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prepare for CRAN

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dr. M.S. (Matthijs) Berends
2023-10-20 14:51:48 +02:00
parent 7dc96794be
commit 7cda9e575b
46 changed files with 7863 additions and 5663 deletions
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8
man/antibiotics.Rd
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@ -21,13 +21,13 @@
\item \code{oral_units}\cr Units of \code{oral_ddd}
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 146 drugs
\item \code{iv_units}\cr Units of \code{iv_ddd}
\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug. Use \code{\link[=ab_loinc]{ab_loinc()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
\item \code{loinc}\cr All codes associated with the name of the antimicrobial drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use \code{\link[=ab_loinc]{ab_loinc()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
}
}
\subsection{For the \link{antivirals} data set: a \link[tibble:tibble]{tibble} with 120 observations and 11 variables:}{
\itemize{
\item \code{av}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{This is a unique identifier.}
\item \code{av}\cr Antiviral ID as used in this package (such as \code{ACI}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{This is a unique identifier.} Combinations are codes that contain a \code{+} to indicate this, such as \code{ATA+COBI} for atazanavir/cobicistat.
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{This is a unique identifier.}
\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
\item \code{cid}\cr Compound ID as found in PubChem. \emph{This is a unique identifier.}
@ -37,7 +37,7 @@
\item \code{oral_units}\cr Units of \code{oral_ddd}
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment
\item \code{iv_units}\cr Units of \code{iv_ddd}
\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug.
\item \code{loinc}\cr All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use \code{\link[=av_loinc]{av_loinc()}} to retrieve them quickly, see \code{\link[=av_property]{av_property()}}.
}
}
@ -46,7 +46,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w
\source{
\itemize{
\item World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
\item Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022). Accessed from \url{https://loinc.org} on October 30th, 2022.
\item Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Accessed from \url{https://loinc.org} on October 19th, 2023.
\item European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
}
}

2
man/microorganisms.Rd
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@ -12,7 +12,7 @@ A \link[tibble:tibble]{tibble} with 52 171 observations and 23 variables:
\item \code{status} \cr Status of the taxon, either "accepted" or "synonym"
\item \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}\cr Taxonomic rank of the microorganism
\item \code{rank}\cr Text of the taxonomic rank of the microorganism, such as \code{"species"} or \code{"genus"}
\item \code{ref}\cr Author(s) and year of related scientific publication. This contains only the \emph{first surname} and year of the \emph{latest} authors, e.g. "Wallis \emph{et al.} 2006 \emph{emend.} Smith and Jones 2018" becomes "Smith \emph{et al.}, 2018". This field is directly retrieved from the source specified in the column \code{source}. Moreover, accents were removed to comply with CRAN that only allows ASCII characters, e.g. "Váňová" becomes "Vanova".
\item \code{ref}\cr Author(s) and year of related scientific publication. This contains only the \emph{first surname} and year of the \emph{latest} authors, e.g. "Wallis \emph{et al.} 2006 \emph{emend.} Smith and Jones 2018" becomes "Smith \emph{et al.}, 2018". This field is directly retrieved from the source specified in the column \code{source}. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.
\item \code{lpsn}\cr Identifier ('Record number') of the List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, \emph{Acetobacter ascendens} has LPSN Record number 7864 and 11011. Only the first is available in the \code{microorganisms} data set.
\item \code{oxygen_tolerance} \cr Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 73.4\% of all ~37 000 bacteria in the data set contain an oxygen tolerance.
\item \code{lpsn_parent}\cr LPSN identifier of the parent taxon

6
man/proportion.Rd
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@ -97,13 +97,13 @@ These functions can be used to calculate the (co-)resistance or susceptibility o
\code{\link[=resistance]{resistance()}} should be used to calculate resistance, \code{\link[=susceptibility]{susceptibility()}} should be used to calculate susceptibility.\cr
}
\details{
\strong{Remember that you should filter your data to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set with one of the four available algorithms.
The function \code{\link[=resistance]{resistance()}} is equal to the function \code{\link[=proportion_R]{proportion_R()}}. The function \code{\link[=susceptibility]{susceptibility()}} is equal to the function \code{\link[=proportion_SI]{proportion_SI()}}.
Use \code{\link[=sir_confidence_interval]{sir_confidence_interval()}} to calculate the confidence interval, which relies on \code{\link[=binom.test]{binom.test()}}, i.e., the Clopper-Pearson method. This function returns a vector of length 2 at default for antimicrobial \emph{resistance}. Change the \code{side} argument to "left"/"min" or "right"/"max" to return a single value, and change the \code{ab_result} argument to e.g. \code{c("S", "I")} to test for antimicrobial \emph{susceptibility}, see Examples.
\strong{Remember that you should filter your data to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set with one of the four available algorithms.
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[=count]{count()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} argument).}
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[=count]{count_*()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{\link[=count_susceptible]{count_susceptible()}}\code{/}\code{\link[=count_all]{count_all()}}. \emph{Low counts can influence the outcome - the \verb{proportion_*()} functions may camouflage this, since they only return the proportion (albeit dependent on the \code{minimum} argument).}
The function \code{\link[=proportion_df]{proportion_df()}} takes any variable from \code{data} that has an \code{\link{sir}} class (created with \code{\link[=as.sir]{as.sir()}}) and calculates the proportions S, I, and R. It also supports grouped variables. The function \code{\link[=sir_df]{sir_df()}} works exactly like \code{\link[=proportion_df]{proportion_df()}}, but adds the number of isolates.
}

9
man/translate.Rd
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@ -58,17 +58,12 @@ ab_name("Ciprofloxacin")
mo_name("Coagulase-negative Staphylococcus (CoNS)")
# setting another language
set_AMR_locale("Spanish")
set_AMR_locale("Dutch")
ab_name("Ciprofloxacin")
mo_name("Coagulase-negative Staphylococcus (CoNS)")
# setting yet another language
set_AMR_locale("Greek")
ab_name("Ciprofloxacin")
mo_name("Coagulase-negative Staphylococcus (CoNS)")
# setting yet another language
set_AMR_locale("Ukrainian")
set_AMR_locale("German")
ab_name("Ciprofloxacin")
mo_name("Coagulase-negative Staphylococcus (CoNS)")