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(v0.7.1.9081) bug_drug fixes

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dr. M.S. (Matthijs) Berends
2019-09-23 13:53:50 +02:00
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commit 64d9829030
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56
man/as.mo.Rd
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@ -75,59 +75,47 @@ The \code{as.mo()} function gains experience from previously determined microorg
Usually, any guess after the first try runs 80-95\% faster than the first try.
This resets with every update of this \code{AMR} package since results are saved to your local package library folder.
\strong{Intelligent rules} \cr
This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:
The \code{as.mo()} function uses several coercion rules for fast and logical results. It assesses the input matching criteria in the following order:
\itemize{
\item{Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations}
\item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones (see \emph{Microbial prevalence of pathogens in humans} below)}
\item{Taxonomic kingdom: it first searches in Bacteria, then Fungi, then Protozoa, then Archaea, then others}
\item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
\item{Human pathogenic prevalence: the function starts with more prevalent microorganisms, followed by less prevalent ones;}
\item{Taxonomic kingdom: the function starts with determining Bacteria, then Fungi, then Protozoa, then others;}
\item{Breakdown of input values to identify possible matches.}
}
This will lead to the effect that e.g. \code{"E. coli"} (a highly prevalent microorganism found in humans) will return the microbial ID of \emph{Escherichia coli} and not \emph{Entamoeba coli} (a less prevalent microorganism in humans), although the latter would alphabetically come first. In addition, the \code{as.mo()} function can differentiate four levels of uncertainty to guess valid results:
A couple of effects because of these rules:
\itemize{
\item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
\item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae} for the same reason}
\item{Something like \code{"stau"} or \code{"S aur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
}
This means that looking up human pathogenic microorganisms takes less time than looking up human non-pathogenic microorganisms.
\strong{Uncertain results} \cr
The algorithm can additionally use three different levels of uncertainty to guess valid results. The default is \code{allow_uncertain = TRUE}, which is equal to uncertainty level 2. Using \code{allow_uncertain = FALSE} will skip all of these additional rules:
\itemize{
\item{(uncertainty level 1): It tries to look for only matching genera, previously accepted (but now invalid) taxonomic names and misspelled input}
\item{(uncertainty level 2): It removed parts between brackets, strips off words from the end one by one and re-evaluates the input with all previous rules}
\item{(uncertainty level 3): It strips off words from the start one by one and tries any part of the name}
\item{Uncertainty level 0: no additional rules are applied;}
\item{Uncertainty level 1: allow previously accepted (but now invalid) taxonomic names and minor spelling errors;}
\item{Uncertainty level 2: allow all of level 1, strip values between brackets, inverse the words of the input, strip off text elements from the end keeping at least two elements;}
\item{Uncertainty level 3: allow all of level 1 and 2, strip off text elements from the end, allow any part of a taxonomic name.}
}
You can also use e.g. \code{as.mo(..., allow_uncertain = 1)} to only allow up to level 1 uncertainty.
This leads to e.g.:
Examples:
\itemize{
\item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPT_GRPB}) needs review.}
\item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
\item{\code{"Fluoroquinolone-resistant Neisseria gonorrhoeae"}. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result \emph{Neisseria gonorrhoeae} (\code{B_NESSR_GON}) needs review.}
\item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AURS}) needs review.}
\item{\code{"Fluoroquinolone-resistant Neisseria gonorrhoeae"}. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result \emph{Neisseria gonorrhoeae} (\code{B_NESSR_GNRR}) needs review.}
}
Use \code{mo_failures()} to get a vector with all values that could not be coerced to a valid value.
The level of uncertainty can be set using the argument \code{allow_uncertain}. The default is \code{allow_uncertain = TRUE}, which is equal to uncertainty level 2. Using \code{allow_uncertain = FALSE} is equal to uncertainty level 0 and will skip all rules. You can also use e.g. \code{as.mo(..., allow_uncertain = 1)} to only allow up to level 1 uncertainty.
Use \code{mo_uncertainties()} to get a data.frame with all values that were coerced to a valid value, but with uncertainty.
Use \code{mo_renamed()} to get a data.frame with all values that could be coerced based on an old, previously accepted taxonomic name.
Use \code{mo_failures()} to get a vector with all values that could not be coerced to a valid value. \cr
Use \code{mo_uncertainties()} to get a \code{data.frame} with all values that were coerced to a valid value, but with uncertainty. \cr
Use \code{mo_renamed()} to get a \code{data.frame} with all values that could be coerced based on an old, previously accepted taxonomic name.
\strong{Microbial prevalence of pathogens in humans} \cr
The intelligent rules take into account microbial prevalence of pathogens in humans. It uses three groups and all (sub)species are in only one group. These groups are:
\itemize{
\item{1 (most prevalent): class is Gammaproteobacteria \strong{or} genus is one of: \emph{Enterococcus}, \emph{Staphylococcus}, \emph{Streptococcus}.}
\item{2: phylum is one of: Proteobacteria, Firmicutes, Actinobacteria, Sarcomastigophora \strong{or} genus is one of: \emph{Aspergillus}, \emph{Bacteroides}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Chryseobacterium}, \emph{Cryptococcus}, \emph{Elisabethkingia}, \emph{Flavobacterium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Leptotrichia}, \emph{Mycoplasma}, \emph{Prevotella}, \emph{Rhodotorula}, \emph{Treponema}, \emph{Trichophyton}, \emph{Ureaplasma}.}
\item{3 (least prevalent): all others.}
}
The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the \code{prevalence} columns in the \code{\link{microorganisms}} and \code{\link{microorganisms.old}} data sets. The grouping into prevalence groups is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence.
Group 1 contains all common Gram positives and Gram negatives, like all Enterobacteriaceae and e.g. \emph{Pseudomonas} and \emph{Legionella}.
Group 1 (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacteriales.
Group 2 contains probably less pathogenic microorganisms; all other members of phyla that were found in humans in the Northern Netherlands between 2001 and 2018.
Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Aspergillus}, \emph{Bacteroides}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Chryseobacterium}, \emph{Cryptococcus}, \emph{Elisabethkingia}, \emph{Flavobacterium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Leptotrichia}, \emph{Mycoplasma}, \emph{Prevotella}, \emph{Rhodotorula}, \emph{Treponema}, \emph{Trichophyton} or \emph{Ureaplasma}.
Group 3 (least prevalent microorganisms) consists of all other microorganisms.
}
\section{Source}{

30
man/bug_drug_combinations.Rd
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@ -8,10 +8,12 @@
\strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
}
\usage{
bug_drug_combinations(x, col_mo = NULL, minimum = 30)
bug_drug_combinations(x, col_mo = NULL, minimum = 30,
FUN = mo_shortname, ...)
\method{format}{bug_drug_combinations}(x, combine_IR = FALSE,
add_ab_group = TRUE, ...)
add_ab_group = TRUE, decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","))
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
@ -20,17 +22,28 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30)
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.}
\item{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link{mo_shortname}}}
\item{...}{argumments passed on to \code{FUN}}
\item{combine_IR}{logical to indicate whether values R and I should be summed}
\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
\item{...}{argumments passed on to \code{\link{mo_name}}}
\item{decimal.mark}{the character to be used to indicate the numeric
decimal point.}
\item{big.mark}{character; if not empty used as mark between every
\code{big.interval} decimals \emph{before} (hence \code{big}) the
decimal point.}
}
\description{
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
}
\details{
The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.
}
\section{Read more on our website!}{
@ -42,5 +55,14 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
x <- bug_drug_combinations(example_isolates)
x
format(x)
# Use FUN to change to transformation of microorganism codes
x <- bug_drug_combinations(example_isolates,
FUN = mo_gramstain)
x <- bug_drug_combinations(example_isolates,
FUN = function(x) ifelse(x == "B_ESCHR_COLI",
"E. coli",
"Others"))
}
}