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(v1.8.0.9001) as.mo improvement, fixes #52
This commit is contained in:
@ -8,7 +8,7 @@ These functions are so-called '\link{Deprecated}'. \strong{They will be removed
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}
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\section{Retired Lifecycle}{
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\if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
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\if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
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}
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@ -8,7 +8,7 @@ All antimicrobial drugs and their official names, ATC codes, ATC groups and defi
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}
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\section{WHOCC}{
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\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
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\if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr}
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This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}).
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These have become the gold standard for international drug utilisation monitoring and research.
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@ -59,7 +59,7 @@ With using \code{collapse}, this function will return a \link{character}:\cr
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}
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
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If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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@ -97,7 +97,7 @@ The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column ren
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}
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
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If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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@ -30,7 +30,7 @@ This function vectorises over both \code{x} and \code{reference}, meaning that e
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}
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
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If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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@ -35,7 +35,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
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}
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
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If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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@ -166,7 +166,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
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If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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@ -80,7 +80,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation,
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\section{WHOCC}{
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\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
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\if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr}
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This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}).
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These have become the gold standard for international drug utilisation monitoring and research.
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@ -49,7 +49,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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@ -57,7 +57,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
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\section{WHOCC}{
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||||
|
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\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
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||||
\if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr}
|
||||
This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}).
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These have become the gold standard for international drug utilisation monitoring and research.
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@ -35,7 +35,7 @@ Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It sup
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}
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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|
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@ -67,7 +67,7 @@ The following \link[=groupGeneric]{generic functions} are implemented for the MI
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}
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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12
man/as.mo.Rd
12
man/as.mo.Rd
@ -36,9 +36,9 @@ mo_renamed()
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This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
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\item{Lancefield}{a \link{logical} to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
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\item{Lancefield}{a \link{logical} to indicate whether a beta-haemolytic \emph{Streptococcus} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These streptococci will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
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This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
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This excludes enterococci at default (who are in group D), use \code{Lancefield = "all"} to also categorise all enterococci as group D.}
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\item{allow_uncertain}{a number between \code{0} (or \code{"none"}) and \code{3} (or \code{"all"}), or \code{TRUE} (= \code{2}) or \code{FALSE} (= \code{0}) to indicate whether the input should be checked for less probable results, see \emph{Details}}
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@ -138,7 +138,7 @@ The intelligent rules consider the prevalence of microorganisms in humans groupe
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\section{Stable Lifecycle}{
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||||
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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@ -148,7 +148,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
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With ambiguous user input in \code{\link[=as.mo]{as.mo()}} and all the \code{\link[=mo_property]{mo_*}} functions, the returned results are chosen based on their matching score using \code{\link[=mo_matching_score]{mo_matching_score()}}. This matching score \eqn{m}, is calculated as:
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\ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300px" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
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\ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
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where:
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\itemize{
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@ -165,11 +165,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
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All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
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All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
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Since \code{AMR} version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.
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}
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\section{Catalogue of Life}{
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\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
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\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
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This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
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\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
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@ -152,7 +152,7 @@ This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{su
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\section{Stable Lifecycle}{
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||||
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
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@ -71,7 +71,7 @@ Abbreviations of return values when using \code{property = "U"} (unit):
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}
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\section{Stable Lifecycle}{
|
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|
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
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@ -22,7 +22,7 @@ The function returns a \link{data.frame} with columns \code{"resistant"} and \co
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||||
}
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||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -65,7 +65,7 @@ The function \code{\link[=format]{format()}} calculates the resistance per bug-d
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||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -8,7 +8,7 @@ This package contains the complete taxonomic tree (last updated: 5 October 2021)
|
||||
}
|
||||
\section{Catalogue of Life}{
|
||||
|
||||
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
|
||||
|
||||
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
|
||||
|
||||
@ -17,7 +17,7 @@ For LPSN, see \link{microorganisms}.
|
||||
}
|
||||
\section{Catalogue of Life}{
|
||||
|
||||
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
|
||||
|
||||
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
|
||||
|
||||
@ -74,7 +74,7 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -102,7 +102,7 @@ It is possible to define antibiotic groups instead of single antibiotics for the
|
||||
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -107,7 +107,7 @@ Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&sho
|
||||
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -166,7 +166,7 @@ The default method is phenotype-based (using \code{type = "points"}) and episode
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -99,7 +99,7 @@ If there are more than two categories and you want to find out which ones are si
|
||||
}
|
||||
\section{Questioning Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
}
|
||||
|
||||
|
||||
@ -34,7 +34,7 @@ The \code{dplyr} package is not required for these functions to work, but these
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -110,7 +110,7 @@ The colours for labels and points can be changed by adding another scale layer f
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -142,7 +142,7 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -31,7 +31,7 @@ You can look for an antibiotic (trade) name or abbreviation and it will search \
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -26,7 +26,7 @@ This function also supports abbreviation of the genus if it is followed by a spe
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -45,7 +45,7 @@ If the \code{dplyr} package is installed, their join functions will be used. Oth
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -109,7 +109,7 @@ The default antimicrobial agents used for \strong{fungi} (set in \code{antifunga
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -27,7 +27,7 @@ Kurtosis is a measure of the "tailedness" of the probability distribution of a r
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -6,24 +6,24 @@
|
||||
\description{
|
||||
Functions in this \code{AMR} package are categorised using \href{https://lifecycle.r-lib.org/articles/stages.html}{the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle}.
|
||||
|
||||
\if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_tidyverse.svg}{options: height="200" style=margin-bottom:"5"} \cr}
|
||||
This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions.
|
||||
}
|
||||
\section{Experimental Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
|
||||
}
|
||||
|
||||
\section{Maturing Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
|
||||
}
|
||||
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
@ -31,13 +31,13 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
|
||||
|
||||
\section{Retired Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
|
||||
}
|
||||
|
||||
\section{Questioning Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
}
|
||||
|
||||
|
||||
@ -47,7 +47,7 @@ Using RStudio? The \verb{\%like\%}/\verb{\%unlike\%} functions can also be direc
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -157,7 +157,7 @@ The rules set (the \code{custom} object in this case) could be exported to a sha
|
||||
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -84,7 +84,7 @@ As of February 2020, the regularly augmented LPSN database at DSMZ is the basis
|
||||
|
||||
\section{Catalogue of Life}{
|
||||
|
||||
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
|
||||
|
||||
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
|
||||
|
||||
@ -24,7 +24,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation,
|
||||
|
||||
\section{Catalogue of Life}{
|
||||
|
||||
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
|
||||
|
||||
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
|
||||
|
||||
@ -26,7 +26,7 @@ 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}
|
||||
\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
|
||||
|
||||
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
|
||||
|
||||
@ -18,7 +18,7 @@ This algorithm is used by \code{\link[=as.mo]{as.mo()}} and all the \code{\link[
|
||||
|
||||
With ambiguous user input in \code{\link[=as.mo]{as.mo()}} and all the \code{\link[=mo_property]{mo_*}} functions, the returned results are chosen based on their matching score using \code{\link[=mo_matching_score]{mo_matching_score()}}. This matching score \eqn{m}, is calculated as:
|
||||
|
||||
\ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300px" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
||||
\ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
||||
|
||||
where:
|
||||
\itemize{
|
||||
@ -35,11 +35,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
|
||||
All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
|
||||
|
||||
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
|
||||
|
||||
Since \code{AMR} version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.
|
||||
}
|
||||
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
@ -63,5 +65,5 @@ mo_matching_score(x = "E. coli",
|
||||
n = c("Escherichia coli", "Entamoeba coli"))
|
||||
}
|
||||
\author{
|
||||
Dr. Matthijs Berends
|
||||
Dr Matthijs Berends
|
||||
}
|
||||
|
||||
@ -141,7 +141,7 @@ SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition o
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
@ -151,7 +151,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
|
||||
|
||||
With ambiguous user input in \code{\link[=as.mo]{as.mo()}} and all the \code{\link[=mo_property]{mo_*}} functions, the returned results are chosen based on their matching score using \code{\link[=mo_matching_score]{mo_matching_score()}}. This matching score \eqn{m}, is calculated as:
|
||||
|
||||
\ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300px" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
||||
\ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
||||
|
||||
where:
|
||||
\itemize{
|
||||
@ -168,11 +168,13 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f
|
||||
All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
|
||||
|
||||
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.079}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
|
||||
|
||||
Since \code{AMR} version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: AIEC, ATEC, BORSA, CRSM, DAEC, EAEC, EHEC, EIEC, EPEC, ETEC, GISA, MRPA, MRSA, MRSE, MSSA, MSSE, NMEC, PISP, PRSP, STEC, UPEC, VISA, VISP, VRE, VRSA and VRSP.
|
||||
}
|
||||
|
||||
\section{Catalogue of Life}{
|
||||
|
||||
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
|
||||
|
||||
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
|
||||
|
||||
@ -97,7 +97,7 @@ If the original file (in the previous case an Excel file) is moved or deleted, t
|
||||
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -61,7 +61,7 @@ The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object,
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -131,7 +131,7 @@ Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -120,7 +120,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
|
||||
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -37,7 +37,7 @@ Generated values are based on the latest EUCAST guideline implemented in the \li
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -112,7 +112,7 @@ Valid options for the statistical model (argument \code{model}) are:
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -27,7 +27,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
@ -29,7 +29,7 @@ Thus, if the R option \code{AMR_locale} is set, the system variables \code{LANGU
|
||||
}
|
||||
\section{Stable Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
|
||||
If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
|
||||
Reference in New Issue
Block a user