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(v0.7.0.9005) ab algorithm update

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dr. M.S. (Matthijs) Berends
2019-06-11 14:18:25 +02:00
parent f6c47c8c88
commit 8f674e19bb
36 changed files with 274 additions and 248 deletions
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2
man/antibiotics.Rd
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@ -4,7 +4,7 @@
\name{antibiotics}
\alias{antibiotics}
\title{Data set with ~450 antibiotics}
\format{A \code{\link{data.frame}} with 454 observations and 13 variables:
\format{A \code{\link{data.frame}} with 453 observations and 13 variables:
\describe{
\item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}

6
man/catalogue_of_life.Rd
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@ -61,9 +61,9 @@ mo_ref("E. coli")
# [1] "Castellani et al., 1919"
# Do not get mistaken - the package only includes microorganisms
mo_phylum("C. elegans")
# [1] "Cyanobacteria" # Bacteria?!
mo_fullname("C. elegans")
mo_kingdom("C. elegans")
# [1] "Bacteria" # Bacteria?!
mo_name("C. elegans")
# [1] "Chroococcus limneticus elegans" # Because a microorganism was found
}
\seealso{

4
man/catalogue_of_life_version.Rd
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@ -10,11 +10,9 @@ catalogue_of_life_version()
a \code{list}, which prints in pretty format
}
\description{
This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.
This function returns information about the included data from the Catalogue of Life.
}
\details{
The list item \code{...$catalogue_of_life$is_latest_annual_release} is based on the system date.
For DSMZ, see \code{?microorganisms}.
}
\section{Catalogue of Life}{

42
man/key_antibiotics.Rd
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@ -5,19 +5,22 @@
\alias{key_antibiotics_equal}
\title{Key antibiotics for first \emph{weighted} isolates}
\usage{
key_antibiotics(x, col_mo = NULL, universal_1 = guess_ab_col(x, "AMX"),
universal_2 = guess_ab_col(x, "AMC"), universal_3 = guess_ab_col(x,
"CXM"), universal_4 = guess_ab_col(x, "TZP"),
universal_5 = guess_ab_col(x, "CIP"), universal_6 = guess_ab_col(x,
"SXT"), GramPos_1 = guess_ab_col(x, "VAN"),
GramPos_2 = guess_ab_col(x, "TEC"), GramPos_3 = guess_ab_col(x,
"TCY"), GramPos_4 = guess_ab_col(x, "ERY"),
GramPos_5 = guess_ab_col(x, "OXA"), GramPos_6 = guess_ab_col(x,
"RIF"), GramNeg_1 = guess_ab_col(x, "GEN"),
GramNeg_2 = guess_ab_col(x, "TOB"), GramNeg_3 = guess_ab_col(x,
"COL"), GramNeg_4 = guess_ab_col(x, "CTX"),
GramNeg_5 = guess_ab_col(x, "CAZ"), GramNeg_6 = guess_ab_col(x,
"MEM"), warnings = TRUE, ...)
key_antibiotics(x, col_mo = NULL, universal_1 = guess_ab_col(x,
"amoxicillin"), universal_2 = guess_ab_col(x,
"amoxicillin/clavulanic acid"), universal_3 = guess_ab_col(x,
"cefuroxime"), universal_4 = guess_ab_col(x,
"piperacillin/tazobactam"), universal_5 = guess_ab_col(x,
"ciprofloxacin"), universal_6 = guess_ab_col(x,
"trimethoprim/sulfamethoxazole"), GramPos_1 = guess_ab_col(x,
"vancomycin"), GramPos_2 = guess_ab_col(x, "teicoplanin"),
GramPos_3 = guess_ab_col(x, "tetracycline"),
GramPos_4 = guess_ab_col(x, "erythromycin"),
GramPos_5 = guess_ab_col(x, "oxacillin"), GramPos_6 = guess_ab_col(x,
"rifampin"), GramNeg_1 = guess_ab_col(x, "gentamicin"),
GramNeg_2 = guess_ab_col(x, "tobramycin"),
GramNeg_3 = guess_ab_col(x, "colistin"), GramNeg_4 = guess_ab_col(x,
"cefotaxime"), GramNeg_5 = guess_ab_col(x, "ceftazidime"),
GramNeg_6 = guess_ab_col(x, "meropenem"), warnings = TRUE, ...)
key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"),
ignore_I = TRUE, points_threshold = 2, info = FALSE)
@ -29,9 +32,9 @@ key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"),
\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
\item{GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6}{column names of antibiotics for \strong{Gram positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
\item{GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6}{column names of antibiotics for \strong{Gram-positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
\item{GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6}{column names of antibiotics for \strong{Gram negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
\item{GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6}{column names of antibiotics for \strong{Gram-negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
\item{warnings}{give warning about missing antibiotic columns, they will anyway be ignored}
@ -53,11 +56,11 @@ These function can be used to determine first isolates (see \code{\link{first_is
\details{
The function \code{key_antibiotics} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{key_antibiotics_equal}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link{first_isolate}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link{first_isolate}}). Without key antibiotic comparison it would not.
At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
\code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"vanc"}, \code{"teic"}, \code{"tetr"}, \code{"eryt"}, \code{"oxac"}, \code{"rifa"}.
At default, the antibiotics that are used for \strong{Gram-positive bacteria} are: \cr
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampin.
At default, the antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
\code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"gent"}, \code{"tobr"}, \code{"coli"}, \code{"cfot"}, \code{"cfta"}, \code{"mero"}.
At default, the antibiotics that are used for \strong{Gram-negative bacteria} are: \cr
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem.
The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical vector.
@ -81,6 +84,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
\examples{
# septic_patients is a dataset available in the AMR package
?septic_patients
library(dplyr)
# set key antibiotics to a new variable
my_patients <- septic_patients \%>\%

11
man/mo_property.Rd
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@ -20,6 +20,7 @@
\alias{mo_year}
\alias{mo_rank}
\alias{mo_taxonomy}
\alias{mo_info}
\alias{mo_url}
\title{Property of a microorganism}
\usage{
@ -59,6 +60,8 @@ mo_rank(x, ...)
mo_taxonomy(x, language = get_locale(), ...)
mo_info(x, language = get_locale(), ...)
mo_url(x, open = FALSE, ...)
mo_property(x, property = "fullname", language = get_locale(), ...)
@ -140,8 +143,8 @@ mo_fullname("E. coli") # "Escherichia coli", same as mo_name()
mo_shortname("E. coli") # "E. coli"
## other properties
mo_gramstain("E. coli") # "Gram negative"
mo_type("E. coli") # "Bacteria" (equal to kingdom)
mo_gramstain("E. coli") # "Gram-negative"
mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
mo_rank("E. coli") # "species"
mo_url("E. coli") # get the direct url to the online database entry
@ -155,7 +158,7 @@ mo_year("E. coli") # 1919
mo_genus("MRSA") # "Staphylococcus"
mo_species("MRSA") # "aureus"
mo_shortname("MRSA") # "S. aureus"
mo_gramstain("MRSA") # "Gram positive"
mo_gramstain("MRSA") # "Gram-positive"
mo_genus("VISA") # "Staphylococcus"
mo_species("VISA") # "aureus"
@ -204,6 +207,8 @@ mo_fullname("S. pyogenes",
# get a list with the complete taxonomy (from kingdom to subspecies)
mo_taxonomy("E. coli")
# get a list with the taxonomy, the authors and the URL to the online database
mo_info("E. coli")
}
\seealso{
\code{\link{microorganisms}}