mirror of https://github.com/msberends/AMR.git
add NEWS
This commit is contained in:
parent
d8da8daf9a
commit
10380bcfae
|
|
@ -0,0 +1,6 @@
|
|||
## 0.1.1
|
||||
- EUCAST_rules applies for amoxicillin even if ampicillin is missing
|
||||
- Edited column names to comply with GLIMS, the laboratory information system
|
||||
|
||||
## 0.1.0
|
||||
- First submission to CRAN.
|
||||
69
R/EUCAST.R
69
R/EUCAST.R
|
|
@ -37,11 +37,19 @@
|
|||
#' EUCAST Expert Rules Version 3.1: \cr
|
||||
#' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
|
||||
#' @examples
|
||||
#' \dontrun{
|
||||
#' tbl <- EUCAST_rules(tbl)
|
||||
#' }
|
||||
#' a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
|
||||
#' vanc = "-",
|
||||
#' amox = "-",
|
||||
#' coli = "-",
|
||||
#' cfta = "-",
|
||||
#' cfur = "-",
|
||||
#' stringsAsFactors = FALSE)
|
||||
#' a
|
||||
#'
|
||||
#' b <- EUCAST_rules(a)
|
||||
#' b
|
||||
EUCAST_rules <- function(tbl,
|
||||
col_bactcode = 'bacteriecode',
|
||||
col_bactcode = 'bactid',
|
||||
info = TRUE,
|
||||
amcl = 'amcl',
|
||||
amik = 'amik',
|
||||
|
|
@ -232,61 +240,61 @@ EUCAST_rules <- function(tbl,
|
|||
# Citrobacter
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
|
||||
cols = c(ampi, tica))
|
||||
cols = c(aminopenicillines, tica))
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
|
||||
cols = c(ampi, amcl, czol, cfox))
|
||||
cols = c(aminopenicillines, amcl, czol, cfox))
|
||||
# Enterobacter
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
|
||||
cols = c(ampi, amcl, czol, cfox))
|
||||
cols = c(aminopenicillines, amcl, czol, cfox))
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
|
||||
cols = c(ampi, amcl, czol, cfox))
|
||||
cols = c(aminopenicillines, amcl, czol, cfox))
|
||||
# Escherichia
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Escherichia hermanni'),
|
||||
cols = c(ampi, tica))
|
||||
cols = c(aminopenicillines, tica))
|
||||
# Hafnia
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Hafnia alvei'),
|
||||
cols = c(ampi, amcl, czol, cfox))
|
||||
cols = c(aminopenicillines, amcl, czol, cfox))
|
||||
# Klebsiella
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Klebsiella'),
|
||||
cols = c(ampi, tica))
|
||||
cols = c(aminopenicillines, tica))
|
||||
# Morganella / Proteus
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Morganella morganii'),
|
||||
cols = c(ampi, amcl, czol, tetracyclines, polymyxines, nitr))
|
||||
cols = c(aminopenicillines, amcl, czol, tetracyclines, polymyxines, nitr))
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Proteus mirabilis'),
|
||||
cols = c(tetracyclines, tige, polymyxines, nitr))
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Proteus penneri'),
|
||||
cols = c(ampi, czol, cfur, tetracyclines, tige, polymyxines, nitr))
|
||||
cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Proteus vulgaris'),
|
||||
cols = c(ampi, czol, cfur, tetracyclines, tige, polymyxines, nitr))
|
||||
cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
|
||||
# Providencia
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Providencia rettgeri'),
|
||||
cols = c(ampi, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
|
||||
cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Providencia stuartii'),
|
||||
cols = c(ampi, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
|
||||
cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
|
||||
# Raoultella
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Raoultella'),
|
||||
cols = c(ampi, tica))
|
||||
cols = c(aminopenicillines, tica))
|
||||
# Serratia
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Serratia marcescens'),
|
||||
cols = c(ampi, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxines, nitr))
|
||||
cols = c(aminopenicillines, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxines, nitr))
|
||||
# Yersinia
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
|
||||
cols = c(ampi, amcl, tica, czol, cfox))
|
||||
cols = c(aminopenicillines, amcl, tica, czol, cfox))
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
|
||||
cols = c(poly, coli))
|
||||
|
|
@ -313,32 +321,32 @@ EUCAST_rules <- function(tbl,
|
|||
# Acinetobacter
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
|
||||
cols = c(ampi, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
|
||||
cols = c(aminopenicillines, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
|
||||
# Achromobacter
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
|
||||
cols = c(ampi, czol, cfot, cftr, erta))
|
||||
cols = c(aminopenicillines, czol, cfot, cftr, erta))
|
||||
# Burkholderia
|
||||
edit_rsi(to = 'R',
|
||||
# onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
|
||||
rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
|
||||
cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosiden, trim, fosf, polymyxines))
|
||||
cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosiden, trim, fosf, polymyxines))
|
||||
# Elizabethkingia
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
|
||||
cols = c(ampi, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxines))
|
||||
cols = c(aminopenicillines, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxines))
|
||||
# Ochrobactrum
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
|
||||
cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
|
||||
cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
|
||||
# Pseudomonas
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
|
||||
cols = c(ampi, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
|
||||
cols = c(aminopenicillines, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
|
||||
# Stenotrophomonas
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
|
||||
cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosiden, trim, fosf, tetr))
|
||||
cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosiden, trim, fosf, tetr))
|
||||
|
||||
|
||||
# Table 3: Intrinsic resistance in other Gram-negative bacteria ----
|
||||
|
|
@ -448,6 +456,12 @@ EUCAST_rules <- function(tbl,
|
|||
& tbl[, ampi] == 'R'),
|
||||
cols = c(ureidopenicillines, carbapenems))
|
||||
}
|
||||
if (!is.na(amox)) {
|
||||
edit_rsi(to = 'R',
|
||||
rows = which(tbl$genus == 'Enterococcus'
|
||||
& tbl[, amox] == 'R'),
|
||||
cols = c(ureidopenicillines, carbapenems))
|
||||
}
|
||||
|
||||
# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
|
||||
if (info == TRUE) {
|
||||
|
|
@ -579,7 +593,7 @@ EUCAST_rules <- function(tbl,
|
|||
cols = trim)
|
||||
}
|
||||
if (!is.na(ampi) & !is.na(amox)) {
|
||||
tbl[, amox] <- tbl[, ampi]
|
||||
tbl[, amox] <- tbl %>% pull(ampi)
|
||||
}
|
||||
|
||||
# Toegevoegde kolommen weer verwijderen
|
||||
|
|
@ -596,6 +610,7 @@ EUCAST_rules <- function(tbl,
|
|||
tbl
|
||||
}
|
||||
|
||||
#' @name EUCAST
|
||||
#' @rdname EUCAST
|
||||
#' @export
|
||||
interpretive_reading <- function(...) {
|
||||
|
|
|
|||
53
README.md
53
README.md
|
|
@ -40,14 +40,37 @@ library(AMR)
|
|||
# For a list of functions:
|
||||
help(package = "AMR")
|
||||
```
|
||||
|
||||
### Databases included in package
|
||||
### Overwrite/force resistance based on EUCAST rules
|
||||
This is also called *interpretive reading*.
|
||||
```r
|
||||
# Dataset with ATC antibiotics codes, official names and DDD's (oral and parenteral)
|
||||
ablist # A tibble: 420 x 12
|
||||
before <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
|
||||
"ENCFAE" # Enterococcus faecalis
|
||||
"ESCCOL", # Escherichia coli
|
||||
"KLEPNE", # Klebsiella pneumoniae
|
||||
"PSEAER"), # Pseudomonas aeruginosa
|
||||
vanc = "-", # Vancomycin
|
||||
amox = "-", # Amoxicillin
|
||||
coli = "-", # Colistin
|
||||
cfta = "-", # Ceftazidime
|
||||
cfur = "-", # Cefuroxime
|
||||
stringsAsFactors = FALSE)
|
||||
before
|
||||
# bactid vanc amox coli cfta cfur
|
||||
# 1 STAAUR - - - - -
|
||||
# 2 ENCFAE - - - - -
|
||||
# 3 ESCCOL - - - - -
|
||||
# 4 KLEPNE - - - - -
|
||||
# 5 PSEAER - - - - -
|
||||
|
||||
# Dataset with bacteria codes and properties like gram stain and aerobic/anaerobic
|
||||
bactlist # A tibble: 2,507 x 10
|
||||
# Now apply those rules; just need a column with bacteria ID's and antibiotic results:
|
||||
after <- EUCAST_rules(before)
|
||||
after
|
||||
# bactid vanc amox coli cfta cfur
|
||||
# 1 STAAUR - - R R -
|
||||
# 2 ENCFAE - - R R R
|
||||
# 3 ESCCOL R - - - -
|
||||
# 4 KLEPNE R R - - -
|
||||
# 5 PSEAER R R - - R
|
||||
```
|
||||
|
||||
### New classes
|
||||
|
|
@ -94,18 +117,13 @@ plot(rsi_data)
|
|||
Other epidemiological functions:
|
||||
|
||||
```r
|
||||
# Apply EUCAST Expert Rules v3.1 (latest) to antibiotic columns
|
||||
EUCAST_rules(...)
|
||||
|
||||
# Determine key antibiotic based on bacteria ID
|
||||
key_antibiotics(...)
|
||||
# Check if key antibiotics are equal
|
||||
key_antibiotics_equal(...)
|
||||
|
||||
# Selection of first isolates of any patient
|
||||
first_isolate(...)
|
||||
|
||||
# Calculate resistance levels of antibiotics
|
||||
# Calculate resistance levels of antibiotics, can be used with `summarise` (dplyr)
|
||||
rsi(...)
|
||||
# Predict resistance levels of antibiotics
|
||||
rsi_predict(...)
|
||||
|
|
@ -115,6 +133,17 @@ abname(...)
|
|||
abname("J01CR02", from = "atc", to = "umcg") # "AMCL"
|
||||
```
|
||||
|
||||
### Databases included in package
|
||||
Datasets to work with antibiotics and bacteria properties.
|
||||
```r
|
||||
# Dataset with ATC antibiotics codes, official names and DDD's (oral and parenteral)
|
||||
ablist # A tibble: 420 x 12
|
||||
|
||||
# Dataset with bacteria codes and properties like gram stain and aerobic/anaerobic
|
||||
bactlist # A tibble: 2,507 x 10
|
||||
```
|
||||
|
||||
|
||||
## Authors
|
||||
|
||||
- [Berends MS](https://github.com/msberends)<sup>1,2</sup>, PhD Student
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@
|
|||
\name{EUCAST}
|
||||
\alias{EUCAST}
|
||||
\alias{EUCAST_rules}
|
||||
\alias{EUCAST}
|
||||
\alias{interpretive_reading}
|
||||
\title{EUCAST expert rules}
|
||||
\source{
|
||||
|
|
@ -14,22 +15,22 @@ EUCAST Expert Rules Version 2.0: \cr
|
|||
\url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
|
||||
}
|
||||
\usage{
|
||||
EUCAST_rules(tbl, col_bactcode = "bacteriecode", info = TRUE,
|
||||
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
|
||||
azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
|
||||
cfep = "cfep", cfot = "cfot", cfox = "cfox", 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", 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")
|
||||
EUCAST_rules(tbl, col_bactcode = "bactid", info = TRUE, amcl = "amcl",
|
||||
amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
|
||||
aztr = "aztr", cefa = "cefa", cfra = "cfra", cfep = "cfep",
|
||||
cfot = "cfot", cfox = "cfox", 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", 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")
|
||||
|
||||
interpretive_reading(...)
|
||||
}
|
||||
|
|
@ -51,7 +52,15 @@ table with edited variables of antibiotics.
|
|||
Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
|
||||
}
|
||||
\examples{
|
||||
\dontrun{
|
||||
tbl <- EUCAST_rules(tbl)
|
||||
}
|
||||
a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
|
||||
vanc = "-",
|
||||
amox = "-",
|
||||
coli = "-",
|
||||
cfta = "-",
|
||||
cfur = "-",
|
||||
stringsAsFactors = FALSE)
|
||||
a
|
||||
|
||||
b <- EUCAST_rules(a)
|
||||
b
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue