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(v0.9.0.9029) add uti to as.rsi()

new-mo-algorithm
parent
commit
c6184a0fb8
  1. 4
      DESCRIPTION
  2. 16
      NEWS.md
  3. 5
      R/disk.R
  4. 10
      R/mic.R
  5. 17
      R/misc.R
  6. 363
      R/rsi.R
  7. 12
      data-raw/antibiotics.txt
  8. 32
      data-raw/read_EUCAST.R
  9. 7
      data-raw/reproduction_of_antibiotics.R
  10. 4
      data-raw/reproduction_of_rsi_translation.R
  11. 194
      data-raw/rsi_translation.txt
  12. BIN
      data/antibiotics.rda
  13. BIN
      data/rsi_translation.rda
  14. 2
      docs/404.html
  15. 2
      docs/LICENSE-text.html
  16. 412
      docs/articles/AMR.html
  17. BIN
      docs/articles/AMR_files/figure-html/plot 1-1.png
  18. BIN
      docs/articles/AMR_files/figure-html/plot 3-1.png
  19. BIN
      docs/articles/AMR_files/figure-html/plot 4-1.png
  20. BIN
      docs/articles/AMR_files/figure-html/plot 5-1.png
  21. 4
      docs/articles/EUCAST.html
  22. 2
      docs/articles/index.html
  23. 2
      docs/authors.html
  24. 4
      docs/index.html
  25. 512
      docs/news/index.html
  26. 2
      docs/reference/AMR-deprecated.html
  27. 2
      docs/reference/AMR.html
  28. 2
      docs/reference/WHOCC.html
  29. 2
      docs/reference/WHONET.html
  30. 2
      docs/reference/ab_property.html
  31. 2
      docs/reference/age.html
  32. 2
      docs/reference/age_groups.html
  33. 2
      docs/reference/antibiotics.html
  34. 2
      docs/reference/as.ab.html
  35. 2
      docs/reference/as.disk.html
  36. 2
      docs/reference/as.mic.html
  37. 2
      docs/reference/as.mo.html
  38. 69
      docs/reference/as.rsi.html
  39. 2
      docs/reference/atc_online.html
  40. 2
      docs/reference/availability.html
  41. 2
      docs/reference/bug_drug_combinations.html
  42. 2
      docs/reference/catalogue_of_life.html
  43. 2
      docs/reference/catalogue_of_life_version.html
  44. 2
      docs/reference/count.html
  45. 2
      docs/reference/eucast_rules.html
  46. 2
      docs/reference/example_isolates.html
  47. 2
      docs/reference/extended-functions.html
  48. 2
      docs/reference/first_isolate.html
  49. 2
      docs/reference/g.test.html
  50. 2
      docs/reference/ggplot_rsi.html
  51. 2
      docs/reference/guess_ab_col.html
  52. 2
      docs/reference/index.html
  53. 2
      docs/reference/join.html
  54. 2
      docs/reference/key_antibiotics.html
  55. 2
      docs/reference/kurtosis.html
  56. 2
      docs/reference/like.html
  57. 2
      docs/reference/mdro.html
  58. 2
      docs/reference/microorganisms.codes.html
  59. 2
      docs/reference/microorganisms.html
  60. 2
      docs/reference/microorganisms.old.html
  61. 2
      docs/reference/mo_property.html
  62. 2
      docs/reference/mo_source.html
  63. 2
      docs/reference/p_symbol.html
  64. 2
      docs/reference/proportion.html
  65. 2
      docs/reference/read.4D.html
  66. 2
      docs/reference/resistance_predict.html
  67. 2
      docs/reference/rsi_translation.html
  68. 2
      docs/reference/skewness.html
  69. 2
      docs/reference/translate.html
  70. 69
      man/as.rsi.Rd
  71. 13
      tests/testthat/test-rsi.R

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.0.0
Date: 2020-02-17
Version: 1.0.0.9000
Date: 2020-02-20
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

16
NEWS.md

@ -1,3 +1,19 @@ @@ -1,3 +1,19 @@
# AMR 1.0.0.9000
## <small>Last updated: 20-Feb-2020</small>
### Changed
* Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
* Fixed floating point error for some MIC compa in EUCAST 2020 guideline
* Interpretation from MIC values to R/SI can now be used with `mutate_at()` of the dplyr package:
```r
yourdata %>%
mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = "E. coli")
yourdata %>%
mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = .$mybacteria)
```
* Added `uti` (as abbreviation of urinary tract infections) as parameter to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
# AMR 1.0.0
This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.

5
R/disk.R

@ -85,6 +85,11 @@ as.disk <- function(x, na.rm = FALSE) { @@ -85,6 +85,11 @@ as.disk <- function(x, na.rm = FALSE) {
}
}
all_valid_disks <- function(x) {
x_disk <- suppressWarnings(as.disk(x[!is.na(x)]))
!any(is.na(x_disk)) & !all(is.na(x))
}
#' @rdname as.disk
#' @export
#' @importFrom dplyr %>%

10
R/mic.R

@ -65,11 +65,14 @@ as.mic <- function(x, na.rm = FALSE) { @@ -65,11 +65,14 @@ as.mic <- function(x, na.rm = FALSE) {
# comma to period
x <- gsub(",", ".", x, fixed = TRUE)
# transform Unicode for >= and <=
x <- gsub("\u2264", "<=", x, fixed = TRUE)
x <- gsub("\u2265", ">=", x, fixed = TRUE)
# remove space between operator and number ("<= 0.002" -> "<=0.002")
x <- gsub("(<|=|>) +", "\\1", x)
# transform => to >= and =< to <=
x <- gsub("=>", ">=", x, fixed = TRUE)
x <- gsub("=<", "<=", x, fixed = TRUE)
x <- gsub("=>", ">=", x, fixed = TRUE)
# starting dots must start with 0
x <- gsub("^[.]+", "0.", x)
# <=0.2560.512 should be 0.512
@ -126,6 +129,11 @@ as.mic <- function(x, na.rm = FALSE) { @@ -126,6 +129,11 @@ as.mic <- function(x, na.rm = FALSE) {
}
}
all_valid_mics <- function(x) {
x_mic <- suppressWarnings(as.mic(x[!is.na(x)]))
!any(is.na(x_mic)) & !all(is.na(x))
}
#' @rdname as.mic
#' @export
#' @importFrom dplyr %>%

17
R/misc.R

@ -117,7 +117,22 @@ search_type_in_df <- function(x, type) { @@ -117,7 +117,22 @@ search_type_in_df <- function(x, type) {
found <- colnames(x)[colnames(x) %like% "^(specimen)"][1]
}
}
# -- UTI (urinary tract infection)
if (type == "uti") {
if (any(colnames(x) == "uti")) {
found <- colnames(x)[colnames(x) == "uti"][1]
} else if (any(colnames(x) %like% "(urine|urinary)")) {
found <- colnames(x)[colnames(x) %like% "(urine|urinary)"][1]
}
if (!is.null(found)) {
if (!is.logical(x[, found, drop = TRUE])) {
message(red(paste0("NOTE: Column `", bold(found), "` found as input for `col_", type,
"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.")))
found <- NULL
}
}
}
if (!is.null(found)) {
msg <- paste0("NOTE: Using column `", bold(found), "` as input for `col_", type, "`.")
if (type %in% c("keyantibiotics", "specimen")) {

363
R/rsi.R

@ -27,6 +27,7 @@ @@ -27,6 +27,7 @@
#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See *Examples*.
#' @inheritParams first_isolate
#' @param guideline defaults to the latest included EUCAST guideline, run `unique(rsi_translation$guideline)` for all options
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
@ -52,13 +53,45 @@ @@ -52,13 +53,45 @@
#' @return Ordered factor with new class [`rsi`]
#' @aliases rsi
#' @export
#' @importFrom dplyr %>% desc arrange filter
#' @seealso [as.mic()]
#' @inheritSection AMR Read more on our website!
#' @examples
#' # For INTERPRETING disk diffusion and MIC values -----------------------
#'
#' # a whole data set, even with combined MIC values and disk zones
#' df <- data.frame(microorganism = "E. coli",
#' AMP = as.mic(8),
#' CIP = as.mic(0.256),
#' GEN = as.disk(18),
#' TOB = as.disk(16),
#' NIT = as.mic(32))
#' as.rsi(df)
#'
#' # single values
#' # the dplyr way
#' library(dplyr)
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
#'
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = .$microorganism)
#'
#' # to include information about urinary tract infections (UTI)
#' data.frame(mo = "E. coli",
#' NIT = c("<= 2", 32),
#' from_the_bladder = c(TRUE, FALSE)) %>%
#' as.rsi(uti = "from_the_bladder")
#'
#' data.frame(mo = "E. coli",
#' NIT = c("<= 2", 32),
#' specimen = c("urine", "blood")) %>%
#' as.rsi() # automatically determines urine isolates
#'
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
#'
#'
#'
#' # for single values
#' as.rsi(x = as.mic(2),
#' mo = as.mo("S. pneumoniae"),
#' ab = "AMP",
@ -68,14 +101,6 @@ @@ -68,14 +101,6 @@
#' mo = "Strep pneu", # `mo` will be coerced with as.mo()
#' ab = "ampicillin", # and `ab` with as.ab()
#' guideline = "EUCAST")
#'
#' # a whole data set, even with combined MIC values and disk zones
#' df <- data.frame(microorganism = "E. coli",
#' AMP = as.mic(8),
#' CIP = as.mic(0.256),
#' GEN = as.disk(18),
#' TOB = as.disk(16))
#' as.rsi(df)
#'
#'
#' # For CLEANING existing R/SI values ------------------------------------
@ -114,6 +139,11 @@ as.rsi.default <- function(x, ...) { @@ -114,6 +139,11 @@ as.rsi.default <- function(x, ...) {
x
} else if (identical(levels(x), c("S", "I", "R"))) {
structure(x, class = c("rsi", "ordered", "factor"))
} else if (all_valid_mics(x) & !all(is.na(x))) {
as.rsi(as.mic(x), ab = deparse(substitute(x)), ...)
} else if (all_valid_disks(x) & !all(is.na(x))) {
#message("These values seem to be disk diffusion diameters and were treated as such.")
as.rsi(as.disk(x), ab = deparse(substitute(x)), ...)
} else if (identical(class(x), "integer") & all(x %in% c(1:3, NA))) {
x[x == 1] <- "S"
x[x == 2] <- "I"
@ -164,6 +194,7 @@ as.rsi.default <- function(x, ...) { @@ -164,6 +194,7 @@ as.rsi.default <- function(x, ...) {
}
}
#' @importFrom dplyr %>%
input_resembles_mic <- function(x) {
mic <- x %>%
gsub("[^0-9.,]+", "", .) %>%
@ -178,26 +209,184 @@ input_resembles_mic <- function(x) { @@ -178,26 +209,184 @@ input_resembles_mic <- function(x) {
}
#' @rdname as.rsi
#' @importFrom dplyr case_when
#' @export
as.rsi.mic <- function(x, mo, ab, guideline = "EUCAST", ...) {
exec_as.rsi(method = "mic",
x = x,
mo = mo,
ab = ab,
guideline = guideline)
as.rsi.mic <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, ...) {
if (missing(mo)) {
stop('No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use\n",
"`data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n\n",
"To tranform all MIC variables in a data set, use `as.rsi(data)` or `data %>% as.rsi()`.", call. = FALSE)
}
ab_coerced <- suppressWarnings(as.ab(ab))
mo_coerced <- suppressWarnings(as.mo(mo))
guideline_coerced <- get_guideline(guideline)
if (is.na(ab_coerced)) {
message(red(paste0("Unknown drug: `", bold(ab), "`. Rename this column to a drug name or code, and check the output with as.ab().")))
return(as.rsi(rep(NA, length(x))))
}
if (length(mo_coerced) == 1) {
mo_coerced <- rep(mo_coerced, length(x))
}
if (length(uti) == 1) {
uti <- rep(uti, length(x))
}
message(blue(paste0("=> Interpreting MIC values of column `", bold(ab), "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") using guideline ", bold(guideline_coerced), " ... ")),
appendLF = FALSE)
result <- exec_as.rsi(method = "mic",
x = x,
mo = mo_coerced,
ab = ab_coerced,
guideline = guideline_coerced,
uti = uti) # exec_as.rsi will return message(blue(" OK."))
result
}
#' @rdname as.rsi
#' @export
as.rsi.disk <- function(x, mo, ab = deparse(substitute(x)), guideline = "EUCAST", uti = FALSE, ...) {
if (missing(mo)) {
stop('No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use\n",
"`data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n\n",
"To tranform all disk diffusion zones in a data set, use `as.rsi(data)` or `data %>% as.rsi()`.", call. = FALSE)
}
ab_coerced <- suppressWarnings(as.ab(ab))
mo_coerced <- suppressWarnings(as.mo(mo))
guideline_coerced <- get_guideline(guideline)
if (is.na(ab_coerced)) {
message(red(paste0("Unknown drug: `", bold(ab), "`. Rename this column to a drug name or code, and check the output with as.ab().")))
return(as.rsi(rep(NA, length(x))))
}
if (length(mo_coerced) == 1) {
mo_coerced <- rep(mo_coerced, length(x))
}
if (length(uti) == 1) {
uti <- rep(uti, length(x))
}
message(blue(paste0("=> Interpreting disk zones of column `", bold(ab), "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") using guideline ", bold(guideline_coerced), " ... ")),
appendLF = FALSE)
result <- exec_as.rsi(method = "disk",
x = x,
mo = mo_coerced,
ab = ab_coerced,
guideline = guideline_coerced,
uti = uti) # exec_as.rsi will return message(blue(" OK."))
result
}
#' @rdname as.rsi
#' @importFrom crayon red blue bold
#' @export
as.rsi.disk <- function(x, mo, ab, guideline = "EUCAST", ...) {
exec_as.rsi(method = "disk",
x = x,
mo = mo,
ab = ab,
guideline = guideline)
as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", uti = NULL, ...) {
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
# -- UTIs
col_uti <- uti
if (is.null(col_uti)) {
col_uti <- search_type_in_df(x = x, type = "uti")
}
if (!is.null(col_uti)) {
if (is.logical(col_uti)) {
# already a logical vector as input
if (length(col_uti) == 1) {
uti <- rep(col_uti, NROW(x))
} else {
uti <- col_uti
}
} else {
# column found, transform to logical
uti <- as.logical(x[, col_uti, drop = TRUE])
}
} else {
# look for specimen column and make logicals of the urines
col_specimen <- suppressMessages(search_type_in_df(x = x, type = "specimen"))
if (!is.null(col_specimen)) {
uti <- x[, col_specimen, drop = TRUE] %like% "urin"
values <- sort(unique(x[uti, col_specimen, drop = TRUE]))
if (length(values) > 1) {
plural <- c("s", "", "")
} else {
plural <- c("", "s", "a ")
}
message(blue(paste0("NOTE: Assuming value", plural[1], " ",
paste(paste0('"', values, '"'), collapse = ", "),
" in column `", bold(col_specimen),
"` reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1], ".\n Use `as.rsi(uti = FALSE)` to prevent this.")))
} else {
# no data about UTI's found
uti <- FALSE
}
}
i <- 0
ab_cols <- colnames(x)[sapply(x, function(y) {
i <<- i + 1
check <- is.mic(y) | is.disk(y)
ab <- colnames(x)[i]
ab_coerced <- suppressWarnings(as.ab(ab))
if (is.na(ab_coerced)) {
# not even a valid AB code
return(FALSE)
} else if (!check & all_valid_mics(y)) {
message(blue(paste0("NOTE: Assuming column `", ab, "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") contains MIC values.")))
return(TRUE)
} else if (!check & all_valid_disks(y)) {
message(blue(paste0("NOTE: Assuming column `", ab, "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") contains disk zones.")))
return(TRUE)
} else {
return(check)
}
})]
if (length(ab_cols) == 0) {
stop("No columns with MIC values or disk zones found in this data set. Use as.mic() or as.disk() to transform antimicrobial columns.", call. = FALSE)
}
# set type per column
types <- character(length(ab_cols))
types[sapply(x[, ab_cols], is.mic)] <- "mic"
types[types == "" & sapply(x[, ab_cols], all_valid_mics)] <- "mic"
types[sapply(x[, ab_cols], is.disk)] <- "disk"
types[types == "" & sapply(x[, ab_cols], all_valid_disks)] <- "disk"
for (i in seq_len(length(ab_cols))) {
if (types[i] == "mic") {
x[, ab_cols[i]] <- as.rsi.mic(x = x %>% pull(ab_cols[i]),
mo = x %>% pull(col_mo),
ab = ab_cols[i],
guideline = guideline,
uti = uti)
} else if (types[i] == "disk") {
x[, ab_cols[i]] <- as.rsi.disk(x = x %>% pull(ab_cols[i]),
mo = x %>% pull(col_mo),
ab = ab_cols[i],
guideline = guideline,
uti = uti)
}
}
x
}
#' @importFrom dplyr %>% filter pull
get_guideline <- function(guideline) {
guideline_param <- toupper(guideline)
if (guideline_param %in% c("CLSI", "EUCAST")) {
@ -216,19 +405,20 @@ get_guideline <- function(guideline) { @@ -216,19 +405,20 @@ get_guideline <- function(guideline) {
}
guideline_param
}
exec_as.rsi <- function(method, x, mo, ab, guideline) {
#' @importFrom dplyr %>% case_when desc arrange filter n_distinct
#' @importFrom crayon green red bold
exec_as.rsi <- function(method, x, mo, ab, guideline, uti) {
if (method == "mic") {
x <- as.double(as.mic(x)) # when as.rsi.mic is called directly
method_param <- "MIC"
x <- as.mic(x) # when as.rsi.mic is called directly
} else if (method == "disk") {
x <- as.double(as.disk(x)) # when as.rsi.disk is called directly
method_param <- "DISK"
x <- as.disk(x) # when as.rsi.disk is called directly
}
mo <- as.mo(mo)
ab <- as.ab(ab)
warned <- FALSE
method_param <- toupper(method)
mo_genus <- as.mo(mo_genus(mo))
mo_family <- as.mo(mo_family(mo))
@ -243,8 +433,9 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) { @@ -243,8 +433,9 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
}
new_rsi <- rep(NA_character_, length(x))
ab_param <- ab
trans <- rsi_translation %>%
filter(guideline == guideline_coerced & method == method_param) %>%
filter(guideline == guideline_coerced & method == method_param & ab == ab_param) %>%
mutate(lookup = paste(mo, ab))
lookup_mo <- paste(mo, ab)
@ -255,110 +446,62 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) { @@ -255,110 +446,62 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
lookup_lancefield <- paste(mo_lancefield, ab)
lookup_other <- paste(mo_other, ab)
if (all(trans$uti == TRUE, na.rm = TRUE) & all(uti == FALSE)) {
message(red("WARNING."))
warning("Interpretation of ", bold(ab_name(ab, tolower = TRUE)), " for some microorganisms is only available for (uncomplicated) urinary tract infections (UTI).\n Use parameter 'uti' to set which isolates are from urine. See ?as.rsi.", call. = FALSE)
warned <- TRUE
}
for (i in seq_len(length(x))) {
get_record <- trans %>%
# no UTI for now
filter(lookup %in% c(lookup_mo[i],
lookup_genus[i],
lookup_family[i],
lookup_order[i],
lookup_becker[i],
lookup_lancefield[i],
lookup_other[i])) %>%
# be as specific as possible (i.e. prefer species over genus):
arrange(desc(nchar(mo))) %>%
.[1L, ]
lookup_other[i]))
if (isTRUE(uti[i])) {
get_record <- get_record %>%
# be as specific as possible (i.e. prefer species over genus):
# desc(uti) = TRUE on top and FALSE on bottom
arrange(desc(uti), desc(nchar(mo))) %>% # 'uti' is a column in rsi_translation
.[1L, ]
} else {
get_record <- get_record %>%
filter(uti == FALSE) %>% # 'uti' is a column in rsi_translation
arrange(desc(nchar(mo))) %>%
.[1L, ]
}
if (NROW(get_record) > 0) {
if (is.na(x[i])) {
new_rsi[i] <- NA_character_
} else if (method == "mic") {
new_rsi[i] <- case_when(isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
mic_input <- x[i]
mic_S <- as.mic(get_record$breakpoint_S)
mic_R <- as.mic(get_record$breakpoint_R)
new_rsi[i] <- case_when(isTRUE(which(levels(mic_input) == mic_input) <= which(levels(mic_S) == mic_S)) ~ "S",
isTRUE(which(levels(mic_input) == mic_input) >= which(levels(mic_R) == mic_R)) ~ "R",
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
TRUE ~ NA_character_)
} else if (method == "disk") {
new_rsi[i] <- case_when(isTRUE(x[i] >= get_record$breakpoint_S) ~ "S",
isTRUE(x[i] <= get_record$breakpoint_R) ~ "R",
new_rsi[i] <- case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
TRUE ~ NA_character_)
}
}
}
if (warned == FALSE) {
message(green("OK."))
}
structure(.Data = factor(new_rsi, levels = c("S", "I", "R"), ordered = TRUE),
class = c("rsi", "ordered", "factor"))
}
#' @rdname as.rsi
#' @importFrom crayon red blue bold
#' @export
as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
x <- x
ab_cols <- colnames(x)[sapply(x, function(y) is.mic(y) | is.disk(y))]
if (length(ab_cols) == 0) {
stop("No columns with MIC values or disk zones found in this data set. Use as.mic or as.disk to transform antimicrobial columns.", call. = FALSE)
}
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
guideline_coerced <- get_guideline(guideline)
if (guideline_coerced != guideline) {
message(blue(paste0("Note: Using guideline ", bold(guideline_coerced), " as input for `guideline`.")))
}
# transform all MICs
ab_cols <- colnames(x)[sapply(x, is.mic)]
if (length(ab_cols) > 0) {
for (i in seq_len(length(ab_cols))) {
ab_col_coerced <- suppressWarnings(as.ab(ab_cols[i]))
if (is.na(ab_col_coerced)) {
message(red(paste0("Unknown drug: `", bold(ab_cols[i]), "`. Rename this column to a drug name or code, and check the output with as.ab().")))
next
}
message(blue(paste0("Interpreting MIC values of column `", bold(ab_cols[i]), "` (",
ifelse(ab_col_coerced != ab_cols[i], paste0(ab_col_coerced, ", "), ""),
ab_name(ab_col_coerced, tolower = TRUE), ")...")),
appendLF = FALSE)
x[, ab_cols[i]] <- exec_as.rsi(method = "mic",
x = x %>% pull(ab_cols[i]),
mo = x %>% pull(col_mo),
ab = ab_col_coerced,
guideline = guideline_coerced)
message(blue(" OK."))
}
}
# transform all disks
ab_cols <- colnames(x)[sapply(x, is.disk)]
if (length(ab_cols) > 0) {
for (i in seq_len(length(ab_cols))) {
ab_col_coerced <- suppressWarnings(as.ab(ab_cols[i]))
if (is.na(ab_col_coerced)) {
message(red(paste0("Unknown drug: `", bold(ab_cols[i]), "`. Rename this column to a drug name or code, and check the output with as.ab().")))
next
}
message(blue(paste0("Interpreting disk zones of column `", bold(ab_cols[i]), "` (",
ifelse(ab_col_coerced != ab_cols[i], paste0(ab_col_coerced, ", "), ""),
ab_name(ab_col_coerced, tolower = TRUE), ")...")),
appendLF = FALSE)
x[, ab_cols[i]] <- exec_as.rsi(method = "disk",
x = x %>% pull(ab_cols[i]),
mo = x %>% pull(col_mo),
ab = ab_col_coerced,
guideline = guideline_coerced)
message(blue(" OK."))
}
}
x
}
#' @rdname as.rsi
#' @export
is.rsi <- function(x) {

12
data-raw/antibiotics.txt

@ -62,7 +62,7 @@ @@ -62,7 +62,7 @@
"CDR" "J01DD15" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cdn\", \"cdr\", \"din\", \"cd\", \"cfd\")" "c(\"Cefdinir\", \"Cefdinirum\", \"Cefdinyl\", \"Cefdirnir\", \"Ceftinex\", \"Cefzon\", \"Omnicef\")" 0.6 "g"
"DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "Cefditoren" 0.4 "g"
"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "c(\"Cefditoren\", \"Cefditoren PI voxil\", \"Cefditoren pivoxil\", \"Cefditoren Pivoxil\", \"Cefditorin\", \"CEFDITORIN PIVOXIL\", \"Meiact\", \"Spectracef\")"
"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cpe\", \"fep\", \"pm\", \"cpm\", \"cfep\", \"xpm\")" "c(\"Axepim\", \"Cefepima\", \"Cefepime\", \"Cefepimum\", \"Cepimax\", \"Cepimex\", \"Maxcef\", \"Maxipime\")" 2 "g" "38363-8"
"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cpe\", \"fep\", \"pm\", \"cpm\", \"cfep\", \"xpm\", \"cfpi\")" "c(\"Axepim\", \"Cefepima\", \"Cefepime\", \"Cefepimum\", \"Cepimax\", \"Cepimex\", \"Maxcef\", \"Maxipime\")" 2 "g" "38363-8"
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "xpml" ""
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" ""
"FPZ" "Cefepime/zidebactam" "Other antibacterials" ""
@ -81,14 +81,14 @@ @@ -81,14 +81,14 @@
"CSL" "J01DD62" "Cefoperazone/sulbactam" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "" 4 "g"
"CND" "J01DC11" 43507 "Ceforanide" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"Ceforanide\", \"Ceforanido\", \"Ceforanidum\", \"Precef\", \"Radacef\")" 4 "g"
"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "c(\"Cefoselis\", \"Cefoselis sulfate\", \"Winsef\")"
"CTX" "J01DD01" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cft\", \"ctx\", \"tax\", \"fot\", \"ct\", \"cfot\", \"xct\")" "c(\"Cefotaxim\", \"Cefotaxim Hikma\", \"Cefotaxima\", \"Cefotaxime\", \"Cefotaxime acid\", \"Cefotaximum\", \"Cephotaxime\", \"Claforan\", \"Omnatax\")" 4 "g" "c(\"25238-7\", \"3446-2\", \"80961-6\")"
"CTX" "J01DD01" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cft\", \"ctx\", \"tax\", \"fot\", \"ct\", \"cfot\", \"xct\", \"cftx\")" "c(\"Cefotaxim\", \"Cefotaxim Hikma\", \"Cefotaxima\", \"Cefotaxime\", \"Cefotaxime acid\", \"Cefotaximum\", \"Cephotaxime\", \"Claforan\", \"Omnatax\")" 4 "g" "c(\"25238-7\", \"3446-2\", \"80961-6\")"
"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.)" "xctl" ""
"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" ""
"CTT" "J01DC05" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"ctn\", \"ctt\", \"cte\", \"tans\", \"cn\")" "c(\"Apacef\", \"Cefotetan\", \"Cefotetan free acid\", \"Cefotetanum\")" 4 "g" "c(\"25239-5\", \"3447-0\")"
"CTF" "J01DC07" 43708 "Cefotiam" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"Cefotiam\", \"Cefotiam?\", \"Cefotiamum\", \"Ceradolan\", \"Ceradon\", \"Haloapor\")" 1.2 "g" 4 "g"
"CHE" 125846 "Cefotiam hexetil" "Cephalosporins (3rd gen.)" "c(\"Cefotiam cilexetil\", \"Pansporin T\")"
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" ""
"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfx\", \"fox\", \"cx\", \"fx\", \"cfox\")" "c(\"Cefoxitin\", \"Cefoxitina\", \"Cefoxitine\", \"Cefoxitinum\", \"Cefoxotin\", \"CEPHOXITIN\", \"Mefoxin\", \"Mefoxitin\", \"Rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")"
"FOX" "J01DC01" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfx\", \"fox\", \"cx\", \"fx\", \"cfox\", \"cfxt\")" "c(\"Cefoxitin\", \"Cefoxitina\", \"Cefoxitine\", \"Cefoxitinum\", \"Cefoxotin\", \"CEPHOXITIN\", \"Mefoxin\", \"Mefoxitin\", \"Rephoxitin\")" 6 "g" "c(\"25240-3\", \"3448-8\")"
"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "Cefozopran"
"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "c(\"Cefpimizol\", \"Cefpimizole\", \"Cefpimizole sodium\", \"Cefpimizolum\")"
"CPM" "J01DD11" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"Cefpiramide\", \"Cefpiramide acid\", \"Cefpiramido\", \"Cefpiramidum\")" 2 "g"
@ -103,7 +103,7 @@ @@ -103,7 +103,7 @@
"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "c(\"Cefsumide\", \"Cefsumido\", \"Cefsumidum\")"
"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "c(\"Teflaro\", \"Zinforo\")"
"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" ""
"CAZ" "J01DD02" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"caz\", \"taz\", \"tz\", \"cfta\", \"xtz\", \"cefta\")" "c(\"Ceftazidim\", \"Ceftazidima\", \"Ceftazidime\", \"CEFTAZIDIME\", \"Ceftazidimum\", \"Ceptaz\", \"Fortaz\", \"Fortum\", \"Pentacef\", \"Tazicef\", \"Tazidime\")" 4 "g" "c(\"21151-6\", \"3449-6\", \"80960-8\")"
"CAZ" "J01DD02" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"caz\", \"taz\", \"tz\", \"cfta\", \"xtz\", \"cefta\", \"cftz\")" "c(\"Ceftazidim\", \"Ceftazidima\", \"Ceftazidime\", \"CEFTAZIDIME\", \"Ceftazidimum\", \"Ceptaz\", \"Fortaz\", \"Fortum\", \"Pentacef\", \"Tazicef\", \"Tazidime\")" 4 "g" "c(\"21151-6\", \"3449-6\", \"80960-8\")"
"CZA" "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" ""
"CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "xtzl" ""
"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "c(\"Cefteram\", \"Cefterame\", \"Cefteramum\", \"Ceftetrame\")"
@ -118,7 +118,7 @@ @@ -118,7 +118,7 @@
"CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" ""
"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" ""
"CRO" "J01DD04" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cax\", \"cro\", \"ctr\", \"frx\", \"axo\", \"tx\", \"cftr\")" "c(\"Biotrakson\", \"Cefatriaxone\", \"Cefatriaxone hydrate\", \"Ceftriaxon\", \"Ceftriaxona\", \"Ceftriaxone\", \"CEFTRIAXONE SODIUM\", \"Ceftriaxonum\", \"Ceftriazone\", \"Cephtriaxone\", \"Longacef\", \"Rocefin\", \"Rocephalin\", \"Rocephin\", \"Rocephine\", \"Rophex\")" 2 "g" "c(\"25244-5\", \"3451-2\", \"80957-4\")"
"CXM" "J01DC02" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"crm\", \"cxm\", \"cfx\", \"rox\", \"fur\", \"xm\", \"cfur\")" "c(\"Biofuroksym\", \"Cefuril\", \"Cefuroxim\", \"Cefuroxime\", \"Cefuroximine\", \"Cefuroximo\", \"Cefuroximum\", \"Cephuroxime\", \"Kefurox\", \"Sharox\", \"Zinacef\", \"Zinacef Danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
"CXM" "J01DC02" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"crm\", \"cxm\", \"cfx\", \"rox\", \"fur\", \"xm\", \"cfur\", \"cfrx\")" "c(\"Biofuroksym\", \"Cefuril\", \"Cefuroxim\", \"Cefuroxime\", \"Cefuroximine\", \"Cefuroximo\", \"Cefuroximum\", \"Cephuroxime\", \"Kefurox\", \"Sharox\", \"Zinacef\", \"Zinacef Danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
"CXA" 6321416 "Cefuroxime axetil" "Cephalosporins (2nd gen.)" "c(\"Altacef\", \"Bioracef\", \"Cefaks\", \"Cefazine\", \"Ceftin\", \"Cefuroximaxetil\", \"Cefuroxime axetil\", \"Celocid\", \"Cepazine\", \"Cethixim\", \"Cetoxil\", \"Coliofossim\", \"Elobact\", \"Forcef\", \"Furoxime\", \"Kalcef\", \"Maxitil\", \"Medoxm\", \"Nivador\", \"Zinnat\")"
"CFM2" "J01RA03" "Cefuroxime/metronidazole" "Other antibacterials" "Combinations of antibacterials" "Combinations of antibacterials" ""
"ZON" 6336505 "Cefuzonam" "Other antibacterials" "c(\"Cefuzonam\", \"Cefuzonam sodium\", \"Cefuzoname\", \"Cefuzonamum\")"
@ -490,7 +490,7 @@ @@ -490,7 +490,7 @@
"TMP" "J01EA01" 5578 "Trimethoprim" "Trimethoprims" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "c(\"t\", \"tmp\", \"tr\", \"w\", \"trim\")" "c(\"Abaprim\", \"Alprim\", \"Anitrim\", \"Antrima\", \"Antrimox\", \"Bacdan\", \"Bacidal\", \"Bacide\", \"Bacterial\", \"Bacticel\", \"Bactifor\", \"Bactin\", \"Bactoprim\", \"Bactramin\", \"Bactrim\", \"Bencole\", \"Bethaprim\", \"Biosulten\", \"Briscotrim\", \"Chemotrin\", \"Colizole\", \"Colizole DS\", \"Conprim\", \"Cotrimel\", \"CoTrimoxizole\", \"Deprim\", \"Dosulfin\", \"Duocide\", \"Esbesul\", \"Espectrin\", \"Euctrim\", \"Exbesul\", \"Fermagex\", \"Fortrim\", \"Idotrim\", \"Ikaprim\", \"Instalac\", \"Kombinax\", \"Lagatrim\", \"Lagatrim Forte\", \"Lastrim\", \"Lescot\",
\"Methoprim\", \"Metoprim\", \"Monoprim\", \"Monotrim\", \"Monotrimin\", \"Novotrimel\", \"Omstat\", \"Oraprim\", \"Pancidim\", \"Polytrim\", \"Priloprim\", \"Primosept\", \"Primsol\", \"Proloprim\", \"Protrin\", \"Purbal\", \"Resprim\", \"Resprim Forte\", \"Roubac\", \"Roubal\", \"Salvatrim\", \"Septrin DS\", \"Septrin Forte\", \"Septrin S\", \"Setprin\", \"Sinotrim\", \"Stopan\", \"Streptoplus\", \"Sugaprim\", \"Sulfamar\", \"Sulfamethoprim\", \"Sulfoxaprim\", \"Sulthrim\", \"Sultrex\", \"Syraprim\", \"Tiempe\", \"Tmp Smx\", \"Toprim\", \"Trimanyl\", \"Trimethioprim\", \"Trimethopim\",
\"Trimethoprim\", \"TRIMETHOPRIM\", \"Trimethoprime\", \"Trimethoprimum\", \"Trimethopriom\", \"Trimetoprim\", \"Trimetoprima\", \"Trimexazole\", \"Trimexol\", \"Trimezol\", \"Trimogal\", \"Trimono\", \"Trimopan\", \"Trimpex\", \"Triprim\", \"Trisul\", \"Trisulcom\", \"Trisulfam\", \"Trisural\", \"Uretrim\", \"Urobactrim\", \"Utetrin\", \"Velaten\", \"Wellcoprim\", \"Wellcoprin\", \"Xeroprim\", \"Zamboprim\")" 0.4 "g" 0.4 "g" "c(\"11005-6\", \"17747-7\", \"25273-4\", \"32342-8\", \"4079-0\", \"4080-8\", \"4081-6\", \"55584-7\", \"80552-3\", \"80973-1\")"
"SXT" "J01EE01" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "c(\"t/s\", \"sxt\", \"ts\", \"cot\", \"trsu\")" "c(\"Bactrim\", \"Bactrimel\", \"Belcomycine\", \"Colimycin\", \"Colimycin sulphate\", \"Colisticin\", \"Colistimethate\", \"Colistimethate Sodium\", \"Colistin sulfate\", \"Colistin sulphate\", \"Colomycin\", \"Coly-Mycin\", \"Cotrimazole\", \"Cotrimoxazole\", \"Polymyxin E\", \"Polymyxin E. Sulfate\", \"Promixin\", \"Septra\", \"Totazina\")"
"SXT" "J01EE01" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "c(\"t/s\", \"sxt\", \"ts\", \"cot\", \"trsu\", \"trsx\")" "c(\"Bactrim\", \"Bactrimel\", \"Belcomycine\", \"Colimycin\", \"Colimycin sulphate\", \"Colisticin\", \"Colistimethate\", \"Colistimethate Sodium\", \"Colistin sulfate\", \"Colistin sulphate\", \"Colomycin\", \"Coly-Mycin\", \"Cotrimazole\", \"Cotrimoxazole\", \"Polymyxin E\", \"Polymyxin E. Sulfate\", \"Promixin\", \"Septra\", \"Totazina\")"
"TRL" "J01FA08" 202225 "Troleandomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"ACETYLOLEANDOMYCIN\", \"Aovine\", \"Cyclamycin\", \"Evramicina\", \"Matromicina\", \"Matromycin T\", \"Oleandocetine\", \"T.A.O.\", \"Treolmicina\", \"Tribiocillina\", \"Triocetin\", \"Triolan\", \"Troleandomicina\", \"Troleandomycin\", \"Troleandomycine\", \"Troleandomycinum\", \"Viamicina\", \"Wytrion\")" 1 "g"
"TRO" 55886 "Trospectomycin" "Other antibacterials" "c(\"Trospectinomycin\", \"Trospectomicina\", \"Trospectomycin\", \"Trospectomycine\", \"Trospectomycinum\")"
"TVA" "J01MA13" 62959 "Trovafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"Trovafloxacin\", \"Trovan\")" 0.2 "g" 0.2 "g"

32
data-raw/read_EUCAST.R

@ -83,9 +83,23 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx") @@ -83,9 +83,23 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx")
x
}
MICs_with_trailing_superscript <- c(0.0011:0.0019, 11:19, 21:29, 0.51:0.59, 41:49,
81:89, 0.031:0.039, 0.061:0.069, 0.251:0.259,
0.1251:0.1259, 161:169, 321:329)
MICs_with_trailing_superscript <- c(seq(from = 0.0011, to = 0.0019, by = 0.0001),
seq(from = 0.031, to = 0.039, by = 0.001),
seq(from = 0.061, to = 0.069, by = 0.001),
seq(from = 0.1251, to = 0.1259, by = 0.0001),
seq(from = 0.251, to = 0.259, by = 0.001),
seq(from = 0.51, to = 0.59, by = 0.01),
seq(from = 11, to = 19, by = 1),
seq(from = 161, to = 169, by = 01),
seq(from = 21, to = 29, by = 1),
seq(from = 321, to = 329, by = 1),
seq(from = 41, to = 49, by = 1),
seq(from = 81, to = 89, by = 1))
has_superscript <- function(x) {
# because due to floating point error 0.1252 is not in:
# seq(from = 0.1251, to = 0.1259, by = 0.0001)
sapply(x, function(x) any(near(x, MICs_with_trailing_superscript)))
}
has_zone_diameters <- rep(any(unlist(raw_data) %like% "zone diameter"), nrow(raw_data))
@ -101,7 +115,8 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx") @@ -101,7 +115,8 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx")
filter(!is.na(drug),
!(is.na(MIC_S) & is.na(MIC_R) & is.na(disk_S) & is.na(disk_R)),
!MIC_S %like% "(MIC|S ≤|note)",
drug != MIC_S) %>%
!MIC_S %like% "^[-]",
drug != MIC_S,) %>%
mutate(administration = case_when(drug %like% "[( ]oral" ~ "oral",
drug %like% "[( ]iv" ~ "iv",
TRUE ~ NA_character_),
@ -120,12 +135,15 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx") @@ -120,12 +135,15 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx")
disk_S = clean_integer(disk_S),
disk_R = clean_integer(disk_R),
# invalid MIC values have a superscript text, delete those
MIC_S = ifelse(MIC_S %in% MICs_with_trailing_superscript,
MIC_S = ifelse(has_superscript(MIC_S),
substr(MIC_S, 1, nchar(MIC_S) - 1),
MIC_S),
MIC_R = ifelse(MIC_R %in% MICs_with_trailing_superscript,
MIC_R = ifelse(has_superscript(MIC_R),
substr(MIC_R, 1, nchar(MIC_R) - 1),
MIC_R)
MIC_R),
# and some are just awful
MIC_S = ifelse(MIC_S == 43.4, 4, MIC_S),
MIC_R = ifelse(MIC_R == 43.4, 4, MIC_R),
) %>%
# clean drug names
mutate(drug = gsub(" ?[(, ].*$", "", drug),

7
data-raw/reproduction_of_antibiotics.R

@ -317,6 +317,13 @@ antibiotics <- filter(antibiotics, ab != "PME") @@ -317,6 +317,13 @@ antibiotics <- filter(antibiotics, ab != "PME")
antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME"
# Remove Sinecatechins
antibiotics <- filter(antibiotics, ab != "SNC")
# GLIMS codes
antibiotics[which(antibiotics$ab == as.ab("cefuroxim")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefuroxim")), "abbreviations"][[1]], "cfrx"))
antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]], "cftx"))
antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]], "cftz"))
antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]], "cfpi"))
antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt"))
antibiotics[which(antibiotics$ab == as.ab("cotrimoxazol")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cotrimoxazol")), "abbreviations"][[1]], "trsx"))
# ESBL E-test codes:
antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))

4
data-raw/reproduction_of_rsi_translation.R

@ -21,7 +21,9 @@ rsi_translation <- DRGLST1 %>% @@ -21,7 +21,9 @@ rsi_translation <- DRGLST1 %>%
R_disk = as.disk(DISK_R),
S_mic = as.mic(MIC_S),
R_mic = as.mic(MIC_R)) %>%
filter(!is.na(mo) & !is.na(ab) & !mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP", "F_FUNGUS", "F_YEAST")) %>%
filter(!is.na(mo),
!is.na(ab),
!mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP", "F_FUNGUS", "F_YEAST")) %>%
arrange(desc(guideline), mo, ab)
print(mo_failures())

194
data-raw/rsi_translation.txt

@ -19,7 +19,7 @@ @@ -19,7 +19,7 @@
"EUCAST 2020" "DISK" "iv" "Haemophilus influenzae" "Amoxicillin/clavulanic acid" "H.influenzae" "2-1ug" 15 15 FALSE
"EUCAST 2020" "DISK" "oral" "Haemophilus influenzae" "Amoxicillin/clavulanic acid" "H.influenzae" "2-1ug" 50 15 FALSE
"EUCAST 2020" "MIC" "iv" "Haemophilus influenzae" "Amoxicillin/clavulanic acid" "H.influenzae" 2 2 FALSE
"EUCAST 2020" "MIC" "oral" "Haemophilus influenzae" "Amoxicillin/clavulanic acid" "H.influenzae" 0.0015 2 FALSE
"EUCAST 2020" "MIC" "oral" "Haemophilus influenzae" "Amoxicillin/clavulanic acid" "H.influenzae" 0.001 2 FALSE
"EUCAST 2020" "MIC" "Lactobacillus" "Amoxicillin/clavulanic acid" "Anaerobes, Grampositive" 4 8 FALSE
"EUCAST 2020" "MIC" "Mobiluncus" "Amoxicillin/clavulanic acid" "Anaerobes, Gramnegative" 4 8 FALSE
"EUCAST 2020" "DISK" "Moraxella catarrhalis" "Amoxicillin/clavulanic acid" "M.catarrhalis" "2-1ug" 19 19 FALSE
@ -70,12 +70,11 @@ @@ -70,12 +70,11 @@
"EUCAST 2020" "MIC" "Fusobacterium" "Ampicillin" "Anaerobes, Gramnegative" 0.5 2 FALSE
"EUCAST 2020" "DISK" "Haemophilus influenzae" "Ampicillin" "H.influenzae" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Haemophilus influenzae" "Ampicillin" "H.influenzae" 1 1 FALSE
"EUCAST 2020" "MIC" "Kingella kingae" "Ampicillin" "K.kingae" 0.062 0.062 FALSE
"EUCAST 2020" "MIC" "Kingella kingae" "Ampicillin" "K.kingae" 0.06 0.06 FALSE
"EUCAST 2020" "MIC" "Lactobacillus" "Ampicillin" "Anaerobes, Grampositive" 4 8 FALSE
"EUCAST 2020" "DISK" "iv" "Listeria monocytogenes" "Ampicillin" "L.monocytogenes" "2ug" 16 16 FALSE
"EUCAST 2020" "MIC" "iv" "Listeria monocytogenes" "Ampicillin" "L.monocytogenes" 1 1 FALSE
"EUCAST 2020" "MIC" "Mobiluncus" "Ampicillin" "Anaerobes, Gramnegative" 0.5 2 FALSE
"EUCAST 2020" "MIC" "Moraxella catarrhalis" "Ampicillin" "M.catarrhalis" -1 -1 FALSE
"EUCAST 2020" "MIC" "Neisseria meningitidis" "Ampicillin" "N.meningitidis" 0.125 1 FALSE
"EUCAST 2020" "MIC" "Parabacteroides" "Ampicillin" "Anaerobes, Gramnegative" 0.5 2 FALSE
"EUCAST 2020" "MIC" "Porphyromonas" "Ampicillin" "Anaerobes, Gramnegative" 0.5 2 FALSE
@ -103,10 +102,9 @@ @@ -103,10 +102,9 @@
"EUCAST 2020" "MIC" "oral" "Helicobacter pylori" "Amoxicillin" "H.pylori" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "iv" "Haemophilus influenzae" "Amoxicillin" "H.influenzae" 2 2 FALSE
"EUCAST 2020" "MIC" "oral" "Haemophilus influenzae" "Amoxicillin" "H.influenzae" 0.001 2 FALSE
"EUCAST 2020" "MIC" "Kingella kingae" "Amoxicillin" "K.kingae" 0.1252 0.1252 FALSE
"EUCAST 2020" "MIC" "Kingella kingae" "Amoxicillin" "K.kingae" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Lactobacillus" "Amoxicillin" "Anaerobes, Grampositive" 4 8 FALSE
"EUCAST 2020" "MIC" "Mobiluncus" "Amoxicillin" "Anaerobes, Gramnegative" 0.5 2 FALSE
"EUCAST 2020" "MIC" "Moraxella catarrhalis" "Amoxicillin" "M.catarrhalis" -1 -1 FALSE
"EUCAST 2020" "MIC" "Neisseria meningitidis" "Amoxicillin" "N.meningitidis" 0.125 1 FALSE
"EUCAST 2020" "MIC" "Parabacteroides" "Amoxicillin" "Anaerobes, Gramnegative" 0.5 2 FALSE
"EUCAST 2020" "MIC" "Porphyromonas" "Amoxicillin" "Anaerobes, Gramnegative" 0.5 2 FALSE
@ -465,29 +463,29 @@ @@ -465,29 +463,29 @@
"EUCAST 2020" "MIC" "Haemophilus influenzae" "Ceftolozane/tazobactam" "H.influenzae" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Pseudomonas aeruginosa" "Ceftolozane/tazobactam" "Pseudomonas" "30-10ug" 24 24 FALSE
"EUCAST 2020" "MIC" "Pseudomonas aeruginosa" "Ceftolozane/tazobactam" "Pseudomonas" 4 4 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Ceftolozane/tazobactam" "PK PD breakpoints" 43.4 43.4 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Dalbavancin" "Staphylococcus" 0.125 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Dalbavancin" "Viridans group streptococci" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae dysgalactiae" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae equisimilis" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi equi" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi ruminatorum" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi zooepidemicus" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group A" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group B" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group C" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group D" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group F" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group G" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group H" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group K" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus pyogenes" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.1252 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Ceftolozane/tazobactam" "PK PD breakpoints" 4 4 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Dalbavancin" "Staphylococcus" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Dalbavancin" "Viridans group streptococci" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae dysgalactiae" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae equisimilis" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi equi" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi ruminatorum" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi zooepidemicus" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus group A" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus group B" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus group C" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus group D" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus group F" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus group G" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus group H" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus group K" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus pyogenes" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Dalbavancin" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Dalbavancin" "PK PD breakpoints" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Daptomycin" "Staphylococcus" 1 1 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Daptomycin" "Streptococcus A,B,C,G" 1 1 FALSE
@ -671,7 +669,6 @@ @@ -671,7 +669,6 @@
"EUCAST 2020" "MIC" "iv" "Enterobacterales" "Fosfomycin" "Enterobacterales" 32 32 FALSE
"EUCAST 2020" "MIC" "UTI" "Enterobacterales" "Fosfomycin" "Enterobacterales" 32 32 TRUE
"EUCAST 2020" "MIC" "iv" "Staphylococcus" "Fosfomycin" "Staphylococcus" 32 32 FALSE
"EUCAST 2020" "MIC" "Clostridium difficile" "Fusidic acid" "C.difficile" -3 -3 FALSE
"EUCAST 2020" "DISK" "Staphylococcus" "Fusidic acid" "Staphylococcus" "10ug" 24 24 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Fusidic acid" "Staphylococcus" 1 1 FALSE
"EUCAST 2020" "DISK" "Systemic" "Enterobacterales" "Gentamicin" "Enterobacterales" "10ug" 17 17 FALSE
@ -928,7 +925,6 @@ @@ -928,7 +925,6 @@
"EUCAST 2020" "MIC" "Enterobacterales" "Moxifloxacin" "Enterobacterales" 0.25 0.25 FALSE
"EUCAST 2020" "DISK" "Corynebacterium" "Moxifloxacin" "Corynebacterium" "5ug" 25 25 FALSE
"EUCAST 2020" "MIC" "Corynebacterium" "Moxifloxacin" "Corynebacterium" 0.5 0.5 FALSE
"EUCAST 2020" "MIC" "Clostridium difficile" "Moxifloxacin" "C.difficile" -1 -1 FALSE
"EUCAST 2020" "DISK" "Haemophilus influenzae" "Moxifloxacin" "H.influenzae" "5ug" 28 28 FALSE
"EUCAST 2020" "MIC" "Haemophilus influenzae" "Moxifloxacin" "H.influenzae" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Moraxella catarrhalis" "Moxifloxacin" "M.catarrhalis" "5ug" 26 26 FALSE
@ -1076,28 +1072,28 @@ @@ -1076,28 +1072,28 @@
"EUCAST 2020" "DISK" "Staphylococcus aureus" "Ofloxacin" "Staphylococcus" "5ug" 50 20 FALSE
"EUCAST 2020" "MIC" "Staphylococcus aureus" "Ofloxacin" "Staphylococcus" 0.001 1 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Ofloxacin" "PK PD breakpoints" 0.25 0.5 FALSE
"EUCAST 2020" "MIC" "Staphylococcus aureus" "Oritavancin" "Staphylococcus" 0.125 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Oritavancin" "Viridans group streptococci" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae dysgalactiae" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae equisimilis" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi equi" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi ruminatorum" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi zooepidemicus" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group A" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group B" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group C" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group D" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group F" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group G" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group H" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus group K" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus pyogenes" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.252 FALSE
"EUCAST 2020" "MIC" "Staphylococcus aureus" "Oritavancin" "Staphylococcus" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Oritavancin" "Viridans group streptococci" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae dysgalactiae" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae equisimilis" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi equi" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi ruminatorum" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi zooepidemicus" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus group A" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus group B" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus group C" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus group D" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus group F" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus group G" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus group H" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus group K" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus pyogenes" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Oritavancin" "Streptococcus A,B,C,G" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Oritavancin" "PK PD breakpoints" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Aerococcus sanguinicola" "Penicillin G" "A.sanguinicola_A.urinae" "1ug" 21 21 FALSE
"EUCAST 2020" "MIC" "Aerococcus sanguinicola" "Penicillin G" "A.sanguinicola_A.urinae" 0.125 0.125 FALSE
@ -1192,7 +1188,6 @@ @@ -1192,7 +1188,6 @@
"EUCAST 2020" "MIC" "Fusobacterium" "Piperacillin" "Anaerobes, Gramnegative" 1 1 FALSE
"EUCAST 2020" "MIC" "Lactobacillus" "Piperacillin" "Anaerobes, Grampositive" 8 1 FALSE
"EUCAST 2020" "MIC" "Mobiluncus" "Piperacillin" "Anaerobes, Gramnegative" 1 1 FALSE
"EUCAST 2020" "MIC" "Moraxella catarrhalis" "Piperacillin" "M.catarrhalis" -1 -1 FALSE
"EUCAST 2020" "MIC" "Parabacteroides" "Piperacillin" "Anaerobes, Gramnegative" 1 1 FALSE
"EUCAST 2020" "MIC" "Porphyromonas" "Piperacillin" "Anaerobes, Gramnegative" 1 1 FALSE
"EUCAST 2020" "MIC" "Propionibacterium" "Piperacillin" "Anaerobes, Grampositive" 8 1 FALSE
@ -1211,7 +1206,6 @@ @@ -1211,7 +1206,6 @@
"EUCAST 2020" "MIC" "Aerococcus urinae" "Rifampicin" "A.sanguinicola_A.urinae" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Corynebacterium" "Rifampicin" "Corynebacterium" "5ug" 30 25 FALSE
"EUCAST 2020" "MIC" "Corynebacterium" "Rifampicin" "Corynebacterium" 0.06 0.5 FALSE
"EUCAST 2020" "MIC" "Clostridium difficile" "Rifampicin" "C.difficile" -6 -6 FALSE
"EUCAST 2020" "MIC" "Helicobacter pylori" "Rifampicin" "H.pylori" 1 1 FALSE
"EUCAST 2020" "DISK" "Haemophilus influenzae" "Rifampicin" "H.influenzae" "5ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Haemophilus influenzae" "Rifampicin" "H.influenzae" 1 1 FALSE
@ -1392,7 +1386,7 @@ @@ -1392,7 +1386,7 @@
"EUCAST 2020" "MIC" "Propionibacterium" "Ticarcillin/clavulanic acid" "Anaerobes, Grampositive" 8 16 FALSE
"EUCAST 2020" "MIC" "Prevotella" "Ticarcillin/clavulanic acid" "Anaerobes, Gramnegative" 8 16 FALSE
"EUCAST 2020" "DISK" "Pseudomonas" "Ticarcillin/clavulanic acid" "Pseudomonas" "75-10ug" 50 18 FALSE
"EUCAST 2020" "MIC" "Pseudomonas" "Ticarcillin/clavulanic acid" "Pseudomonas" 0.0012 16 FALSE
"EUCAST 2020" "MIC" "Pseudomonas" "Ticarcillin/clavulanic acid" "Pseudomonas" 0.001 16 FALSE
"EUCAST 2020" "MIC" "Staphylococcus saccharolyticus" "Ticarcillin/clavulanic acid" "Anaerobes, Grampositive" 8 16 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Ticarcillin/clavulanic acid" "PK PD breakpoints" 8 16 FALSE
"EUCAST 2020" "DISK" "Campylobacter coli" "Tetracycline" "C.jejuni_C.coli" "30ug" 30 30 FALSE
@ -1505,53 +1499,53 @@ @@ -1505,53 +1499,53 @@
"EUCAST 2020" "DISK" "Citrobacter koseri" "Tigecycline" "Enterobacterales" "15ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Citrobacter koseri" "Tigecycline" "Enterobacterales" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Enterococcus faecium" "Tigecycline" "Enterococcus" "15ug" 22 22 FALSE
"EUCAST 2020" "MIC" "Enterococcus faecium" "Tigecycline" "Enterococcus" 0.252 0.252 FALSE
"EUCAST 2020" "MIC" "Enterococcus faecium" "Tigecycline" "Enterococcus" 0.25 0.25 FALSE
"EUCAST 2020" "DISK" "Enterococcus faecalis" "Tigecycline" "Enterococcus" "15ug" 20 20 FALSE
"EUCAST 2020" "MIC" "Enterococcus faecalis" "Tigecycline" "Enterococcus" 0.252 0.252 FALSE
"EUCAST 2020" "MIC" "Enterococcus faecalis" "Tigecycline" "Enterococcus" 0.25 0.25 FALSE
"EUCAST 2020" "DISK" "Escherichia coli" "Tigecycline" "Enterobacterales" "15ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Escherichia coli" "Tigecycline" "Enterobacterales" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Staphylococcus" "Tigecycline" "Staphylococcus" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Tigecycline" "Staphylococcus" 0.53 0.53 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Tigecycline" "Staphylococcus" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus agalactiae" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus anginosus" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus dysgalactiae" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus dysgalactiae dysgalactiae" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae dysgalactiae" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae dysgalactiae" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus dysgalactiae equisimilis" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae equisimilis" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae equisimilis" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus equi" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus equi equi" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi equi" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi equi" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus equi ruminatorum" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi ruminatorum" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi ruminatorum" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus equi zooepidemicus" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi zooepidemicus" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi zooepidemicus" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus group A" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus group A" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus group A" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus group B" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus group B" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus group B" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus group C" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus group C" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus group C" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus group D" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus group D" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus group D" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus group F" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus group F" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus group F" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus group G" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus group G" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus group G" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus group H" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus group H" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus group H" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus group K" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus group K" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus group K" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus pyogenes" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus pyogenes" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus pyogenes" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus salivarius" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "Streptococcus sanguinis" "Tigecycline" "Streptococcus A,B,C,G" "15ug" 19 19 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Tigecycline" "Streptococcus A,B,C,G" 0.1253 0.1253 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Tigecycline" "Streptococcus A,B,C,G" 0.125 0.125 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Tigecycline" "PK PD breakpoints" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Enterobacterales" "Ticarcillin" "Enterobacterales" "75ug" 23 20 FALSE
"EUCAST 2020" "MIC" "Enterobacterales" "Ticarcillin" "Enterobacterales" 8 1 FALSE
@ -1619,7 +1613,7 @@ @@ -1619,7 +1613,7 @@
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Telithromycin" "Streptococcus A,B,C,G" 0.25 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus sanguinis" "Telithromycin" "Streptococcus A,B,C,G" "15ug" 20 17 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Telithromycin" "Streptococcus A,B,C,G" 0.25 0.5 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Telavancin" "Staphylococcus" 0.125 0.1253 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Telavancin" "Staphylococcus" 0.125 0.125 FALSE
"EUCAST 2020" "DISK" "UTI" "Enterobacterales" "Trimethoprim" "Enterobacterales" "5ug" 15 15 TRUE
"EUCAST 2020" "MIC" "UTI" "Enterobacterales" "Trimethoprim" "Enterobacterales" 4 4 TRUE
"EUCAST 2020" "DISK" "UTI" "Staphylococcus" "Trimethoprim" "Staphylococcus" "5ug" 14 14 TRUE
@ -1645,47 +1639,47 @@ @@ -1645,47 +1639,47 @@
"EUCAST 2020" "DISK" "Staphylococcus" "Tedizolid" "Staphylococcus" "2ug" 21 21 FALSE
"EUCAST 2020" "MIC" "Staphylococcus" "Tedizolid" "Staphylococcus" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus agalactiae" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus agalactiae" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus anginosus" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "DISK" "Streptococcus anginosus" "Tedizolid" "Viridans group streptococci" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus anginosus" "Tedizolid" "Viridans group streptococci" 0.25 0.25 FALSE
"EUCAST 2020" "DISK" "Streptococcus dysgalactiae" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus dysgalactiae dysgalactiae" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae dysgalactiae" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae dysgalactiae" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus dysgalactiae equisimilis" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae equisimilis" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus dysgalactiae equisimilis" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus equi" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus equi equi" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi equi" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi equi" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus equi ruminatorum" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi ruminatorum" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi ruminatorum" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus equi zooepidemicus" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi zooepidemicus" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus equi zooepidemicus" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus group A" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus group A" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus group A" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus group B" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus group B" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus group B" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus group C" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus group C" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus group C" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus group D" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus group D" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus group D" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus group F" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus group F" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus group F" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus group G" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus group G" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus group G" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus group H" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus group H" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus group H" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus group K" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus group K" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus group K" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus pyogenes" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus pyogenes" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus pyogenes" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus salivarius" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus salivarius" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Streptococcus sanguinis" "Tedizolid" "Streptococcus A,B,C,G" "2ug" 18 18 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Tedizolid" "Streptococcus A,B,C,G" 0.52 0.5 FALSE
"EUCAST 2020" "MIC" "Streptococcus sanguinis" "Tedizolid" "Streptococcus A,B,C,G" 0.5 0.5 FALSE
"EUCAST 2020" "DISK" "Enterobacterales" "Piperacillin/tazobactam" "Enterobacterales" "30-6ug" 20 17 FALSE
"EUCAST 2020" "MIC" "Enterobacterales" "Piperacillin/tazobactam" "Enterobacterales" 8 16 FALSE
"EUCAST 2020" "MIC" "Actinomyces" "Piperacillin/tazobactam" "Anaerobes, Grampositive" 8 16 FALSE
@ -1699,7 +1693,7 @@ @@ -1699,7 +1693,7 @@
"EUCAST 2020" "MIC" "Eggerthella" "Piperacillin/tazobactam" "Anaerobes, Grampositive" 8 16 FALSE
"EUCAST 2020" "MIC" "Fusobacterium" "Piperacillin/tazobactam" "Anaerobes, Gramnegative" 8 16 FALSE
"EUCAST 2020" "DISK" "Haemophilus influenzae" "Piperacillin/tazobactam" "H.influenzae" "30-6ug" 27 27 FALSE
"EUCAST 2020" "MIC" "Haemophilus influenzae" "Piperacillin/tazobactam" "H.influenzae" 0.256 0.256 FALSE
"EUCAST 2020" "MIC" "Haemophilus influenzae" "Piperacillin/tazobactam" "H.influenzae" 0.25 0.25 FALSE
"EUCAST 2020" "MIC" "Lactobacillus" "Piperacillin/tazobactam" "Anaerobes, Grampositive" 8 16 FALSE
"EUCAST 2020" "MIC" "Mobiluncus" "Piperacillin/tazobactam" "Anaerobes, Gramnegative" 8 16 FALSE
"EUCAST 2020" "MIC" "Parabacteroides" "Piperacillin/tazobactam" "Anaerobes, Gramnegative" 8 16 FALSE

BIN
data/antibiotics.rda

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BIN
data/rsi_translation.rda

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2
docs/404.html

@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9000</span>
</span>
</div>

2
docs/LICENSE-text.html

@ -78,7 +78,7 @@ @@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9000</span>
</span>
</div>

412
docs/articles/AMR.html

@ -39,7 +39,7 @@ @@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9029</span>
</span>
</div>
@ -179,7 +179,7 @@ @@ -179,7 +179,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 February 2020</h4>
<h4 class="date">20 February 2020</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -188,7 +188,7 @@ @@ -188,7 +188,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 17 February 2020.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 20 February 2020.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -219,21 +219,21 @@ @@ -219,21 +219,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2020-02-17</td>
<td align="center">2020-02-20</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2020-02-17</td>
<td align="center">2020-02-20</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2020-02-17</td>
<td align="center">2020-02-20</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -328,30 +328,30 @@ @@ -328,30 +328,30 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-11-17</td>
<td align="center">D1</td>
<td align="center">2010-01-05</td>
<td align="center">F4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-03-23</td>
<td align="center">N2</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2012-08-23</td>
<td align="center">J5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>