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(v1.5.0.9011) small dosage update

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dr. M.S. (Matthijs) Berends 2021-01-24 23:27:11 +01:00
parent 286eaa9699
commit 24eb4453db
29 changed files with 207 additions and 110 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.5.0.9010
Version: 1.5.0.9011
Date: 2021-01-24
Title: Antimicrobial Resistance Analysis
Authors@R: c(

4
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.5.0.9010
# AMR 1.5.0.9011
## <small>Last updated: 24 January 2021</small>
### New
@ -38,7 +38,7 @@
### Other
* Big documentation updates
* Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before
* Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before, in costs of package size (increased with ~3 MB)
# AMR 1.5.0

4
R/ab_class_selectors.R
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@ -207,12 +207,12 @@ ab_selector <- function(ab_class, function_name) {
} else {
agents_formatted <- paste0("column '", font_bold(agents, collapse = NULL), "'")
agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
need_name <- tolower(agents) != tolower(agents_names)
need_name <- tolower(gsub("[^a-zA-Z]", "", agents)) != tolower(gsub("[^a-zA-Z]", "", agents_names))
agents_formatted[need_name] <- paste0(agents_formatted[need_name],
" (", agents_names[need_name], ")")
message_("Selecting ", ab_group, ": ", paste(agents_formatted, collapse = ", "),
as_note = FALSE,
extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
extra_indent = 4)
}
remember_thrown_message(function_name)
}

8
R/episode.R
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@ -29,7 +29,7 @@
#' @inheritSection lifecycle Stable Lifecycle
#' @param x vector of dates (class `Date` or `POSIXt`)
#' @param episode_days required episode length in days, can also be less than a day, see *Details*
#' @param ... arguments passed on to [as.POSIXct()]
#' @param ... currently not used
#' @details
#' Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least `episode_days` days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least `episode_days` days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
#'
@ -106,8 +106,6 @@
get_episode <- function(x, episode_days, ...) {
meet_criteria(x, allow_class = c("Date", "POSIXt"))
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
stop_if(inherits(x, "Date") & episode_days < 1,
"argument `episode_days` must be at least 1 (day) when `x` is not a date-time object")
exec_episode(type = "sequential",
x = x,
@ -120,8 +118,6 @@ get_episode <- function(x, episode_days, ...) {
is_new_episode <- function(x, episode_days, ...) {
meet_criteria(x, allow_class = c("Date", "POSIXt"))
meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
stop_if(inherits(x, "Date") & episode_days < 1,
"argument `episode_days` must be at least 1 (day) when `x` is not a date-time object")
exec_episode(type = "logical",
x = x,
@ -130,7 +126,7 @@ is_new_episode <- function(x, episode_days, ...) {
}
exec_episode <- function(type, x, episode_days, ...) {
x <- as.double(as.POSIXct(x, ...)) # as.POSIXct() for Date classes
x <- as.double(as.POSIXct(x)) # as.POSIXct() for Date classes
# since x is now in seconds, get seconds from episode_days as well
episode_seconds <- episode_days * 60 * 60 * 24

2
R/eucast_rules.R
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@ -1196,7 +1196,7 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0)
ab <- as.ab(ab)
df <- AMR::dosage[which(AMR::dosage$ab %in% ab & AMR::dosage$administration %in% administration), , drop = FALSE]
df <- df[match(ab, df$ab), colnames(df)[colnames(df) != "administration"], drop = FALSE]
df <- df[which(df$ab == ab), colnames(df)[colnames(df) != "administration"], drop = FALSE]
rownames(df) <- NULL
df$ab <- ab
df

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data-raw/AMR_1.5.0.9010.tar.gz → data-raw/AMR_1.5.0.9011.tar.gz
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data-raw/dosage.dta
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data-raw/dosage.md5
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42d032c419117561e5c4b5b402e16f01
58d6a0589aea598420e37045fb04a5ae

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data-raw/dosage.sas
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data-raw/dosage.txt
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@ -14,19 +14,20 @@
"AMP" "Ampicillin" "standard_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 11
"SAM" "Ampicillin/sulbactam" "high_dosage" "2 g + 1 g" 4 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 4 iv" 11
"SAM" "Ampicillin/sulbactam" "standard_dosage" "2 g + 1 g" 3 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 3 iv" 11
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "or 0.5 g x 1 iv" "0.5 g x 1 oral or 0.5 g x 1 iv" 11
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 11
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 11
"ATM" "Aztreonam" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 11
"ATM" "Aztreonam" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 11
"PEN" "Benzylpenicillin" "high_dosage" "1.2 g" 4 "iv" "" "1.2 g (2 MU) x 4-6 iv" 11
"PEN" "Benzylpenicillin" "standard_dosage" "0.6 g" 4 "iv" "" "0.6 g (1 MU) x 4 iv" 11
"CEC" "Cefaclor" "high_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 11
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "depending on species and/or infection type" "0.25-0.5 g x 3 oral depending on species and/or infection type" 11
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 11
"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 11
"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 11
"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 11
"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 11
"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 11
"FEP" "Cefepime" "standard_dosage" "1 g" 3 "iv" "or 2 g x 2 iv" "1 g x 3 iv or 2 g x 2 iv" 11
"FEP" "Cefepime" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 11
"FDC" "Cefiderocol" "standard_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 11
"CFM" "Cefixime" "standard_dosage" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 11
"CFM" "Cefixime" "uncomplicated_uti" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 11
@ -36,14 +37,14 @@
"CPD" "Cefpodoxime" "uncomplicated_uti" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 11
"CPT" "Ceftaroline" "high_dosage" "0.6 g" 3 "iv" "over 2 hours" "0.6 g x 3 iv over 2 hours" 11
"CPT" "Ceftaroline" "standard_dosage" "0.6 g" 2 "iv" "over 1 hour" "0.6 g x 2 iv over 1 hour" 11
"CAZ" "Ceftazidime" "high_dosage" "2 g" 3 "iv" "or 1 g x 6 iv" "2 g x 3 iv or 1 g x 6 iv" 11
"CAZ" "Ceftazidime" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 11
"CAZ" "Ceftazidime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 11
"CZA" "Ceftazidime/avibactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 2 hours" "(2 g ceftazidime + 0.5 g avibactam) x 3 iv over 2 hours" 11
"CTB" "Ceftibuten" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 11
"BPR" "Ceftobiprole" "standard_dosage" "0.5 g" 3 "iv" "over 2 hours" "0.5 g x 3 iv over 2 hours" 11
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "1 g + 0.5 g" 3 "iv" "over 1 hour" "(1 g ceftolozane + 0.5 g tazobactam) x 3 iv over 1 hour" 11
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "2 g + 1 g" 3 "iv" "over 1 hour" "(2 g ceftolozane + 1 g tazobactam) x 3 iv over 1 hour" 11
"CRO" "Ceftriaxone" "high_dosage" "2 g" 2 "iv" "or 4 g x 1 iv" "2 g x 2 iv or 4 g x 1 iv" 11
"CRO" "Ceftriaxone" "high_dosage" "4 g" 1 "iv" "" "4 g x 1 iv" 11
"CRO" "Ceftriaxone" "standard_dosage" "2 g" 1 "iv" "" "2 g x 1 iv" 11
"CXM" "Cefuroxime" "high_dosage" "1.5 g" 3 "iv" "" "1.5 g x 3 iv" 11
"CXM" "Cefuroxime" "standard_dosage" "0.75 g" 3 "iv" "" "0.75 g x 3 iv" 11
@ -52,70 +53,100 @@
"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
"LEX" "Cephalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
"LEX" "Cephalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "or 2 g x 4 iv" "2 g x 4 oral or 2 g x 4 iv" 11
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "or 1 g x 4 iv" "1 g x 4 oral or 1 g x 4 iv" 11
"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "or 0.4 g x 3 iv" "0.75 g x 2 oral or 0.4 g x 3 iv" 11
"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "or 0.4 g x 2 iv" "0.5 g x 2 oral or 0.4 g x 2 iv" 11
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 11
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 11
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 11
"CIP" "Ciprofloxacin" "high_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 11
"CIP" "Ciprofloxacin" "standard_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 11
"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "" "0.75 g x 2 oral" 11
"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
"CLR" "Clarithromycin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
"CLR" "Clarithromycin" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
"CLI" "Clindamycin" "high_dosage" "0.3 g" 4 "oral" "or 0.9 g x 3 iv" "0.3 g x 4 oral or 0.9 g x 3 iv" 11
"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "or 0.6 g x 3 iv" "0.3 g x 2 oral or 0.6 g x 3 iv" 11
"CLO" "Cloxacillin" "high_dosage" "1 g" 4 "oral" "or 2 g x 6 iv" "1 g x 4 oral or 2 g x 6 iv" 11
"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "or 1 g x 4 iv" "0.5 g x 4 oral or 1 g x 4 iv" 11
"CLI" "Clindamycin" "high_dosage" "0.9 g" 3 "iv" "" "0.9 g x 3 iv" 11
"CLI" "Clindamycin" "standard_dosage" "0.6 g" 3 "iv" "" "0.6 g x 3 iv" 11
"CLI" "Clindamycin" "high_dosage" "0.3 g" 4 "oral" "" "0.3 g x 4 oral" 11
"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "" "0.3 g x 2 oral" 11
"CLO" "Cloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 11
"CLO" "Cloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"CLO" "Cloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 11
"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 11
"COL" "Colistin" "standard_dosage" "4.5 MU" 2 "iv" "loading dose of 9 MU" "4.5 MU x 2 iv with a loading dose of 9 MU" 11
"DAL" "Dalbavancin" "standard_dosage" "1 g" 1 "iv" "over 30 minutes on day 8" "1 g x 1 iv over 30 minutes on day 1 If needed, 0.5 g x 1 iv over 30 minutes on day 8" 11
"DAP" "Daptomycin" "standard_dosage" "4 mg/kg" 1 "iv" "" "4 mg/kg x 1 iv" 11
"DAP" "Daptomycin" "standard_dosage" "6 mg/kg" 1 "iv" "" "6 mg/kg x 1 iv" 11
"DFX" "Delafloxacin" "standard_dosage" "0.45 g" 2 "oral" "or 0.3 g x 2 iv" "0.45 g x 2 oral or 0.3 g x 2 iv" 11
"DIC" "Dicloxacillin" "high_dosage" "2 g" 4 "oral" "or 2 g x 6 iv" "2 g x 4 oral or 2 g x 6 iv" 11
"DIC" "Dicloxacillin" "standard_dosage" "0.5-1 g" 4 "oral" "or 1 g x 4 iv" "0.5-1 g x 4 oral or 1 g x 4 iv" 11
"DFX" "Delafloxacin" "standard_dosage" "0.3 g" 2 "iv" "" "0.3 g x 2 iv" 11
"DFX" "Delafloxacin" "standard_dosage" "0.45 g" 2 "oral" "" "0.45 g x 2 oral" 11
"DIC" "Dicloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 11
"DIC" "Dicloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"DIC" "Dicloxacillin" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 11
"DIC" "Dicloxacillin" "standard_dosage" "0.5-1 g" 4 "oral" "" "0.5-1 g x 4 oral" 11
"DOR" "Doripenem" "high_dosage" "1 g" 3 "iv" "over 1 hour" "1 g x 3 iv over 1 hour" 11
"DOR" "Doripenem" "standard_dosage" "0.5 g" 3 "iv" "over 1 hour" "0.5 g x 3 iv over 1 hour" 11
"DOX" "Doxycycline" "high_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 11
"DOX" "Doxycycline" "standard_dosage" "0.1 g" 1 "oral" "" "0.1 g x 1 oral" 11
"ERV" "Eravacycline" "standard_dosage" "1 mg/kg" 2 "iv" "" "1 mg/kg x 2 iv" 11
"ETP" "Ertapenem" "standard_dosage" "1 g" 1 "iv" "over 30 minutes" "1 g x 1 iv over 30 minutes" 11
"ERY" "Erythromycin" "high_dosage" "1 g" 4 "oral" "or 1 g x 4 iv" "1 g x 4 oral or 1 g x 4 iv" 11
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "oral" "or 0.5 g x 2-4 iv" "0.5 g x 2-4 oral or 0.5 g x 2-4 iv" 11
"ERY" "Erythromycin" "high_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2-4 iv" 11
"ERY" "Erythromycin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 11
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2-4 oral" 11
"FDX" "Fidaxomicin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 11
"FLC" "Flucloxacillin" "high_dosage" "1 g" 4 "oral" "or 2 g x 6 iv" "1 g x 4 oral or 2 g x 6 iv" 11
"FLC" "Flucloxacillin" "standard_dosage" "1 g" 3 "oral" "or 2 g x 4 iv (or 1 g x 6 iv)" "1 g x 3 oral or 2 g x 4 iv (or 1 g x 6 iv)" 11
"FLC" "Flucloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 11
"FLC" "Flucloxacillin" "standard_dosage" "2 g" 4 "iv" "" "2 g x 4 iv (or 1 g x 6 iv)" 11
"FLC" "Flucloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 11
"FLC" "Flucloxacillin" "standard_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 11
"FOS" "Fosfomycin" "high_dosage" "8 g" 3 "iv" "" "8 g x 3 iv" 11
"FOS" "Fosfomycin" "standard_dosage" "4 g" 3 "iv" "" "4 g x 3 iv" 11
"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "oral" "or 0.5 g x 3 iv" "0.5 g x 3 oral or 0.5 g x 3 iv" 11
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "oral" "or 0.5 g x 2 iv" "0.5 g x 2 oral or 0.5 g x 2 iv" 11
"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 11
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 11
"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 11
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
"GEN" "Gentamicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 11
"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 11
"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 11
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 11
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 11
"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 11
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "or 0.5 g x 2 iv" "0.5 g x 2 oral or 0.5 g x 2 iv" 11
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "or 0.5 g x 1 iv" "0.5 g x 1 oral or 0.5 g x 1 iv" 11
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "or 0.6 g x 2 iv" "0.6 g x 2 oral or 0.6 g x 2 iv" 11
"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 11
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 11
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 11
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 11
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 11
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 11
"MEM" "Meropenem" "high_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 11
"MEM" "Meropenem" "standard_dosage" "1 g" 3 "iv" "over 30 minutes" "1 g x 3 iv over 30 minutes" 11
"MEV" "Meropenem/vaborbactam" "standard_dosage" "2 g + 2 g" 3 "iv" "over 3 hours" "(2 g meropenem + 2 g vaborbactam) x 3 iv over 3 hours" 11
"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "oral" "or 0.5 g x 3 iv" "0.5 g x 3 oral or 0.5 g x 3 iv" 11
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "or 0.4 g x 3 iv" "0.4 g x 3 oral or 0.4 g x 3 iv" 11
"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 11
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 11
"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 11
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "" "0.4 g x 3 oral" 11
"MNO" "Minocycline" "standard_dosage" "0.1 g" 2 "oral" "" "0.1 g x 2 oral" 11
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "or 0.4 g x 1 iv" "0.4 g x 1 oral or 0.4 g x 1 iv" 11
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "or 0.4 g x 2 iv" "0.4 g x 2 oral or 0.4 g x 2 iv" 11
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "or 0.2 g x 2 iv" "0.2 g x 2 oral or 0.2 g x 2 iv" 11
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 11
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 11
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 11
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "iv" "" "0.2 g x 2 iv" 11
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "" "0.4 g x 2 oral" 11
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 11
"ORI" "Oritavancin" "standard_dosage" "1.2 g" 1 "iv" "" "1.2 g x 1 (single dose) iv over 3 hours" 11
"OXA" "Oxacillin" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 11
"OXA" "Oxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "depending on species and/or infection type" "0.5-2 g x 3-4 oral depending on species and/or infection type" 11
"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "" "0.5-2 g x 3-4 oral" 11
"PIP" "Piperacillin" "high_dosage" "4 g" 4 "iv" "" "4 g x 4 iv by extended 3-hour infusion" 11
"PIP" "Piperacillin" "standard_dosage" "4 g" 4 "iv" "" "4 g x 4 iv" 11
"TZP" "Piperacillin/tazobactam" "high_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam) x 4 iv by extended 3-hour infusion" 11
"TZP" "Piperacillin/tazobactam" "standard_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam) x 4 iv or x 3 by extended 4-hour infusion" 11
"QDA" "Quinupristin/dalfopristin" "high_dosage" "7.5 mg/kg" 3 "iv" "" "7.5 mg/kg x 3 iv" 11
"QDA" "Quinupristin/dalfopristin" "standard_dosage" "7.5 mg/kg" 2 "iv" "" "7.5 mg/kg x 2 iv" 11
"RIF" "Rifampicin" "high_dosage" "0.6 g" 2 "oral" "or 0.6 g x 2 iv" "0.6 g x 2 oral or 0.6 g x 2 iv" 11
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "oral" "or 0.6 g x 1 iv" "0.6 g x 1 oral or 0.6 g x 1 iv" 11
"RIF" "Rifampicin" "high_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 11
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "iv" "" "0.6 g x 1 iv" 11
"RIF" "Rifampicin" "high_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 11
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "oral" "" "0.6 g x 1 oral" 11
"RXT" "Roxithromycin" "standard_dosage" "0.15 g" 2 "oral" "" "0.15 g x 2 oral" 11
"SPT" "Spectinomycin" "standard_dosage" "2 g" 1 "im" "" "2 g x 1 im" 11
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "oral" "or 0.2 g x 1 iv" "0.2 g x 1 oral or 0.2 g x 1 iv" 11
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "iv" "" "0.2 g x 1 iv" 11
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 11
"TEC" "Teicoplanin" "high_dosage" "0.8 g" 1 "iv" "" "0.8 g x 1 iv" 11
"TEC" "Teicoplanin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 11
"TLV" "Telavancin" "standard_dosage" "10 mg/kg" 1 "iv" "over 1 hour" "10 mg/kg x 1 iv over 1 hour" 11
@ -130,7 +161,10 @@
"TCC" "Ticarcillin/clavulanic acid" "standard_dosage" "3 g + 0.1-0.2 g" 4 "iv" "" "(3 g ticarcillin + 0.1-0.2 g clavulanic acid) x 4 iv" 11
"TGC" "Tigecycline" "standard_dosage" "0.1 g" "loading dose followed by 50 mg x 2 iv" "0.1 g loading dose followed by 50 mg x 2 iv" 11
"TOB" "Tobramycin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 11
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral" 11
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral or (0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 iv" 11
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 11
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
"VAN" "Vancomycin" "standard_dosage" "0.5 g" 4 "iv" "or 1 g x 2 iv or 2 g x 1 by continuous infusion" "0.5 g x 4 iv or 1 g x 2 iv or 2 g x 1 by continuous infusion" 11
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv or 2 g x 1 by continuous infusion" 11

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@ -44,6 +44,28 @@ dosage_source <- read_excel("data-raw/Dosages_v_11.0_Breakpoint_Tables.xlsx", sk
mutate(ab = as.ab(drug),
ab_name = ab_name(ab, language = NULL))
dosage_source <- bind_rows(
# oral
dosage_source %>%
filter(standard_dosage %like% " oral") %>%
mutate(standard_dosage = gsub("oral.*", "oral", standard_dosage),
high_dosage = if_else(high_dosage %like% "oral",
gsub("oral.*", "oral", high_dosage),
NA_character_)),
# iv
dosage_source %>%
filter(standard_dosage %like% " iv") %>%
mutate(standard_dosage = gsub(".* or ", "", standard_dosage),
high_dosage = if_else(high_dosage %like% "( or | iv)",
gsub(".* or ", "", high_dosage),
NA_character_)),
# im
dosage_source %>%
filter(standard_dosage %like% " im")
) %>%
arrange(drug)
get_dosage_lst <- function(col_data) {
standard <- col_data %>%
# remove new lines
@ -90,6 +112,7 @@ standard <- get_dosage_lst(dosage_source$standard_dosage)
high <- get_dosage_lst(dosage_source$high_dosage)
uti <- get_dosage_lst(dosage_source$uncomplicated_uti)
dosage <- bind_rows(
# standard dose
data.frame(
ab = dosage_source$ab,
name = dosage_source$ab_name,
@ -101,6 +124,7 @@ dosage <- bind_rows(
original_txt = sapply(standard, function(x) x$original_txt),
stringsAsFactors = FALSE
),
# high dose
data.frame(
ab = dosage_source$ab,
name = dosage_source$ab_name,
@ -112,6 +136,7 @@ dosage <- bind_rows(
original_txt = sapply(high, function(x) x$original_txt),
stringsAsFactors = FALSE
),
# UTIs
data.frame(
ab = dosage_source$ab,
name = dosage_source$ab_name,
@ -124,8 +149,11 @@ dosage <- bind_rows(
stringsAsFactors = FALSE
)) %>%
mutate(eucast_version = breakpoints_version,
dose_times = as.integer(dose_times)) %>%
dose_times = as.integer(dose_times),
administration = gsub("([a-z]+) .*", "\\1", administration)) %>%
arrange(name, administration, type) %>%
filter(!is.na(dose), dose != ".")
filter(!is.na(dose), dose != ".") %>%
as.data.frame(stringsAsFactors = FALSE)
rownames(dosage) <- NULL
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2)

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2
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>

2
docs/authors.html
View File

@ -81,7 +81,7 @@
</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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>

50
docs/index.html
View File

@ -43,7 +43,7 @@
</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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>
@ -223,20 +223,20 @@ Since you are one of our users, we would like to know how you use the package an
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; NOTE: Using column 'mo' as input for mo_is_gram_negative()</span>
<span class="co">#&gt; NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()</span>
<span class="co">#&gt; NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and</span>
<span class="co">#&gt; 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 from 2020.</span>
<span class="co">#&gt; 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020).</span>
<span class="co">#&gt; Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), </span>
<span class="co">#&gt; 'KAN' (kanamycin), 'TOB' (tobramycin)</span>
<span class="co">#&gt; Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)</span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<table class="table">
<thead><tr class="header">
<th align="left">mo</th>
<th align="left">bacteria</th>
<th align="center">AMK</th>
<th align="center">GEN</th>
<th align="center">KAN</th>
@ -256,6 +256,24 @@ Since you are one of our users, we would like to know how you use the package an
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center"></td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
@ -299,14 +317,32 @@ Since you are one of our users, we would like to know how you use the package an
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
</tbody>
</table>
<p>A base R equivalent would be:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
<code class="sourceCode R"><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span>
<span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,
<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
</div>
<div id="partners" class="section level4">
<h4 class="hasAnchor">

48
docs/news/index.html
View File

@ -81,7 +81,7 @@
</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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1509010" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9010">
<a href="#amr-1509010" class="anchor"></a>AMR 1.5.0.9010<small> Unreleased </small>
<div id="amr-1509011" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9011">
<a href="#amr-1509011" class="anchor"></a>AMR 1.5.0.9011<small> Unreleased </small>
</h1>
<div id="last-updated-24-january-2021" class="section level2">
<h2 class="hasAnchor">
@ -296,7 +296,7 @@
<a href="#other" class="anchor"></a>Other</h3>
<ul>
<li>Big documentation updates</li>
<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before</li>
<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (increased with ~3 MB)</li>
</ul>
</div>
</div>
@ -615,7 +615,7 @@
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p>
<ul>
<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@ -952,7 +952,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div>
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
</li>
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
@ -1221,7 +1221,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
</li>
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
<li>Frequency tables (<code>freq()</code>):
<ul>
<li><p>speed improvement for microbial IDs</p></li>
<li><p>fixed factor level names for R Markdown</p></li>
@ -1231,12 +1231,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># grouped boxplots:</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</li>
</ul>
@ -1246,7 +1246,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
</li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@ -1487,7 +1487,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</li>
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
<li>Frequency tables (<code>freq()</code> function):
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@ -1497,15 +1497,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co"># OLD WAY</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
<span class="co"># NEW WAY</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
<span class="co"># Even supports grouping variables:</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
</li>
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@ -1588,7 +1588,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
<li>
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
<p>Frequency tables - <code>freq()</code>:</p>
<ul>
<li>
<p>Support for grouping variables, test with:</p>
@ -1596,14 +1596,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
</li>
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@ -1621,7 +1621,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
<li>
<p>AI improvements for <code>as.mo</code>:</p>
@ -1789,13 +1789,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
</li>
</ul>
</div>
@ -1869,13 +1869,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
</li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-01-24T13:47Z
last_built: 2021-01-24T22:17Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

4
docs/reference/dosage.html
View File

@ -82,7 +82,7 @@
</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">1.5.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>
@ -247,7 +247,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 135 observations and 9 variables:</p><ul>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 169 observations and 9 variables:</p><ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>name</code><br /> Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>type</code><br /> Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti"</p></li>

6
docs/reference/get_episode.html
View File

@ -82,7 +82,7 @@
</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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>
@ -255,11 +255,11 @@
</tr>
<tr>
<th>episode_days</th>
<td><p>length of the required episode length in days, can also be less than a day, see <em>Details</em></p></td>
<td><p>required episode length in days, can also be less than a day, see <em>Details</em></p></td>
</tr>
<tr>
<th>...</th>
<td><p>arguments passed on to <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXct()</a></code></p></td>
<td><p>currently not used</p></td>
</tr>
</table>

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</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">1.5.0.9010</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9011</span>
</span>
</div>

31
index.md
View File

@ -32,13 +32,13 @@ library(AMR)
library(dplyr)
example_isolates %>%
mutate(mo = mo_fullname(mo)) %>%
mutate(bacteria = mo_fullname(mo)) %>%
filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
select(mo, aminoglycosides(), carbapenems())
select(bacteria, aminoglycosides(), carbapenems())
#> NOTE: Using column 'mo' as input for mo_is_gram_negative()
#> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()
#> NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and
#> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 from 2020.
#> 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020).
#> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin),
#> 'KAN' (kanamycin), 'TOB' (tobramycin)
#> Selecting carbapenems: 'IPM' (imipenem), 'MEM' (meropenem)
@ -46,23 +46,26 @@ example_isolates %>%
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
| mo | AMK | GEN | KAN | TOB | IPM | MEM |
|:------------------------------|:---------:|:---------:|:---------:|:---------:|:---------:|:---------:|
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|*Stenotrophomonas maltophilia* | R | R | R | R | R | R |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|bacteria | AMK | GEN | KAN | TOB | IPM | MEM |
|:------------------------------|:---:|:---:|:---:|:---:|:---:|:---:|
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|*Stenotrophomonas maltophilia* | R | R | R | R | R | R |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
A base R equivalent would be:
```r
example_isolates$mo <- mo_fullname(example_isolates$mo)
example_isolates$bacteria <- mo_fullname(example_isolates$mo)
example_isolates[which(mo_is_gram_negative() &
mo_is_intrinsic_resistant(ab = "cefotax")),
c("mo", aminoglycosides(), carbapenems())]
c("bacteria", aminoglycosides(), carbapenems())]
```
#### Partners

2
man/dosage.Rd
View File

@ -5,7 +5,7 @@
\alias{dosage}
\title{Data Set with Treatment Dosages as Defined by EUCAST}
\format{
A \link{data.frame} with 135 observations and 9 variables:
A \link{data.frame} with 169 observations and 9 variables:
\itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{name}\cr Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO

4
man/get_episode.Rd
View File

@ -12,9 +12,9 @@ is_new_episode(x, episode_days, ...)
\arguments{
\item{x}{vector of dates (class \code{Date} or \code{POSIXt})}
\item{episode_days}{length of the required episode length in days, can also be less than a day, see \emph{Details}}
\item{episode_days}{required episode length in days, can also be less than a day, see \emph{Details}}
\item{...}{arguments passed on to \code{\link[=as.POSIXct]{as.POSIXct()}}}
\item{...}{currently not used}
}
\value{
\itemize{