were:
\itemize{
\item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
\item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
\item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
\item{8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
}
@ -47,9 +47,9 @@ From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloa
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{

4
man/microorganisms.codes.Rd
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@ -18,9 +18,9 @@ A data set containing commonly used codes for microorganisms, from laboratory sy
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{

4
man/microorganisms.old.Rd
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@ -23,9 +23,9 @@ A data set containing old (previously valid or accepted) taxonomic names accordi
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{

4
man/mo_property.Rd
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@ -108,9 +108,9 @@ The function \code{mo_url()} will return the direct URL to the online database e
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Source}{