mirror of https://github.com/msberends/AMR
(v0.9.0.9012) Support for LOINC codes
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Package: AMR
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Version: 0.9.0.9011
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Date: 2020-01-15
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Version: 0.9.0.9012
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Date: 2020-01-26
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -66,6 +66,7 @@ export(ab_cid)
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export(ab_ddd)
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export(ab_group)
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export(ab_info)
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export(ab_loinc)
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export(ab_name)
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export(ab_property)
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export(ab_synonyms)
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14
NEWS.md
14
NEWS.md
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@ -1,8 +1,18 @@
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# AMR 0.9.0.9011
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## <small>Last updated: 15-Jan-2020</small>
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# AMR 0.9.0.9012
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## <small>Last updated: 26-Jan-2020</small>
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### New
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* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use LOINC code for input in any `ab_*` function:
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```r
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ab_loinc("ampicillin")
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#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"
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ab_name("21066-6")
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#> [1] "Ampicillin"
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```
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### Changes
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* Speed improvement for `as.mo()` (and consequently all `mo_*` functions that use `as.mo()` internally), especially for the *G. species* format (G for genus), like *E. coli* and *K penumoniae*
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* Better support for determination of *Salmonella* biovars
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* Input values for `as.disk()` limited to a maximum of 50 millimeters
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* Added a lifecycle state to every function, following [the lifecycle circle of the `tidyverse`](https://www.tidyverse.org/lifecycle)
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* For in `as.ab()`: support for drugs starting with "co-" like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)
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13
R/ab.R
13
R/ab.R
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@ -143,6 +143,19 @@ as.ab <- function(x, ...) {
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x_new[i] <- found[1L]
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next
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}
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# exact LOINC code
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loinc_found <- unlist(lapply(AMR::antibiotics$loinc,
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function(s) if (x[i] %in% s) {
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TRUE
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} else {
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FALSE
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}))
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found <- AMR::antibiotics$ab[loinc_found == TRUE]
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if (length(found) > 0) {
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x_new[i] <- found[1L]
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next
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}
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# exact synonym
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synonym_found <- unlist(lapply(AMR::antibiotics$synonyms,
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@ -47,18 +47,18 @@
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#' ab_name("AMX") # "Amoxicillin"
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#' ab_atc("AMX") # J01CA04 (ATC code from the WHO)
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#' ab_cid("AMX") # 33613 (Compound ID from PubChem)
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#'
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#' ab_synonyms("AMX") # a list with brand names of amoxicillin
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#' ab_tradenames("AMX") # same
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#'
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#' ab_group("AMX") # "Beta-lactams/penicillins"
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#' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
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#' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
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#'
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#' # smart lowercase tranformation
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#' ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
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#' ab_name(x = c("AMC", "PLB"),
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#' tolower = TRUE) # "amoxicillin/clavulanic acid" "polymyxin B"
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#'
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#' # defined daily doses (DDD)
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#' ab_ddd("AMX", "oral") # 1
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#' ab_ddd("AMX", "oral", units = TRUE) # "g"
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#' ab_ddd("AMX", "iv") # 1
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@ -66,12 +66,13 @@
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#'
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#' ab_info("AMX") # all properties as a list
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#'
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#' # all ab_* functions use as.ab() internally:
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#' ab_name("Fluclox") # "Flucloxacillin"
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#' ab_name("fluklox") # "Flucloxacillin"
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#' ab_name("floxapen") # "Flucloxacillin"
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#' ab_name(21319) # "Flucloxacillin" (using CID)
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#' ab_name("J01CF05") # "Flucloxacillin" (using ATC)
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#' # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
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#' ab_atc("AMP") # ATC code of AMP (ampicillin)
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#' ab_group("J01CA01") # Drug group of ampicillins ATC code
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#' ab_loinc("ampicillin") # LOINC codes of ampicillin
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#' ab_name("21066-6") # "Ampicillin" (using LOINC)
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#' ab_name(6249) # "Ampicillin" (using CID)
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#' ab_name("J01CA01") # "Ampicillin" (using ATC)
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#'
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#' # spelling from different languages and dyslexia are no problem
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#' ab_atc("ceftriaxon")
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@ -137,6 +138,18 @@ ab_atc_group2 <- function(x, language = get_locale(), ...) {
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translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
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}
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#' @rdname ab_property
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#' @export
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ab_loinc <- function(x, ...) {
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loincs <- ab_validate(x = x, property = "loinc", ...)
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names(loincs) <- x
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if (length(loincs) == 1) {
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unname(unlist(loincs))
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} else {
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loincs
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}
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}
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#' @rdname ab_property
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#' @export
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ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
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3
R/data.R
3
R/data.R
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@ -23,7 +23,7 @@
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#'
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#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
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#' @format
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#' ### For the [antibiotics] data set: a [`data.frame`] with 452 observations and 13 variables:
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#' ### For the [antibiotics] data set: a [`data.frame`] with 452 observations and 14 variables:
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#' - `ab`\cr Antibiotic ID as used in this package (like `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
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#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
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#' - `cid`\cr Compound ID as found in PubChem
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@ -37,6 +37,7 @@
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#' - `oral_units`\cr Units of `oral_ddd`
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#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
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#' - `iv_units`\cr Units of `iv_ddd`
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#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the antimicrobial name of the drug. Use [ab_loic()] to retrieve them quickly, see [ab_property()].
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#'
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#' ### For the [antivirals] data set: a [`data.frame`] with 102 observations and 9 variables:
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#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
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@ -23,7 +23,7 @@
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EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019"
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EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' EUCAST rules
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#' Apply EUCAST rules
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#'
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#' @description
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#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <http://eucast.org>), see *Source*. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
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@ -49,6 +49,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' - Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
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#' - Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
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#' - Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
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#'
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#' To *not* use these rules, please use `eucast_rules(..., rules = c("breakpoints", "expert"))`.
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#'
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#' The file containing all EUCAST rules is located here: <https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
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4
R/mo.R
4
R/mo.R
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@ -922,8 +922,10 @@ exec_as.mo <- function(x,
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set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
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}
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next
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} else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE)) {
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} else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE) &
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!x_backup[i] %like% "t[iy](ph|f)[iy]") {
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# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
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# except for S. typhi, S. paratyphi, S. typhimurium
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x[i] <- microorganismsDT[mo == "B_SLMNL_ENTR",
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..property][[1]][1L]
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if (initial_search == TRUE) {
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
File diff suppressed because one or more lines are too long
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@ -59,9 +59,6 @@ for (i in 2:length(unique_ip)) {
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ip_tbl.bak <- ip_tbl
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# how many?
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n_distinct(ip_tbl$country)
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# add long and lat
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ip_tbl <- ip_tbl %>%
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separate(loc, into = c("y", "x"), sep = ",", remove = FALSE, convert = TRUE)
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@ -118,7 +115,7 @@ countries_plot_big <- countries_plot +
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theme(plot.title = element_text(size = 16, hjust = 0.5),
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plot.subtitle = element_text(size = 12, hjust = 0.5)) +
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geom_text(aes(x = -170,
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y = -70,
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y = -75,
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label = stringr::str_wrap(paste0("Countries (n = ",
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length(countries_name[!is.na(countries_name)]), "): ",
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paste(countries_name[!is.na(countries_name)], collapse = ", ")),
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@ -0,0 +1,52 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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# last updated: 20 January 2020 - Loinc_2.67
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# Steps to reproduce:
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# 1. Create a fake account at https://loinc.org (sad you have to create one...)
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# 2. Download the CSV from https://loinc.org/download/loinc-table-file-csv/ (Loinc_2.67_Text_2.67.zip)
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# 3. Read Loinc.csv that's in this zip file
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loinc_df <- read.csv("data-raw/Loinc.csv",
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row.names = NULL,
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stringsAsFactors = FALSE)
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# 4. Clean and add
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library(dplyr)
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library(cleaner)
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library(AMR)
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loinc_df %>% freq(CLASS) # to find the drugs
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loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
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ab_names <- antibiotics %>% pull(name) %>% paste0(collapse = "|") %>% paste0("(", ., ")")
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antibiotics$loinc <- as.list(rep(NA_character_, nrow(antibiotics)))
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for (i in seq_len(nrow(antibiotics))) {
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loinc_ab <- loinc_df %>%
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filter(COMPONENT %like% paste0("^", antibiotics$name[i])) %>%
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pull(LOINC_NUM)
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if (length(loinc_ab) > 0) {
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antibiotics$loinc[i] <- list(loinc_ab)
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}
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}
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dim(antibiotics) # for R/data.R
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usethis::use_data(antibiotics, overwrite = TRUE)
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rm(antibiotics)
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@ -401,6 +401,8 @@ antibiotics <- antibiotics %>%
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antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
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class(antibiotics$ab) <- "ab"
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# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
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dim(antibiotics) # for R/data.R
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usethis::use_data(antibiotics, overwrite = TRUE)
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rm(antibiotics)
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@ -0,0 +1,80 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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library(AMR)
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library(dplyr)
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baseUrl <- 'https://browser.ihtsdotools.org/snowstorm/snomed-ct'
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edition <- 'MAIN'
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version <- '2019-07-31'
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microorganisms.snomed <- data.frame(conceptid = character(0),
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mo = character(0),
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stringsAsFactors = FALSE)
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microorganisms$snomed <- ""
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# for (i in 1:50) {
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for (i in 1:1000) {
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if (i %% 10 == 0) {
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cat(paste0(i, " - ", cleaner::percentage(i / nrow(microorganisms)), "\n"))
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}
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mo_data <- microorganisms %>%
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filter(mo == microorganisms$mo[i]) %>%
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as.list()
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if (!mo_data$rank %in% c("genus", "species")) {
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next
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}
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searchTerm <- paste0(
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ifelse(mo_data$rank == "genus", "Genus ", ""),
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mo_data$fullname,
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" (organism)")
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url <- paste0(baseUrl, '/browser/',
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edition, '/',
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version,
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'/descriptions?term=', curl::curl_escape(searchTerm),
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'&mode=fullText&activeFilter=true&limit=', 250)
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results <- url %>%
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httr::GET() %>%
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httr::content(type = "text", encoding = "UTF-8") %>%
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jsonlite::fromJSON(flatten = TRUE) %>%
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.$items
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if (NROW(results) == 0) {
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next
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} else {
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message("Adding ", crayon::italic(mo_data$fullname))
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}
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tryCatch(
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microorganisms$snomed[i] <- results %>% filter(term == searchTerm) %>% pull(concept.conceptId),
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error = function(e) invisible()
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)
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if (nrow(results) > 1) {
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microorganisms.snomed <- microorganisms.snomed %>%
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bind_rows(tibble(conceptid = results %>% filter(term != searchTerm) %>% pull(concept.conceptId) %>% unique(),
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mo = as.character(mo_data$mo)))
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}
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}
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Binary file not shown.
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
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</span>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
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</span>
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</div>
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|||
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|
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|
|
@ -45,7 +45,7 @@
|
|||
</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">0.9.0.9011</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -205,8 +205,8 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
|||
<div class="main-content">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
|
||||
<strong>Used over 90 countries</strong><br>
|
||||
Since its first public release in early 2018, this package has been downloaded over 25,000 times from 92 countries <small>(as of January 2020, <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge.</p>
|
||||
<strong>Used in almost 100 countries</strong><br>
|
||||
Since its first public release in early 2018, this package has been downloaded over 25,000 times from 96 countries <small>(as of January 2020, <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge.</p>
|
||||
<br><br>
|
||||
</div>
|
||||
<div id="partners" class="section level4">
|
||||
|
|
@ -238,6 +238,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
|
|||
<li>Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
|
||||
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
|
||||
<li>Get the LOINC code of an antibiotic, or get the name associated with a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
|
||||
</ul>
|
||||
<p>This package is ready-to-use for a professional environment by specialists in the following fields:</p>
|
||||
<p>Medical Microbiology</p>
|
||||
|
|
|
|||
|
|
@ -84,7 +84,7 @@
|
|||
</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">0.9.0.9011</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -231,20 +231,34 @@
|
|||
|
||||
</div>
|
||||
|
||||
<div id="amr-0-9-0-9011" class="section level1">
|
||||
<div id="amr-0-9-0-9012" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0-9-0-9011" class="anchor"></a>AMR 0.9.0.9011<small> Unreleased </small>
|
||||
<a href="#amr-0-9-0-9012" class="anchor"></a>AMR 0.9.0.9012<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-15-jan-2020" class="section level2">
|
||||
<div id="last-updated-26-jan-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-15-jan-2020" class="anchor"></a><small>Last updated: 15-Jan-2020</small>
|
||||
<a href="#last-updated-26-jan-2020" class="anchor"></a><small>Last updated: 26-Jan-2020</small>
|
||||
</h2>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use LOINC code for input in any <code>ab_*</code> function:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)</a>
|
||||
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co">#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span></a>
|
||||
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)</a>
|
||||
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co">#> [1] "Ampicillin"</span></a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changes" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changes" class="anchor"></a>Changes</h3>
|
||||
<ul>
|
||||
<li>Speed improvement for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally), especially for the <em>G. species</em> format (G for genus), like <em>E. coli</em> and <em>K penumoniae</em>
|
||||
</li>
|
||||
<li>Better support for determination of <em>Salmonella</em> biovars</li>
|
||||
<li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li>
|
||||
<li>Added a lifecycle state to every function, following <a href="https://www.tidyverse.org/lifecycle">the lifecycle circle of the <code>tidyverse</code></a>
|
||||
</li>
|
||||
|
|
@ -280,26 +294,26 @@
|
|||
<ul>
|
||||
<li>
|
||||
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="cf">if</span> (<span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(somebugs) <span class="op">==</span><span class="st"> "Enterobacteriaceae"</span>) ...</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="cf">if</span> (<span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(somebugs) <span class="op">==</span><span class="st"> "Enterobacteriaceae"</span>) ...</a></code></pre></div>
|
||||
<p>then please adjust this to:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="cf">if</span> (<span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(somebugs) <span class="op">==</span><span class="st"> "Enterobacterales"</span>) ...</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="cf">if</span> (<span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(somebugs) <span class="op">==</span><span class="st"> "Enterobacterales"</span>) ...</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="new" class="section level3">
|
||||
<div id="new-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new" class="anchor"></a>New</h3>
|
||||
<a href="#new-1" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
|
||||
<a class="sourceLine" id="cb3-2" data-line-number="2">example_isolates <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="dt">bug =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(mo)) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX),</a>
|
||||
<a class="sourceLine" id="cb3-5" data-line-number="5"> <span class="dt">amox_clav =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMC)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(amoxicillin) <span class="op">|</span><span class="st"> </span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(amox_clav))</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
|
||||
<a class="sourceLine" id="cb4-2" data-line-number="2">example_isolates <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="dt">bug =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(mo)) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX),</a>
|
||||
<a class="sourceLine" id="cb4-5" data-line-number="5"> <span class="dt">amox_clav =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMC)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(amoxicillin) <span class="op">|</span><span class="st"> </span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(amox_clav))</a></code></pre></div>
|
||||
</li>
|
||||
<li>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).
|
||||
<ul>
|
||||
|
|
@ -320,16 +334,16 @@
|
|||
<li>More intelligent way of coping with some consonants like “l” and “r”</li>
|
||||
<li>
|
||||
<p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,</a>
|
||||
<a class="sourceLine" id="cb4-2" data-line-number="2"> <span class="st">"staphylokok aureuz"</span>))</a>
|
||||
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co">#> Warning: </span></a>
|
||||
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co">#> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span></a>
|
||||
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co">#> Class 'mo'</span></a>
|
||||
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co">#> [1] B_STPHY_AURS B_STPHY_AURS</span></a>
|
||||
<a class="sourceLine" id="cb4-7" data-line-number="7"></a>
|
||||
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="kw"><a href="../reference/as.mo.html">mo_uncertainties</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-9" data-line-number="9"><span class="co">#> "Stafylococcus aureus" -> Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)</span></a>
|
||||
<a class="sourceLine" id="cb4-10" data-line-number="10"><span class="co">#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,</a>
|
||||
<a class="sourceLine" id="cb5-2" data-line-number="2"> <span class="st">"staphylokok aureuz"</span>))</a>
|
||||
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co">#> Warning: </span></a>
|
||||
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co">#> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span></a>
|
||||
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co">#> Class 'mo'</span></a>
|
||||
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co">#> [1] B_STPHY_AURS B_STPHY_AURS</span></a>
|
||||
<a class="sourceLine" id="cb5-7" data-line-number="7"></a>
|
||||
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="kw"><a href="../reference/as.mo.html">mo_uncertainties</a></span>()</a>
|
||||
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co">#> "Stafylococcus aureus" -> Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)</span></a>
|
||||
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co">#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span></a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -377,81 +391,81 @@
|
|||
<ul>
|
||||
<li>
|
||||
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(..., <span class="dt">include_unknown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(..., <span class="dt">include_unknown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
|
||||
For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</li>
|
||||
<li>
|
||||
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co"># how it works in base R:</span></a>
|
||||
<a class="sourceLine" id="cb6-2" data-line-number="2">x <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)</a>
|
||||
<a class="sourceLine" id="cb6-3" data-line-number="3">x[<span class="dv">1</span>] <-<span class="st"> "B"</span></a>
|
||||
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="co">#> invalid factor level, NA generated</span></a>
|
||||
<a class="sourceLine" id="cb6-6" data-line-number="6"></a>
|
||||
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co"># how it now works similarly for classes 'mo' and 'ab':</span></a>
|
||||
<a class="sourceLine" id="cb6-8" data-line-number="8">x <-<span class="st"> </span><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb6-9" data-line-number="9">x[<span class="dv">1</span>] <-<span class="st"> "testvalue"</span></a>
|
||||
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb6-11" data-line-number="11"><span class="co">#> invalid microorganism code, NA generated</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="co"># how it works in base R:</span></a>
|
||||
<a class="sourceLine" id="cb7-2" data-line-number="2">x <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)</a>
|
||||
<a class="sourceLine" id="cb7-3" data-line-number="3">x[<span class="dv">1</span>] <-<span class="st"> "B"</span></a>
|
||||
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="co">#> invalid factor level, NA generated</span></a>
|
||||
<a class="sourceLine" id="cb7-6" data-line-number="6"></a>
|
||||
<a class="sourceLine" id="cb7-7" data-line-number="7"><span class="co"># how it now works similarly for classes 'mo' and 'ab':</span></a>
|
||||
<a class="sourceLine" id="cb7-8" data-line-number="8">x <-<span class="st"> </span><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb7-9" data-line-number="9">x[<span class="dv">1</span>] <-<span class="st"> "testvalue"</span></a>
|
||||
<a class="sourceLine" id="cb7-10" data-line-number="10"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co">#> invalid microorganism code, NA generated</span></a></code></pre></div>
|
||||
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.</li>
|
||||
<li>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).</li>
|
||||
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="new-1" class="section level3">
|
||||
<div id="new-2" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-1" class="anchor"></a>New</h3>
|
||||
<a href="#new-2" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates)</a>
|
||||
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb7-3" data-line-number="3">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
|
||||
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co">#> mo ab S I R total</span></a>
|
||||
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="co">#> 1 A. baumannii AMC 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="co">#> 2 A. baumannii AMK 0 0 0 0</span></a>
|
||||
<a class="sourceLine" id="cb7-7" data-line-number="7"><span class="co">#> 3 A. baumannii AMP 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb7-8" data-line-number="8"><span class="co">#> 4 A. baumannii AMX 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb7-9" data-line-number="9"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a>
|
||||
<a class="sourceLine" id="cb7-10" data-line-number="10"></a>
|
||||
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># change the transformation with the FUN argument to anything you like:</span></a>
|
||||
<a class="sourceLine" id="cb7-12" data-line-number="12">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates, <span class="dt">FUN =</span> mo_gramstain)</a>
|
||||
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb7-14" data-line-number="14">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
|
||||
<a class="sourceLine" id="cb7-15" data-line-number="15"><span class="co">#> mo ab S I R total</span></a>
|
||||
<a class="sourceLine" id="cb7-16" data-line-number="16"><span class="co">#> 1 Gram-negative AMC 469 89 174 732</span></a>
|
||||
<a class="sourceLine" id="cb7-17" data-line-number="17"><span class="co">#> 2 Gram-negative AMK 251 0 2 253</span></a>
|
||||
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="co">#> 3 Gram-negative AMP 227 0 405 632</span></a>
|
||||
<a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co">#> 4 Gram-negative AMX 227 0 405 632</span></a>
|
||||
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates)</a>
|
||||
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb8-3" data-line-number="3">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
|
||||
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co">#> mo ab S I R total</span></a>
|
||||
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="co">#> 1 A. baumannii AMC 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb8-6" data-line-number="6"><span class="co">#> 2 A. baumannii AMK 0 0 0 0</span></a>
|
||||
<a class="sourceLine" id="cb8-7" data-line-number="7"><span class="co">#> 3 A. baumannii AMP 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb8-8" data-line-number="8"><span class="co">#> 4 A. baumannii AMX 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb8-9" data-line-number="9"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a>
|
||||
<a class="sourceLine" id="cb8-10" data-line-number="10"></a>
|
||||
<a class="sourceLine" id="cb8-11" data-line-number="11"><span class="co"># change the transformation with the FUN argument to anything you like:</span></a>
|
||||
<a class="sourceLine" id="cb8-12" data-line-number="12">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates, <span class="dt">FUN =</span> mo_gramstain)</a>
|
||||
<a class="sourceLine" id="cb8-13" data-line-number="13"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb8-14" data-line-number="14">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
|
||||
<a class="sourceLine" id="cb8-15" data-line-number="15"><span class="co">#> mo ab S I R total</span></a>
|
||||
<a class="sourceLine" id="cb8-16" data-line-number="16"><span class="co">#> 1 Gram-negative AMC 469 89 174 732</span></a>
|
||||
<a class="sourceLine" id="cb8-17" data-line-number="17"><span class="co">#> 2 Gram-negative AMK 251 0 2 253</span></a>
|
||||
<a class="sourceLine" id="cb8-18" data-line-number="18"><span class="co">#> 3 Gram-negative AMP 227 0 405 632</span></a>
|
||||
<a class="sourceLine" id="cb8-19" data-line-number="19"><span class="co">#> 4 Gram-negative AMX 227 0 405 632</span></a>
|
||||
<a class="sourceLine" id="cb8-20" data-line-number="20"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a></code></pre></div>
|
||||
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/format.html">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/format.html">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="co"># --------------------------------------------------------------------</span></a>
|
||||
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span></a>
|
||||
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="co"># ----------------------- -----------------------</span></a>
|
||||
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># Drug A Drug B include as include as include as include as</span></a>
|
||||
<a class="sourceLine" id="cb9-5" data-line-number="5"><span class="co"># numerator denominator numerator denominator</span></a>
|
||||
<a class="sourceLine" id="cb9-6" data-line-number="6"><span class="co"># -------- -------- ---------- ----------- ---------- -----------</span></a>
|
||||
<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="co"># S or I S or I X X X X</span></a>
|
||||
<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="co"># R S or I X X X X</span></a>
|
||||
<a class="sourceLine" id="cb9-9" data-line-number="9"><span class="co"># <NA> S or I X X - -</span></a>
|
||||
<a class="sourceLine" id="cb9-10" data-line-number="10"><span class="co"># S or I R X X X X</span></a>
|
||||
<a class="sourceLine" id="cb9-11" data-line-number="11"><span class="co"># R R - X - X</span></a>
|
||||
<a class="sourceLine" id="cb9-12" data-line-number="12"><span class="co"># <NA> R - - - -</span></a>
|
||||
<a class="sourceLine" id="cb9-13" data-line-number="13"><span class="co"># S or I <NA> X X - -</span></a>
|
||||
<a class="sourceLine" id="cb9-14" data-line-number="14"><span class="co"># R <NA> - - - -</span></a>
|
||||
<a class="sourceLine" id="cb9-15" data-line-number="15"><span class="co"># <NA> <NA> - - - -</span></a>
|
||||
<a class="sourceLine" id="cb9-16" data-line-number="16"><span class="co"># --------------------------------------------------------------------</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="co"># --------------------------------------------------------------------</span></a>
|
||||
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span></a>
|
||||
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="co"># ----------------------- -----------------------</span></a>
|
||||
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="co"># Drug A Drug B include as include as include as include as</span></a>
|
||||
<a class="sourceLine" id="cb10-5" data-line-number="5"><span class="co"># numerator denominator numerator denominator</span></a>
|
||||
<a class="sourceLine" id="cb10-6" data-line-number="6"><span class="co"># -------- -------- ---------- ----------- ---------- -----------</span></a>
|
||||
<a class="sourceLine" id="cb10-7" data-line-number="7"><span class="co"># S or I S or I X X X X</span></a>
|
||||
<a class="sourceLine" id="cb10-8" data-line-number="8"><span class="co"># R S or I X X X X</span></a>
|
||||
<a class="sourceLine" id="cb10-9" data-line-number="9"><span class="co"># <NA> S or I X X - -</span></a>
|
||||
<a class="sourceLine" id="cb10-10" data-line-number="10"><span class="co"># S or I R X X X X</span></a>
|
||||
<a class="sourceLine" id="cb10-11" data-line-number="11"><span class="co"># R R - X - X</span></a>
|
||||
<a class="sourceLine" id="cb10-12" data-line-number="12"><span class="co"># <NA> R - - - -</span></a>
|
||||
<a class="sourceLine" id="cb10-13" data-line-number="13"><span class="co"># S or I <NA> X X - -</span></a>
|
||||
<a class="sourceLine" id="cb10-14" data-line-number="14"><span class="co"># R <NA> - - - -</span></a>
|
||||
<a class="sourceLine" id="cb10-15" data-line-number="15"><span class="co"># <NA> <NA> - - - -</span></a>
|
||||
<a class="sourceLine" id="cb10-16" data-line-number="16"><span class="co"># --------------------------------------------------------------------</span></a></code></pre></div>
|
||||
Since this is a major change, usage of the old <code>also_single_tested</code> will throw an informative error that it has been replaced by <code>only_all_tested</code>.</li>
|
||||
<li>
|
||||
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
|
||||
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
|
||||
<a class="sourceLine" id="cb10-3" data-line-number="3">example_isolates <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb10-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
|
||||
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
|
||||
<a class="sourceLine" id="cb11-3" data-line-number="3">example_isolates <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb11-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
|
@ -522,20 +536,20 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
|
|||
<h1 class="page-header">
|
||||
<a href="#amr-0-7-1" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
|
||||
</h1>
|
||||
<div id="new-2" class="section level4">
|
||||
<div id="new-3" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-2" class="anchor"></a>New</h4>
|
||||
<a href="#new-3" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(AMX, CIP) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">rsi_df</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</span></a>
|
||||
<a class="sourceLine" id="cb11-5" data-line-number="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a>
|
||||
<a class="sourceLine" id="cb11-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a>
|
||||
<a class="sourceLine" id="cb11-7" data-line-number="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a>
|
||||
<a class="sourceLine" id="cb11-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(AMX, CIP) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb12-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">rsi_df</a></span>()</a>
|
||||
<a class="sourceLine" id="cb12-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</span></a>
|
||||
<a class="sourceLine" id="cb12-5" data-line-number="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a>
|
||||
<a class="sourceLine" id="cb12-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a>
|
||||
<a class="sourceLine" id="cb12-7" data-line-number="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a>
|
||||
<a class="sourceLine" id="cb12-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
|
||||
|
|
@ -553,12 +567,12 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
|
|||
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
|
||||
</ul>
|
||||
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="co"># B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb12-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb12-4" data-line-number="4"><span class="co"># "Escherichia coli"</span></a>
|
||||
<a class="sourceLine" id="cb12-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb12-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="co"># B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb13-4" data-line-number="4"><span class="co"># "Escherichia coli"</span></a>
|
||||
<a class="sourceLine" id="cb13-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb13-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
|
||||
|
|
@ -603,9 +617,9 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
|
|||
<h1 class="page-header">
|
||||
<a href="#amr-0-7-0" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
|
||||
</h1>
|
||||
<div id="new-3" class="section level4">
|
||||
<div id="new-4" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-3" class="anchor"></a>New</h4>
|
||||
<a href="#new-4" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
|
||||
<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
|
||||
|
|
@ -657,14 +671,14 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
|
|||
<li>when all values are unique it now shows a message instead of a warning</li>
|
||||
<li>
|
||||
<p>support for boxplots:</p>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a>
|
||||
<a class="sourceLine" id="cb13-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
|
||||
<a class="sourceLine" id="cb13-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb13-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
|
||||
<a class="sourceLine" id="cb14-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb14-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -720,9 +734,9 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
|
|||
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
|
||||
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
|
||||
</ul>
|
||||
<div id="new-4" class="section level4">
|
||||
<div id="new-5" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-4" class="anchor"></a>New</h4>
|
||||
<a href="#new-5" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
|
||||
|
|
@ -749,32 +763,32 @@ This data is updated annually - check the included version with the new function
|
|||
</li>
|
||||
<li>
|
||||
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-4" data-line-number="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-5" data-line-number="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-7" data-line-number="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-8" data-line-number="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-9" data-line-number="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-10" data-line-number="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb14-11" data-line-number="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-3" data-line-number="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-5" data-line-number="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-6" data-line-number="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-7" data-line-number="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-8" data-line-number="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-9" data-line-number="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb15-11" data-line-number="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
||||
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||
<a class="sourceLine" id="cb15-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-2" data-line-number="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||
<a class="sourceLine" id="cb16-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-4" data-line-number="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1">ab_property -><span class="st"> </span><span class="kw">atc_property</span>()</a>
|
||||
<a class="sourceLine" id="cb16-2" data-line-number="2">ab_name -><span class="st"> </span><span class="kw">atc_name</span>()</a>
|
||||
<a class="sourceLine" id="cb16-3" data-line-number="3">ab_official -><span class="st"> </span><span class="kw">atc_official</span>()</a>
|
||||
<a class="sourceLine" id="cb16-4" data-line-number="4">ab_trivial_nl -><span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
|
||||
<a class="sourceLine" id="cb16-5" data-line-number="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
||||
<a class="sourceLine" id="cb16-6" data-line-number="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
||||
<a class="sourceLine" id="cb16-7" data-line-number="7">ab_tradenames -><span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">ab_property -><span class="st"> </span><span class="kw">atc_property</span>()</a>
|
||||
<a class="sourceLine" id="cb17-2" data-line-number="2">ab_name -><span class="st"> </span><span class="kw">atc_name</span>()</a>
|
||||
<a class="sourceLine" id="cb17-3" data-line-number="3">ab_official -><span class="st"> </span><span class="kw">atc_official</span>()</a>
|
||||
<a class="sourceLine" id="cb17-4" data-line-number="4">ab_trivial_nl -><span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
|
||||
<a class="sourceLine" id="cb17-5" data-line-number="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
||||
<a class="sourceLine" id="cb17-6" data-line-number="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
||||
<a class="sourceLine" id="cb17-7" data-line-number="7">ab_tradenames -><span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div>
|
||||
These functions use <code>as.atc()</code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
|
||||
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
|
||||
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
|
||||
|
|
@ -786,20 +800,20 @@ These functions use <code>as.atc()</code> internally. The old <code>atc_property
|
|||
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
|
||||
<li>
|
||||
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||