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(v0.8.0.9007) Enterobacterales order

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-10-30 23:02:50 +01:00
parent 7ff2ad8188
commit 09c4b04cd0
22 changed files with 156 additions and 55 deletions
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34
R/mdro.R
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@ -424,6 +424,9 @@ mdro <- function(x,
}
}
trans_tbl2 <- function(txt, rows, lst) {
if (info == TRUE) {
message(blue(txt, "..."), appendLF = FALSE)
}
# function specific for the CMI paper of 2012 (Magiorakos et al.)
lst_vector <- unlist(lst)[!is.na(unlist(lst))]
x$total_groups <- NA_integer_
@ -447,12 +450,15 @@ mdro <- function(x,
# MDR (=2): >=3 groups affected
x[which(x$row_number %in% rows & x$affected_groups >= 3), "MDRO"] <<- 2
# XDR (=3): all but <=2 groups affected
x[which(x$row_number %in% rows & x$total_groups - x$affected_groups <= 2), "MDRO"] <<- 3
x[which(x$row_number %in% rows & (x$total_groups - x$affected_groups) <= 2), "MDRO"] <<- 3
# PDR (=4): all agents are R
x[filter_at(x[rows, ],
vars(lst_vector),
all_vars(. %in% c("R", "I")))$row_number,
"MDRO"] <<- 4
if (info == TRUE) {
message(blue(" OK"))
}
}
x <- x %>%
@ -461,7 +467,7 @@ mdro <- function(x,
left_join_microorganisms(by = col_mo) %>%
# add unconfirmed to where genus is available
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
row_number = seq_len(nrow(x))) %>%
row_number = seq_len(nrow(.))) %>%
# transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
as.data.frame(stringsAsFactors = FALSE)
@ -572,7 +578,7 @@ mdro <- function(x,
FOS,
QDA,
c(TCY, DOX, MNO)))
trans_tbl2(paste("Table 2 -", italic("Enterococcus"), "spp"),
trans_tbl2(paste("Table 2 -", italic("Enterococcus"), "spp."),
which(x$genus == "Enterococcus"),
list(GEH,
STH,
@ -585,8 +591,10 @@ mdro <- function(x,
AMP,
QDA,
c(DOX, MNO)))
trans_tbl2(paste("Table 3 -", italic("Enterobacteriaceae")),
which(x$family == "Enterobacteriaceae"),
trans_tbl2(paste0("Table 3 - ", italic("Enterobacteriaceae"),
" (before the taxonomic reclassification by Adeolu ", italic("et al."), ", 2016)"),
# this new order was previously 'Enterobacteriales' and contained only the family 'Enterobacteriaceae':
which(x$order == "Enterobacterales"),
list(c(GEN, TOB, AMK, NET),
CPT,
c(TCC, TZP),
@ -615,7 +623,7 @@ mdro <- function(x,
ATM,
FOS,
c(COL, PLB)))
trans_tbl2(paste("Table 5 -", italic("Acinetobacter"), "spp"),
trans_tbl2(paste("Table 5 -", italic("Acinetobacter"), "spp."),
which(x$genus == "Acinetobacter"),
list(c(GEN, TOB, AMK, NET),
c(IPM, MEM, DOR),
@ -632,7 +640,7 @@ mdro <- function(x,
# EUCAST ------------------------------------------------------------------
# Table 5
trans_tbl(3,
which(x$family == "Enterobacteriaceae"
which(x$order == "Enterobacterales"
| x$fullname %like% "^Pseudomonas aeruginosa"
| x$genus == "Acinetobacter"),
COL,
@ -706,7 +714,7 @@ mdro <- function(x,
if (is.na(CIP)) CIP <- "missing"
# Table 1
x[which((x$family == "Enterobacteriaceae" |
x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x$fullname %like% "^Acinetobacter baumannii") &
x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" &
@ -714,7 +722,7 @@ mdro <- function(x,
x[, CIP] == "R"),
"MDRO"] <- 2 # 2 = 3MRGN
x[which((x$family == "Enterobacteriaceae" |
x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x$fullname %like% "^Acinetobacter baumannii") &
x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" &
@ -722,7 +730,7 @@ mdro <- function(x,
x[, CIP] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN, overwrites 3MRGN if applicable
x[which((x$family == "Enterobacteriaceae" |
x[which((x$order == "Enterobacterales" | # following in fact the old Enterobacteriaceae classification
x$fullname %like% "^Acinetobacter baumannii") &
x[, IPM] == "R" | x[, MEM] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN, always when imipenem or meropenem is R
@ -757,17 +765,17 @@ mdro <- function(x,
# Table 1
trans_tbl(3,
which(x$family == "Enterobacteriaceae"),
which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
c(aminoglycosides, fluoroquinolones),
"all")
trans_tbl(2,
which(x$family == "Enterobacteriaceae"),
which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
carbapenems,
"any")
trans_tbl(2,
which(x$family == "Enterobacteriaceae"),
which(x$order == "Enterobacterales"), # following in fact the old Enterobacteriaceae classification
ESBLs,
"all")