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dr. M.S. (Matthijs) Berends
2022-10-03 14:34:45 +02:00
parent 75e05a201a
commit 9cbc1d4f16
23 changed files with 245 additions and 211 deletions
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42
man/as.mo.Rd
View File

@ -16,7 +16,7 @@ as.mo(
Lancefield = FALSE,
minimum_matching_score = NULL,
allow_uncertain = TRUE,
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
reference_df = get_mo_source(),
ignore_pattern = getOption("AMR_ignore_pattern", NULL),
language = get_AMR_locale(),
@ -37,11 +37,11 @@ mo_reset_session()
\arguments{
\item{x}{a \link{character} vector or a \link{data.frame} with one or two columns}
\item{Becker}{a \link{logical} to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} (1,2,3).
\item{Becker}{a \link{logical} to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} (see Source).
This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
\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.
\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 (see Source). 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.
This excludes enterococci at default (who are in group D), use \code{Lancefield = "all"} to also categorise all enterococci as group D.}
@ -49,7 +49,7 @@ This excludes enterococci at default (who are in group D), use \code{Lancefield
\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}}
\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{TRUE}, which will return a note if old taxonomic names are returned. The default can be set with \code{options(AMR_keep_synonyms = ...)}.}
\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
\item{reference_df}{a \link{data.frame} to be used for extra reference when translating \code{x} to a valid \code{\link{mo}}. See \code{\link[=set_mo_source]{set_mo_source()}} and \code{\link[=get_mo_source]{get_mo_source()}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
@ -104,22 +104,17 @@ This will lead to the effect that e.g. \code{"E. coli"} (a microorganism highly
\subsection{Coping with Uncertain Results}{
In addition, the \code{\link[=as.mo]{as.mo()}} function can differentiate four levels of uncertainty to guess valid results:
Users can control the coercion rules by setting the \code{allow_uncertain} argument in the \code{\link[=as.mo]{as.mo()}} function. The following values or levels can be used:
\itemize{
\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.
\item \code{0}: no additional rules are applied;
\item \code{1}: allow previously accepted (but now invalid) taxonomic names
\item \code{2}: allow all of \code{1}, strip values between brackets, inverse the words of the input, strip off text elements from the end keeping at least two elements;
\item \code{3}: allow all of level \code{1} and \code{2}, strip off text elements from the end, allow any part of a taxonomic name;
\item \code{TRUE} (default): equivalent to \code{2};
\item \code{FALSE}: equivalent to `0``.
}
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.
With the default setting (\code{allow_uncertain = TRUE}, level 2), below examples will lead to valid results:
\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_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.
}
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.
There are three helper functions that can be run after using the \code{\link[=as.mo]{as.mo()}} function:
\itemize{
@ -137,12 +132,13 @@ The coercion rules consider the prevalence of microorganisms in humans grouped i
\section{Source}{
\enumerate{
\item Becker K. \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
\item Becker K. \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K. \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield R.C. (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci}. \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Berends M.S. \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019} \emph{Microorganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
\item Parte, A.C. \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 12 September, 2022.
\item Berends MS \emph{et al.} (2022). \strong{AMR: An R Package for Working with Antimicrobial Resistance Data}. \emph{Journal of Statistical Software}, 104(3), 1-31; \doi{10.18637/jss.v104.i03}
\item Becker K \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
\item Becker K \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci}. \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019} \emph{Microorganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 12 September, 2022.
\item GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 12 September, 2022.
\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov}
}

2
man/microorganisms.Rd
View File

@ -26,7 +26,7 @@ A \link[tibble:tibble]{tibble} with 48,787 observations and 22 variables:
}
\source{
\itemize{
\item Parte, A.C. \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 12 September, 2022.
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 12 September, 2022.
\item GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 12 September, 2022.
\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov}
}

77
man/mo_property.Rd
View File

@ -37,126 +37,126 @@
mo_name(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_fullname(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_shortname(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_subspecies(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_species(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_genus(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_family(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_order(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_class(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_phylum(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_kingdom(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_domain(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_type(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_status(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_gramstain(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_gram_negative(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_gram_positive(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_is_yeast(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
@ -164,77 +164,77 @@ mo_is_intrinsic_resistant(
x,
ab,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_snomed(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_ref(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_authors(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_year(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_lpsn(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_gbif(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_rank(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_taxonomy(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_synonyms(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
mo_info(
x,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
@ -242,7 +242,7 @@ mo_url(
x,
open = FALSE,
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
@ -250,7 +250,7 @@ mo_property(
x,
property = "fullname",
language = get_AMR_locale(),
keep_synonyms = getOption("AMR_keep_synonyms", TRUE),
keep_synonyms = getOption("AMR_keep_synonyms", FALSE),
...
)
}
@ -259,7 +259,7 @@ mo_property(
\item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}})}
\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{TRUE}, which will return a note if old taxonomic names are returned. The default can be set with \code{options(AMR_keep_synonyms = ...)}.}
\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'allow_uncertain' and 'ignore_pattern'}
@ -337,12 +337,13 @@ All matches are sorted descending on their matching score and for all user input
\section{Source}{
\enumerate{
\item Becker K. \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
\item Becker K. \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K. \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield R.C. (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci}. \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Berends M.S. \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019} \emph{Microorganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
\item Parte, A.C. \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 12 September, 2022.
\item Berends MS \emph{et al.} (2022). \strong{AMR: An R Package for Working with Antimicrobial Resistance Data}. \emph{Journal of Statistical Software}, 104(3), 1-31; \doi{10.18637/jss.v104.i03}
\item Becker K \emph{et al.} (2014). \strong{Coagulase-Negative Staphylococci.} \emph{Clin Microbiol Rev.} 27(4): 870-926; \doi{10.1128/CMR.00109-13}
\item Becker K \emph{et al.} (2019). \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} \emph{Clin Microbiol Infect}; \doi{10.1016/j.cmi.2019.02.028}
\item Becker K \emph{et al.} (2020). \strong{Emergence of coagulase-negative staphylococci} \emph{Expert Rev Anti Infect Ther.} 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci}. \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
\item Berends MS \emph{et al.} (2022). \strong{Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019} \emph{Microorganisms} 10(9), 1801; \doi{10.3390/microorganisms10091801}
\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on 12 September, 2022.
\item GBIF Secretariat (November 26, 2021). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on 12 September, 2022.
\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://phinvads.cdc.gov}
}