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eucast update

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dr. M.S. (Matthijs) Berends
2018-11-01 20:23:33 +01:00
parent f7687557c9
commit 5476fecc73
16 changed files with 82 additions and 69 deletions
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41
man/EUCAST.Rd
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@ -22,25 +22,24 @@
}
}
\usage{
EUCAST_rules(tbl, col_mo = "mo", info = TRUE,
rules = c("breakpoints", "expert", "other", "all"), amcl = "amcl",
amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
azlo = "azlo", aztr = "aztr", cefa = "cefa", cfep = "cfep",
cfot = "cfot", cfox = "cfox", cfra = "cfra", cfta = "cfta",
cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
clar = "clar", clin = "clin", clox = "clox", coli = "coli",
czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
imip = "imip", kana = "kana", levo = "levo", linc = "linc",
line = "line", mero = "mero", mezl = "mezl", mino = "mino",
moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
nitr = "nitr", norf = "norf", novo = "novo", oflo = "oflo",
oxac = "oxac", peni = "peni", pipe = "pipe", pita = "pita",
poly = "poly", pris = "pris", qida = "qida", rifa = "rifa",
roxi = "roxi", siso = "siso", teic = "teic", tetr = "tetr",
tica = "tica", tige = "tige", tobr = "tobr", trim = "trim",
trsu = "trsu", vanc = "vanc", col_bactid = "bactid",
verbose = FALSE)
EUCAST_rules(tbl, col_mo = NULL, info = TRUE,
rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
azit = "azit", azlo = "azlo", aztr = "aztr", cefa = "cefa",
cfep = "cfep", cfot = "cfot", cfox = "cfox", cfra = "cfra",
cfta = "cfta", cftr = "cftr", cfur = "cfur", chlo = "chlo",
cipr = "cipr", clar = "clar", clin = "clin", clox = "clox",
coli = "coli", czol = "czol", dapt = "dapt", doxy = "doxy",
erta = "erta", eryt = "eryt", fosf = "fosf", fusi = "fusi",
gent = "gent", imip = "imip", kana = "kana", levo = "levo",
linc = "linc", line = "line", mero = "mero", mezl = "mezl",
mino = "mino", moxi = "moxi", nali = "nali", neom = "neom",
neti = "neti", nitr = "nitr", norf = "norf", novo = "novo",
oflo = "oflo", oxac = "oxac", peni = "peni", pipe = "pipe",
pita = "pita", poly = "poly", pris = "pris", qida = "qida",
rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
trim = "trim", trsu = "trsu", vanc = "vanc", col_bactid = NULL)
interpretive_reading(...)
}
@ -53,12 +52,12 @@ interpretive_reading(...)
\item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}}
\item{verbose}{a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected}
\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details}
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
\item{verbose}{a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected}
\item{...}{parameters that are passed on to \code{EUCAST_rules}}
}
\value{

11
man/MDRO.Rd
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@ -19,10 +19,11 @@ MDRO(tbl, country = NULL, col_mo = NULL, info = TRUE,
line = "line", mero = "mero", metr = "metr", mino = "mino",
moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
nitr = "nitr", novo = "novo", norf = "norf", oflo = "oflo",
peni = "peni", pita = "pita", poly = "poly", qida = "qida",
rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
trim = "trim", trsu = "trsu", vanc = "vanc", col_bactid = NULL)
peni = "peni", pipe = "pipe", pita = "pita", poly = "poly",
qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso",
teic = "teic", tetr = "tetr", tica = "tica", tige = "tige",
tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc",
col_bactid = NULL)
BRMO(tbl, country = "nl", ...)
@ -129,6 +130,8 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{peni}{column name of an antibiotic, see Details}
\item{pipe}{column name of an antibiotic, see Details}
\item{pita}{column name of an antibiotic, see Details}
\item{poly}{column name of an antibiotic, see Details}

2
man/as.mo.Rd
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@ -78,7 +78,7 @@ This means that looking up human pathogenic microorganisms takes less time than
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This \strong{allows users to use authoritative taxonomic information} for their data analysis on any microorganism, not only human pathogens. It also helps to \strong{quickly determine the Gram stain of bacteria}, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

2
man/microorganisms.Rd
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@ -36,7 +36,7 @@ A data set containing the complete microbial taxonomy of the kingdoms Bacteria,
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This \strong{allows users to use authoritative taxonomic information} for their data analysis on any microorganism, not only human pathogens. It also helps to \strong{quickly determine the Gram stain of bacteria}, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

2
man/microorganisms.old.Rd
View File

@ -25,7 +25,7 @@ A data set containing old (previously valid or accepted) taxonomic names accordi
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This \strong{allows users to use authoritative taxonomic information} for their data analysis on any microorganism, not only human pathogens. It also helps to \strong{quickly determine the Gram stain of bacteria}, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

2
man/mo_property.Rd
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@ -71,7 +71,7 @@ Use these functions to return a specific property of a microorganism from the \c
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This \strong{allows users to use authoritative taxonomic information} for their data analysis on any microorganism, not only human pathogens. It also helps to \strong{quickly determine the Gram stain of bacteria}, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}