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(v1.6.0.9000) custom EUCAST rules
This commit is contained in:
parent
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11
.github/workflows/check.yaml
vendored
11
.github/workflows/check.yaml
vendored
@ -66,8 +66,8 @@ jobs:
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- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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@ -78,8 +78,8 @@ jobs:
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- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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env:
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@ -162,7 +162,8 @@ jobs:
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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run: |
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R CMD check data-raw/AMR_latest.tar.gz --no-manual --no-build-vignettes
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tar -xvf data-raw/AMR_latest.tar.gz
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R CMD check AMR --no-manual --no-build-vignettes
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- name: Show testthat output
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if: always()
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13
DESCRIPTION
13
DESCRIPTION
@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.6.0
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Date: 2021-03-14
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Version: 1.6.0.9000
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Date: 2021-04-07
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -35,11 +35,10 @@ Authors@R: c(
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family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"),
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person(role = "ctb",
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family = "Underwood", given = "Anthony", email = "au3@sanger.ac.uk"))
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Description: Functions to simplify the analysis and prediction of Antimicrobial
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Resistance (AMR) and to work with microbial and antimicrobial properties by
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using evidence-based methods, like those defined by Leclercq et al. (2013)
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<doi:10.1111/j.1469-0691.2011.03703.x> and containing reference data such as
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LPSN <doi:10.1099/ijsem.0.004332>.
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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using evidence-based methods and reliable reference data such as LPSN
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<doi:10.1099/ijsem.0.004332>.
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Depends:
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R (>= 3.0.0)
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Suggests:
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@ -43,6 +43,8 @@ S3method(as.data.frame,ab)
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S3method(as.data.frame,mo)
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S3method(as.double,mic)
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S3method(as.integer,mic)
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S3method(as.list,custom_eucast_rules)
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S3method(as.list,custom_mdro_guideline)
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S3method(as.matrix,mic)
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S3method(as.numeric,mic)
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S3method(as.rsi,data.frame)
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@ -57,6 +59,8 @@ S3method(barplot,disk)
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S3method(barplot,mic)
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S3method(barplot,rsi)
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S3method(c,ab)
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S3method(c,custom_eucast_rules)
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S3method(c,custom_mdro_guideline)
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S3method(c,disk)
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S3method(c,mic)
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S3method(c,mo)
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@ -97,6 +101,7 @@ S3method(plot,rsi)
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S3method(print,ab)
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S3method(print,bug_drug_combinations)
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S3method(print,catalogue_of_life_version)
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S3method(print,custom_eucast_rules)
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S3method(print,custom_mdro_guideline)
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S3method(print,disk)
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S3method(print,mic)
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@ -184,6 +189,7 @@ export(count_all)
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export(count_df)
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export(count_resistant)
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export(count_susceptible)
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export(custom_eucast_rules)
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export(custom_mdro_guideline)
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export(eucast_dosage)
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export(eucast_exceptional_phenotypes)
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18
NEWS.md
18
NEWS.md
@ -1,5 +1,19 @@
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# AMR 1.6.0
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# AMR 1.6.0.9000
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## <small>Last updated: 7 April 2021</small>
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### New
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* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
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# Changed
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* Custom MDRO guidelines (`mdro()`, `custom_mdro_guideline()`):
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* Custom MDRO guidelines can now be combined with other custom MDRO guidelines using `c()`
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* Fix for applying the rules; in previous versions, rows were interpreted according to the last matched rule. Now, rows are interpreted according to the first matched rule
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* Fix for `age_groups()` for persons aged zero
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* The `example_isolates` data set now contains some (fictitious) zero-year old patients
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* Fix for minor translation errors
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* Printing of microbial codes in a `data.frame` or `tibble` now gives a warning if the data contains old microbial codes (from a previous AMR package version)
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# AMR 1.6.0
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### New
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* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
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@ -59,7 +73,7 @@
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```
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### Changed
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* Updated the bacterial taxonomy to 3 March 2021 (using [LSPN](https://lpsn.dsmz.de))
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* Updated the bacterial taxonomy to 3 March 2021 (using [LPSN](https://lpsn.dsmz.de))
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* Added 3,372 new species and 1,523 existing species became synomyms
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* The URL of a bacterial species (`mo_url()`) will now lead to https://lpsn.dsmz.de
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* Big update for plotting classes `rsi`, `<mic>`, and `<disk>`:
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@ -504,8 +504,8 @@ format_class <- function(class, plural) {
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if ("matrix" %in% class) {
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class <- "a matrix"
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}
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if ("isolate_identifier" %in% class) {
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class <- "created with isolate_identifier()"
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if ("custom_eucast_rules" %in% class) {
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class <- "input created with `custom_eucast_rules()`"
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}
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if (any(c("mo", "ab", "rsi") %in% class)) {
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class <- paste0("of class <", class[1L], ">")
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@ -522,6 +522,7 @@ meet_criteria <- function(object,
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looks_like = NULL,
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is_in = NULL,
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is_positive = NULL,
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is_positive_or_zero = NULL,
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is_finite = NULL,
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contains_column_class = NULL,
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allow_NULL = FALSE,
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@ -594,9 +595,16 @@ meet_criteria <- function(object,
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stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument `", obj_name,
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"` must ",
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ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
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"be a positive number",
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"all be positive numbers"),
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" (higher than zero)",
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"be a number higher than zero",
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"all be numbers higher than zero"),
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call = call_depth)
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}
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if (!is.null(is_positive_or_zero)) {
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stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument `", obj_name,
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"` must ",
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ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
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"be zero or a positive number",
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"all be zero or numbers higher than zero"),
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call = call_depth)
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}
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if (!is.null(is_finite)) {
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4
R/age.R
4
R/age.R
@ -149,8 +149,8 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
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#' }
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#' }
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age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
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meet_criteria(x, allow_class = c("numeric", "integer"), is_positive = TRUE, is_finite = TRUE)
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meet_criteria(split_at, allow_class = c("numeric", "integer", "character"), is_positive = TRUE, is_finite = TRUE)
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meet_criteria(x, allow_class = c("numeric", "integer"), is_positive_or_zero = TRUE, is_finite = TRUE)
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meet_criteria(split_at, allow_class = c("numeric", "integer", "character"), is_positive_or_zero = TRUE, is_finite = TRUE)
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meet_criteria(na.rm, allow_class = "logical", has_length = 1)
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if (any(x < 0, na.rm = TRUE)) {
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247
R/custom_eucast_rules.R
Normal file
247
R/custom_eucast_rules.R
Normal file
@ -0,0 +1,247 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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# 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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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Create Custom EUCAST Rules
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#'
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#' @inheritSection lifecycle Experimental Lifecycle
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#' @param ... rules in formula notation, see *Examples*
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#' @details
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#' This documentation page will be updated shortly. **This function is experimental.**
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#'
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#' @section How it works:
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#' ..
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#'
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#' It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): `r vector_and(tolower(DEFINED_AB_GROUPS), quote = "``")`.
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#' @export
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#' @examples
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#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
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#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
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#' eucast_rules(example_isolates,
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#' rules = "custom",
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#' custom_rules = x,
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#' info = FALSE)
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#'
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#' # combine rule sets
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#' x2 <- c(x,
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#' custom_eucast_rules(TZP == "R" ~ carbapenems == "R"))
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#' x2
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custom_eucast_rules <- function(...) {
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dots <- tryCatch(list(...),
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error = function(e) "error")
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stop_if(identical(dots, "error"),
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"rules must be a valid formula inputs (e.g., using '~'), see `?custom_eucast_rules`")
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n_dots <- length(dots)
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stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?custom_eucast_rules`.")
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out <- vector("list", n_dots)
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for (i in seq_len(n_dots)) {
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stop_ifnot(inherits(dots[[i]], "formula"),
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"rule ", i, " must be a valid formula input (e.g., using '~'), see `?custom_eucast_rules`")
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# Query
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qry <- dots[[i]][[2]]
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if (inherits(qry, "call")) {
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qry <- as.expression(qry)
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}
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qry <- as.character(qry)
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# these will prevent vectorisation, so replace them:
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qry <- gsub("&&", "&", qry, fixed = TRUE)
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qry <- gsub("||", "|", qry, fixed = TRUE)
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# format nicely, setting spaces around operators
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qry <- gsub(" *([&|+-/*^><==]+) *", " \\1 ", qry)
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qry <- gsub(" ?, ?", ", ", qry)
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qry <- gsub("'", "\"", qry, fixed = TRUE)
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out[[i]]$query <- as.expression(qry)
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# Resulting rule
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result <- dots[[i]][[3]]
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stop_ifnot(deparse(result) %like% "==",
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"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`")
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result_group <- as.character(result)[[2]]
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if (paste0(toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
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# support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
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result_group <- paste0(result_group, "s")
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}
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if (toupper(result_group) %in% DEFINED_AB_GROUPS) {
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result_group <- eval(parse(text = toupper(result_group)), envir = asNamespace("AMR"))
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} else {
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result_group <- tryCatch(
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suppressWarnings(as.ab(result_group,
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fast_mode = TRUE,
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info = FALSE,
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flag_multiple_results = FALSE)),
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error = function(e) NA_character_)
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}
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stop_if(any(is.na(result_group)),
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"this result of rule ", i, " could not be translated to a single antimicrobial agent/group: \"",
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as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial agent, or be one of: ",
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vector_or(tolower(DEFINED_AB_GROUPS), quotes = FALSE), ".")
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result_value <- as.character(result)[[3]]
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result_value[result_value == "NA"] <- NA
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stop_ifnot(result_value %in% c("R", "S", "I", NA),
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"the resulting value of rule ", i, " must be either \"R\", \"S\", \"I\" or NA")
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result_value <- as.rsi(result_value)
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out[[i]]$result_group <- result_group
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out[[i]]$result_value <- result_value
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}
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names(out) <- paste0("rule", seq_len(n_dots))
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set_clean_class(out, new_class = c("custom_eucast_rules", "list"))
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}
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#' @method c custom_eucast_rules
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#' @noRd
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#' @export
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c.custom_eucast_rules <- function(x, ...) {
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if (length(list(...)) == 0) {
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return(x)
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}
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out <- unclass(x)
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for (e in list(...)) {
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out <- c(out, unclass(e))
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}
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names(out) <- paste0("rule", seq_len(length(out)))
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set_clean_class(out, new_class = c("custom_eucast_rules", "list"))
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}
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#' @method as.list custom_eucast_rules
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#' @noRd
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#' @export
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as.list.custom_eucast_rules <- function(x, ...) {
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c(x, ...)
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}
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#' @method print custom_eucast_rules
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#' @export
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#' @noRd
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print.custom_eucast_rules <- function(x, ...) {
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cat("A set of custom EUCAST rules:\n")
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for (i in seq_len(length(x))) {
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rule <- x[[i]]
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rule$query <- format_custom_query_rule(rule$query)
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if (rule$result_value == "R") {
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val <- font_rsi_R_bg(font_black(" R "))
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} else if (rule$result_value == "S") {
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val <- font_rsi_S_bg(font_black(" S "))
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} else {
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val <- font_rsi_I_bg(font_black(" I "))
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}
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agents <- paste0(font_blue(ab_name(rule$result_group, language = NULL, tolower = TRUE),
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collapse = NULL),
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" (", rule$result_group, ")")
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agents <- sort(agents)
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rule_if <- word_wrap(paste0(i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then "),
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"set to {result}:"),
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extra_indent = 5)
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rule_if <- gsub("{result}", val, rule_if, fixed = TRUE)
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rule_then <- paste0(" ", word_wrap(paste0(agents, collapse = ", "), extra_indent = 5))
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cat("\n ", rule_if, "\n", rule_then, "\n", sep = "")
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}
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}
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run_custom_eucast_rules <- function(df, rule, info) {
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n_dots <- length(rule)
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stop_if(n_dots == 0, "no custom rules set", call = -2)
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out <- character(length = NROW(df))
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reasons <- character(length = NROW(df))
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for (i in seq_len(n_dots)) {
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qry <- tryCatch(eval(parse(text = rule[[i]]$query), envir = df, enclos = parent.frame()),
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error = function(e) {
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||||
pkg_env$err_msg <- e$message
|
||||
return("error")
|
||||
})
|
||||
if (identical(qry, "error")) {
|
||||
warning_("in custom_eucast_rules(): rule ", i,
|
||||
" (`", as.character(rule[[i]]$query), "`) was ignored because of this error message: ",
|
||||
pkg_env$err_msg,
|
||||
call = FALSE,
|
||||
add_fn = font_red)
|
||||
next
|
||||
}
|
||||
stop_ifnot(is.logical(qry), "in custom_eucast_rules(): rule ", i, " (`", rule[[i]]$query,
|
||||
"`) must return `TRUE` or `FALSE`, not ",
|
||||
format_class(class(qry), plural = FALSE), call = FALSE)
|
||||
|
||||
new_eucasts <- which(qry == TRUE & out == "")
|
||||
|
||||
if (info == TRUE) {
|
||||
cat(word_wrap("- Custom EUCAST rule ", i, ": `", as.character(rule[[i]]$query),
|
||||
"` (", length(new_eucasts), " rows matched)"), "\n", sep = "")
|
||||
}
|
||||
val <- rule[[i]]$value
|
||||
out[new_eucasts] <- val
|
||||
reasons[new_eucasts] <- paste0("matched rule ", gsub("rule", "", names(rule)[i]), ": ", as.character(rule[[i]]$query))
|
||||
}
|
||||
out[out == ""] <- "Negative"
|
||||
reasons[out == "Negative"] <- "no rules matched"
|
||||
|
||||
if (isTRUE(attributes(rule)$as_factor)) {
|
||||
out <- factor(out, levels = attributes(rule)$values, ordered = TRUE)
|
||||
}
|
||||
|
||||
columns_nonsusceptible <- as.data.frame(t(df[, is.rsi(df)] == "R"))
|
||||
columns_nonsusceptible <- vapply(FUN.VALUE = character(1),
|
||||
columns_nonsusceptible,
|
||||
function(x) paste0(rownames(columns_nonsusceptible)[which(x)], collapse = " "))
|
||||
columns_nonsusceptible[is.na(out)] <- NA_character_
|
||||
|
||||
data.frame(row_number = seq_len(NROW(df)),
|
||||
EUCAST = out,
|
||||
reason = reasons,
|
||||
columns_nonsusceptible = columns_nonsusceptible,
|
||||
stringsAsFactors = FALSE)
|
||||
}
|
||||
|
||||
format_custom_query_rule <- function(query, colours = has_colour()) {
|
||||
query <- gsub(" & ", font_black(font_bold(" and ")), query, fixed = TRUE)
|
||||
query <- gsub(" | ", font_black(" or "), query, fixed = TRUE)
|
||||
query <- gsub(" + ", font_black(" plus "), query, fixed = TRUE)
|
||||
query <- gsub(" - ", font_black(" minus "), query, fixed = TRUE)
|
||||
query <- gsub(" / ", font_black(" divided by "), query, fixed = TRUE)
|
||||
query <- gsub(" * ", font_black(" times "), query, fixed = TRUE)
|
||||
query <- gsub(" == ", font_black(" is "), query, fixed = TRUE)
|
||||
query <- gsub(" > ", font_black(" is higher than "), query, fixed = TRUE)
|
||||
query <- gsub(" < ", font_black(" is lower than "), query, fixed = TRUE)
|
||||
query <- gsub(" >= ", font_black(" is higher than or equal to "), query, fixed = TRUE)
|
||||
query <- gsub(" <= ", font_black(" is lower than or equal to "), query, fixed = TRUE)
|
||||
query <- gsub(" ^ ", font_black(" to the power of "), query, fixed = TRUE)
|
||||
query <- gsub(" %in% ", font_black(" is one of "), query, fixed = TRUE)
|
||||
query <- gsub(" %like% ", font_black(" resembles "), query, fixed = TRUE)
|
||||
if (colours == TRUE) {
|
||||
query <- gsub('"R"', font_rsi_R_bg(font_black(" R ")), query, fixed = TRUE)
|
||||
query <- gsub('"S"', font_rsi_S_bg(font_black(" S ")), query, fixed = TRUE)
|
||||
query <- gsub('"I"', font_rsi_I_bg(font_black(" I ")), query, fixed = TRUE)
|
||||
}
|
||||
# replace the black colour 'stops' with blue colour 'starts'
|
||||
query <- gsub("\033[39m", "\033[34m", as.character(query), fixed = TRUE)
|
||||
# start with blue
|
||||
query <- paste0("\033[34m", query)
|
||||
if (colours == FALSE) {
|
||||
query <- font_stripstyle(query)
|
||||
}
|
||||
query
|
||||
}
|
||||
391
R/eucast_rules.R
391
R/eucast_rules.R
@ -51,7 +51,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x data with antibiotic columns, such as `amox`, `AMX` and `AMC`
|
||||
#' @param info a logical to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions
|
||||
#' @param rules a character vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`.
|
||||
#' @param rules a character vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
|
||||
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
|
||||
#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
|
||||
#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
|
||||
@ -60,6 +60,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
|
||||
#' @param administration route of administration, either `r vector_or(dosage$administration)`
|
||||
#' @param only_rsi_columns a logical to indicate whether only antibiotic columns must be detected that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
|
||||
#' @param custom_rules custom rules to apply, created with [custom_eucast_rules()]
|
||||
#' @inheritParams first_isolate
|
||||
#' @details
|
||||
#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
|
||||
@ -67,6 +68,18 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#'
|
||||
#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
|
||||
#'
|
||||
#' ## Custom Rules
|
||||
#'
|
||||
#' Custom rules can be created using [custom_eucast_rules()], e.g.:
|
||||
#'
|
||||
#' ```
|
||||
#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
|
||||
#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
|
||||
#'
|
||||
#' eucast_rules(example_isolates, rules = "custom", custom_rules = x)
|
||||
#' ```
|
||||
#'
|
||||
#'
|
||||
#' ## 'Other' Rules
|
||||
#'
|
||||
#' Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:
|
||||
@ -149,16 +162,31 @@ eucast_rules <- function(x,
|
||||
version_expertrules = 3.2,
|
||||
ampc_cephalosporin_resistance = NA,
|
||||
only_rsi_columns = FALSE,
|
||||
custom_rules = NULL,
|
||||
...) {
|
||||
meet_criteria(x, allow_class = "data.frame")
|
||||
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4), is_in = c("breakpoints", "expert", "other", "all"))
|
||||
meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5), is_in = c("breakpoints", "expert", "other", "all", "custom"))
|
||||
meet_criteria(verbose, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
|
||||
meet_criteria(version_expertrules, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPERT_RULES)))
|
||||
meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "rsi"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE)
|
||||
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
|
||||
|
||||
if ("custom" %in% rules & is.null(custom_rules)) {
|
||||
warning_("No custom rules were set with the `custom_rules` argument",
|
||||
call = FALSE,
|
||||
immediate = TRUE)
|
||||
rules <- rules[rules != "custom"]
|
||||
if (length(rules) == 0) {
|
||||
if (info == TRUE) {
|
||||
message_("No other rules were set, returning original data", add_fn = font_red, as_note = FALSE)
|
||||
}
|
||||
return(x)
|
||||
}
|
||||
}
|
||||
|
||||
x_deparsed <- deparse(substitute(x))
|
||||
if (length(x_deparsed) > 1 || !all(x_deparsed %like% "[a-z]+")) {
|
||||
@ -264,237 +292,12 @@ eucast_rules <- function(x,
|
||||
only_rsi_columns = only_rsi_columns,
|
||||
...)
|
||||
|
||||
AMC <- cols_ab["AMC"]
|
||||
AMK <- cols_ab["AMK"]
|
||||
AMP <- cols_ab["AMP"]
|
||||
AMX <- cols_ab["AMX"]
|
||||
APL <- cols_ab["APL"]
|
||||
APX <- cols_ab["APX"]
|
||||
ATM <- cols_ab["ATM"]
|
||||
AVB <- cols_ab["AVB"]
|
||||
AVO <- cols_ab["AVO"]
|
||||
AZD <- cols_ab["AZD"]
|
||||
AZL <- cols_ab["AZL"]
|
||||
AZM <- cols_ab["AZM"]
|
||||
BAM <- cols_ab["BAM"]
|
||||
BPR <- cols_ab["BPR"]
|
||||
CAC <- cols_ab["CAC"]
|
||||
CAT <- cols_ab["CAT"]
|
||||
CAZ <- cols_ab["CAZ"]
|
||||
CCP <- cols_ab["CCP"]
|
||||
CCV <- cols_ab["CCV"]
|
||||
CCX <- cols_ab["CCX"]
|
||||
CDC <- cols_ab["CDC"]
|
||||
CDR <- cols_ab["CDR"]
|
||||
CDZ <- cols_ab["CDZ"]
|
||||
CEC <- cols_ab["CEC"]
|
||||
CED <- cols_ab["CED"]
|
||||
CEI <- cols_ab["CEI"]
|
||||
CEM <- cols_ab["CEM"]
|
||||
CEP <- cols_ab["CEP"]
|
||||
CFM <- cols_ab["CFM"]
|
||||
CFM1 <- cols_ab["CFM1"]
|
||||
CFP <- cols_ab["CFP"]
|
||||
CFR <- cols_ab["CFR"]
|
||||
CFS <- cols_ab["CFS"]
|
||||
CFZ <- cols_ab["CFZ"]
|
||||
CHE <- cols_ab["CHE"]
|
||||
CHL <- cols_ab["CHL"]
|
||||
CIC <- cols_ab["CIC"]
|
||||
CID <- cols_ab["CID"]
|
||||
CIP <- cols_ab["CIP"]
|
||||
CLI <- cols_ab["CLI"]
|
||||
CLM <- cols_ab["CLM"]
|
||||
CLO <- cols_ab["CLO"]
|
||||
CLR <- cols_ab["CLR"]
|
||||
CMX <- cols_ab["CMX"]
|
||||
CMZ <- cols_ab["CMZ"]
|
||||
CND <- cols_ab["CND"]
|
||||
COL <- cols_ab["COL"]
|
||||
CPD <- cols_ab["CPD"]
|
||||
CPI <- cols_ab["CPI"]
|
||||
CPL <- cols_ab["CPL"]
|
||||
CPM <- cols_ab["CPM"]
|
||||
CPO <- cols_ab["CPO"]
|
||||
CPR <- cols_ab["CPR"]
|
||||
CPT <- cols_ab["CPT"]
|
||||
CPX <- cols_ab["CPX"]
|
||||
CRB <- cols_ab["CRB"]
|
||||
CRD <- cols_ab["CRD"]
|
||||
CRN <- cols_ab["CRN"]
|
||||
CRO <- cols_ab["CRO"]
|
||||
CSL <- cols_ab["CSL"]
|
||||
CTB <- cols_ab["CTB"]
|
||||
CTC <- cols_ab["CTC"]
|
||||
CTF <- cols_ab["CTF"]
|
||||
CTL <- cols_ab["CTL"]
|
||||
CTS <- cols_ab["CTS"]
|
||||
CTT <- cols_ab["CTT"]
|
||||
CTX <- cols_ab["CTX"]
|
||||
CTZ <- cols_ab["CTZ"]
|
||||
CXM <- cols_ab["CXM"]
|
||||
CYC <- cols_ab["CYC"]
|
||||
CZA <- cols_ab["CZA"]
|
||||
CZD <- cols_ab["CZD"]
|
||||
CZO <- cols_ab["CZO"]
|
||||
CZP <- cols_ab["CZP"]
|
||||
CZX <- cols_ab["CZX"]
|
||||
DAL <- cols_ab["DAL"]
|
||||
DAP <- cols_ab["DAP"]
|
||||
DIC <- cols_ab["DIC"]
|
||||
DIR <- cols_ab["DIR"]
|
||||
DIT <- cols_ab["DIT"]
|
||||
DIX <- cols_ab["DIX"]
|
||||
DIZ <- cols_ab["DIZ"]
|
||||
DKB <- cols_ab["DKB"]
|
||||
DOR <- cols_ab["DOR"]
|
||||
DOX <- cols_ab["DOX"]
|
||||
ENX <- cols_ab["ENX"]
|
||||
EPC <- cols_ab["EPC"]
|
||||
ERY <- cols_ab["ERY"]
|
||||
ETP <- cols_ab["ETP"]
|
||||
FEP <- cols_ab["FEP"]
|
||||
FLC <- cols_ab["FLC"]
|
||||
FLE <- cols_ab["FLE"]
|
||||
FLR1 <- cols_ab["FLR1"]
|
||||
FOS <- cols_ab["FOS"]
|
||||
FOV <- cols_ab["FOV"]
|
||||
FOX <- cols_ab["FOX"]
|
||||
FOX1 <- cols_ab["FOX1"]
|
||||
FUS <- cols_ab["FUS"]
|
||||
GAT <- cols_ab["GAT"]
|
||||
GEM <- cols_ab["GEM"]
|
||||
GEN <- cols_ab["GEN"]
|
||||
GRX <- cols_ab["GRX"]
|
||||
HAP <- cols_ab["HAP"]
|
||||
HET <- cols_ab["HET"]
|
||||
IPM <- cols_ab["IPM"]
|
||||
ISE <- cols_ab["ISE"]
|
||||
JOS <- cols_ab["JOS"]
|
||||
KAN <- cols_ab["KAN"]
|
||||
LEN <- cols_ab["LEN"]
|
||||
LEX <- cols_ab["LEX"]
|
||||
LIN <- cols_ab["LIN"]
|
||||
LNZ <- cols_ab["LNZ"]
|
||||
LOM <- cols_ab["LOM"]
|
||||
LOR <- cols_ab["LOR"]
|
||||
LTM <- cols_ab["LTM"]
|
||||
LVX <- cols_ab["LVX"]
|
||||
MAN <- cols_ab["MAN"]
|
||||
MCM <- cols_ab["MCM"]
|
||||
MEC <- cols_ab["MEC"]
|
||||
MEM <- cols_ab["MEM"]
|
||||
MET <- cols_ab["MET"]
|
||||
MEV <- cols_ab["MEV"]
|
||||
MEZ <- cols_ab["MEZ"]
|
||||
MFX <- cols_ab["MFX"]
|
||||
MID <- cols_ab["MID"]
|
||||
MNO <- cols_ab["MNO"]
|
||||
MTM <- cols_ab["MTM"]
|
||||
NAC <- cols_ab["NAC"]
|
||||
NAF <- cols_ab["NAF"]
|
||||
NAL <- cols_ab["NAL"]
|
||||
NEO <- cols_ab["NEO"]
|
||||
NET <- cols_ab["NET"]
|
||||
NIT <- cols_ab["NIT"]
|
||||
NOR <- cols_ab["NOR"]
|
||||
NOV <- cols_ab["NOV"]
|
||||
NVA <- cols_ab["NVA"]
|
||||
OFX <- cols_ab["OFX"]
|
||||
OLE <- cols_ab["OLE"]
|
||||
ORI <- cols_ab["ORI"]
|
||||
OXA <- cols_ab["OXA"]
|
||||
PAZ <- cols_ab["PAZ"]
|
||||
PEF <- cols_ab["PEF"]
|
||||
PEN <- cols_ab["PEN"]
|
||||
PHE <- cols_ab["PHE"]
|
||||
PHN <- cols_ab["PHN"]
|
||||
PIP <- cols_ab["PIP"]
|
||||
PLB <- cols_ab["PLB"]
|
||||
PME <- cols_ab["PME"]
|
||||
PNM <- cols_ab["PNM"]
|
||||
PRC <- cols_ab["PRC"]
|
||||
PRI <- cols_ab["PRI"]
|
||||
PRL <- cols_ab["PRL"]
|
||||
PRP <- cols_ab["PRP"]
|
||||
PRU <- cols_ab["PRU"]
|
||||
PVM <- cols_ab["PVM"]
|
||||
QDA <- cols_ab["QDA"]
|
||||
RAM <- cols_ab["RAM"]
|
||||
RFL <- cols_ab["RFL"]
|
||||
RID <- cols_ab["RID"]
|
||||
RIF <- cols_ab["RIF"]
|
||||
ROK <- cols_ab["ROK"]
|
||||
RST <- cols_ab["RST"]
|
||||
RXT <- cols_ab["RXT"]
|
||||
SAM <- cols_ab["SAM"]
|
||||
SBC <- cols_ab["SBC"]
|
||||
SDI <- cols_ab["SDI"]
|
||||
SDM <- cols_ab["SDM"]
|
||||
SIS <- cols_ab["SIS"]
|
||||
SLF <- cols_ab["SLF"]
|
||||
SLF1 <- cols_ab["SLF1"]
|
||||
SLF10 <- cols_ab["SLF10"]
|
||||
SLF11 <- cols_ab["SLF11"]
|
||||
SLF12 <- cols_ab["SLF12"]
|
||||
SLF13 <- cols_ab["SLF13"]
|
||||
SLF2 <- cols_ab["SLF2"]
|
||||
SLF3 <- cols_ab["SLF3"]
|
||||
SLF4 <- cols_ab["SLF4"]
|
||||
SLF5 <- cols_ab["SLF5"]
|
||||
SLF6 <- cols_ab["SLF6"]
|
||||
SLF7 <- cols_ab["SLF7"]
|
||||
SLF8 <- cols_ab["SLF8"]
|
||||
SLF9 <- cols_ab["SLF9"]
|
||||
SLT1 <- cols_ab["SLT1"]
|
||||
SLT2 <- cols_ab["SLT2"]
|
||||
SLT3 <- cols_ab["SLT3"]
|
||||
SLT4 <- cols_ab["SLT4"]
|
||||
SLT5 <- cols_ab["SLT5"]
|
||||
SLT6 <- cols_ab["SLT6"]
|
||||
SMX <- cols_ab["SMX"]
|
||||
SPI <- cols_ab["SPI"]
|
||||
SPX <- cols_ab["SPX"]
|
||||
SRX <- cols_ab["SRX"]
|
||||
STR <- cols_ab["STR"]
|
||||
STR1 <- cols_ab["STR1"]
|
||||
SUD <- cols_ab["SUD"]
|
||||
SUL <- cols_ab["SUL"]
|
||||
SUT <- cols_ab["SUT"]
|
||||
SXT <- cols_ab["SXT"]
|
||||
SZO <- cols_ab["SZO"]
|
||||
TAL <- cols_ab["TAL"]
|
||||
TAZ <- cols_ab["TAZ"]
|
||||
TCC <- cols_ab["TCC"]
|
||||
TCM <- cols_ab["TCM"]
|
||||
TCY <- cols_ab["TCY"]
|
||||
TEC <- cols_ab["TEC"]
|
||||
TEM <- cols_ab["TEM"]
|
||||
TGC <- cols_ab["TGC"]
|
||||
THA <- cols_ab["THA"]
|
||||
TIC <- cols_ab["TIC"]
|
||||
TIO <- cols_ab["TIO"]
|
||||
TLT <- cols_ab["TLT"]
|
||||
TLV <- cols_ab["TLV"]
|
||||
TMP <- cols_ab["TMP"]
|
||||
TMX <- cols_ab["TMX"]
|
||||
TOB <- cols_ab["TOB"]
|
||||
TRL <- cols_ab["TRL"]
|
||||
TVA <- cols_ab["TVA"]
|
||||
TZD <- cols_ab["TZD"]
|
||||
TZP <- cols_ab["TZP"]
|
||||
VAN <- cols_ab["VAN"]
|
||||
|
||||
ab_missing <- function(ab) {
|
||||
all(ab %in% c(NULL, NA))
|
||||
}
|
||||
|
||||
if (ab_missing(AMP) & !ab_missing(AMX)) {
|
||||
if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) {
|
||||
# ampicillin column is missing, but amoxicillin is available
|
||||
if (info == TRUE) {
|
||||
message_("Using column '", font_bold(AMX), "' as input for ampicillin since many EUCAST rules depend on it.")
|
||||
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
|
||||
}
|
||||
AMP <- AMX
|
||||
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
|
||||
}
|
||||
|
||||
# data preparation ----
|
||||
@ -502,40 +305,23 @@ eucast_rules <- function(x,
|
||||
message_("Preparing data...", appendLF = FALSE, as_note = FALSE)
|
||||
}
|
||||
|
||||
# nolint start
|
||||
# antibiotic classes ----
|
||||
aminoglycosides <- c(AMK, DKB, GEN, ISE, KAN, NEO, NET, RST, SIS, STR, STR1, TOB)
|
||||
aminopenicillins <- c(AMP, AMX)
|
||||
carbapenems <- c(DOR, ETP, IPM, MEM, MEV)
|
||||
cephalosporins <- c(CDZ, CCP, CAC, CEC, CFR, RID, MAN, CTZ, CZD, CZO, CDR, DIT, FEP, CAT, CFM, CMX, CMZ, DIZ, CID, CFP, CSL, CND, CTX, CTT, CTF, FOX, CPM, CPO, CPD, CPR, CRD, CFS, CPT, CAZ, CCV, CTL, CTB, CZX, BPR, CFM1, CEI, CRO, CXM, LEX, CEP, HAP, CED, LTM, LOR)
|
||||
cephalosporins_1st <- c(CAC, CFR, RID, CTZ, CZD, CZO, CRD, CTL, LEX, CEP, HAP, CED)
|
||||
cephalosporins_2nd <- c(CEC, MAN, CMZ, CID, CND, CTT, CTF, FOX, CPR, CXM, LOR)
|
||||
cephalosporins_3rd <- c(CDZ, CCP, CCX, CDR, DIT, DIX, CAT, CPI, CFM, CMX, DIZ, CFP, CSL, CTX, CTC, CTS, CHE, FOV, CFZ, CPM, CPD, CPX, CDC, CFS, CAZ, CZA, CCV, CEM, CPL, CTB, TIO, CZX, CZP, CRO, LTM)
|
||||
cephalosporins_except_CAZ <- cephalosporins[cephalosporins != ifelse(is.null(CAZ), "", CAZ)]
|
||||
fluoroquinolones <- c(CIP, ENX, FLE, GAT, GEM, GRX, LVX, LOM, MFX, NOR, OFX, PAZ, PEF, PRU, RFL, SPX, TMX, TVA)
|
||||
glycopeptides <- c(AVO, NVA, RAM, TEC, TCM, VAN) # dalba/orita/tela are in lipoglycopeptides
|
||||
lincosamides <- c(CLI, LIN, PRL)
|
||||
lipoglycopeptides <- c(DAL, ORI, TLV)
|
||||
macrolides <- c(AZM, CLR, DIR, ERY, FLR1, JOS, MID, MCM, OLE, ROK, RXT, SPI, TLT, TRL)
|
||||
oxazolidinones <- c(CYC, LNZ, THA, TZD)
|
||||
polymyxins <- c(PLB, COL)
|
||||
streptogramins <- c(QDA, PRI)
|
||||
tetracyclines <- c(DOX, MNO, TCY) # since EUCAST v3.1 tigecycline (TGC) is set apart
|
||||
ureidopenicillins <- c(PIP, TZP, AZL, MEZ)
|
||||
all_betalactams <- c(aminopenicillins, cephalosporins, carbapenems, ureidopenicillins, AMC, OXA, FLC, PEN)
|
||||
# nolint end
|
||||
|
||||
# Some helper functions ---------------------------------------------------
|
||||
get_antibiotic_columns <- function(x, df) {
|
||||
x <- trimws(unlist(strsplit(x, ",", fixed = TRUE)))
|
||||
y <- character(0)
|
||||
for (i in seq_len(length(x))) {
|
||||
if (is.function(get(x[i]))) {
|
||||
stop("Column ", x[i], " is also a function. Please create an issue on github.com/msberends/AMR/issues.")
|
||||
get_antibiotic_columns <- function(x, cols_ab) {
|
||||
x <- strsplit(x, ", *")[[1]]
|
||||
x_new <- character()
|
||||
for (val in x) {
|
||||
if (toupper(val) %in% ls(envir = asNamespace("AMR"))) {
|
||||
# antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS`
|
||||
val <- eval(parse(text = toupper(val)), envir = asNamespace("AMR"))
|
||||
} else if (toupper(val) %in% AB_lookup$ab) {
|
||||
# separate drugs, such as `AMX`
|
||||
val <- as.ab(val)
|
||||
} else {
|
||||
stop_("antimicrobial agent (group) not found in EUCAST rules file: ", val, call = FALSE)
|
||||
}
|
||||
y <- c(y, tryCatch(get(x[i]), error = function(e) ""))
|
||||
x_new <- c(x_new, val)
|
||||
}
|
||||
y[y != "" & y %in% colnames(df)]
|
||||
cols_ab[match(x_new, names(cols_ab))]
|
||||
}
|
||||
markup_italics_where_needed <- function(x) {
|
||||
# returns names found in family, genus or species as italics
|
||||
@ -688,7 +474,8 @@ eucast_rules <- function(x,
|
||||
last_verbose_info = verbose_info,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info)
|
||||
info = info,
|
||||
verbose = verbose)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
@ -720,7 +507,8 @@ eucast_rules <- function(x,
|
||||
last_verbose_info = verbose_info,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info)
|
||||
info = info,
|
||||
verbose = verbose)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
@ -740,10 +528,17 @@ eucast_rules <- function(x,
|
||||
} else {
|
||||
if (info == TRUE) {
|
||||
cat("\n")
|
||||
message_("Skipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R. Use `eucast_rules(..., rules = \"all\")` to also apply those rules.")
|
||||
message_("Skipping inheritance rules defined by this AMR package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R. Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
|
||||
}
|
||||
}
|
||||
|
||||
if (!any(c("all", "custom") %in% rules) & !is.null(custom_rules)) {
|
||||
if (info == TRUE) {
|
||||
message_("Skipping custom EUCAST rules, since the `rules` argument does not contain \"custom\".")
|
||||
}
|
||||
custom_rules <- NULL
|
||||
}
|
||||
|
||||
# Official EUCAST rules ---------------------------------------------------
|
||||
eucast_notification_shown <- FALSE
|
||||
if (!is.null(list(...)$eucast_rules_df)) {
|
||||
@ -777,6 +572,7 @@ eucast_rules <- function(x,
|
||||
eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
|
||||
}
|
||||
|
||||
# Go over all rules and apply them ----
|
||||
for (i in seq_len(nrow(eucast_rules_df))) {
|
||||
|
||||
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule", drop = TRUE]
|
||||
@ -904,7 +700,7 @@ eucast_rules <- function(x,
|
||||
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value),
|
||||
error = function(e) integer(0))
|
||||
} else {
|
||||
source_antibiotics <- get_antibiotic_columns(source_antibiotics, x)
|
||||
source_antibiotics <- get_antibiotic_columns(source_antibiotics, cols_ab)
|
||||
if (length(source_value) == 1 & length(source_antibiotics) > 1) {
|
||||
source_value <- rep(source_value, length(source_antibiotics))
|
||||
}
|
||||
@ -932,7 +728,7 @@ eucast_rules <- function(x,
|
||||
}
|
||||
}
|
||||
|
||||
cols <- get_antibiotic_columns(target_antibiotics, x)
|
||||
cols <- get_antibiotic_columns(target_antibiotics, cols_ab)
|
||||
|
||||
# Apply rule on data ------------------------------------------------------
|
||||
# this will return the unique number of changes
|
||||
@ -948,7 +744,8 @@ eucast_rules <- function(x,
|
||||
last_verbose_info = verbose_info,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info)
|
||||
info = info,
|
||||
verbose = verbose)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
@ -962,6 +759,61 @@ eucast_rules <- function(x,
|
||||
n_added <- 0
|
||||
n_changed <- 0
|
||||
}
|
||||
} # end of going over all rules
|
||||
|
||||
# Apply custom rules ----
|
||||
if (!is.null(custom_rules)) {
|
||||
if (info == TRUE) {
|
||||
cat("\n")
|
||||
cat(font_bold("Custom EUCAST rules, set by user"), "\n")
|
||||
}
|
||||
for (i in seq_len(length(custom_rules))) {
|
||||
rule <- custom_rules[[i]]
|
||||
rows <- which(eval(parse(text = rule$query), envir = x))
|
||||
cols <- as.character(rule$result_group)
|
||||
cols <- c(cols[cols %in% colnames(x)], # direct column names
|
||||
unname(cols_ab[names(cols_ab) %in% cols])) # based on previous cols_ab finding
|
||||
cols <- unique(cols)
|
||||
target_value <- as.character(rule$result_value)
|
||||
rule_text <- paste0("report as '", target_value, "' when ",
|
||||
format_custom_query_rule(rule$query, colours = FALSE), ": ",
|
||||
get_antibiotic_names(cols))
|
||||
if (info == TRUE) {
|
||||
# print rule
|
||||
cat(markup_italics_where_needed(word_wrap(format_custom_query_rule(rule$query, colours = FALSE),
|
||||
width = getOption("width") - 30,
|
||||
extra_indent = 6)))
|
||||
warned <- FALSE
|
||||
}
|
||||
run_changes <- edit_rsi(x = x,
|
||||
col_mo = col_mo,
|
||||
to = target_value,
|
||||
rule = c(rule_text,
|
||||
"Custom EUCAST rules",
|
||||
paste0("Custom EUCAST rule ", i),
|
||||
paste0("Object '", deparse(substitute(custom_rules)),
|
||||
"' consisting of ", length(custom_rules), " custom rules")),
|
||||
rows = rows,
|
||||
cols = cols,
|
||||
last_verbose_info = verbose_info,
|
||||
original_data = x.bak,
|
||||
warned = warned,
|
||||
info = info,
|
||||
verbose = verbose)
|
||||
n_added <- n_added + run_changes$added
|
||||
n_changed <- n_changed + run_changes$changed
|
||||
verbose_info <- run_changes$verbose_info
|
||||
x <- run_changes$output
|
||||
warn_lacking_rsi_class <- c(warn_lacking_rsi_class, run_changes$rsi_warn)
|
||||
# Print number of new changes ---------------------------------------------
|
||||
if (info == TRUE & rule_next != rule_current) {
|
||||
# print only on last one of rules in this group
|
||||
txt_ok(n_added = n_added, n_changed = n_changed, warned = warned)
|
||||
# and reset counters
|
||||
n_added <- 0
|
||||
n_changed <- 0
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
# Print overview ----------------------------------------------------------
|
||||
@ -1089,7 +941,8 @@ edit_rsi <- function(x,
|
||||
last_verbose_info,
|
||||
original_data,
|
||||
warned,
|
||||
info) {
|
||||
info,
|
||||
verbose) {
|
||||
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
|
||||
|
||||
# for Verbose Mode, keep track of all changes and return them
|
||||
@ -1146,7 +999,7 @@ edit_rsi <- function(x,
|
||||
)
|
||||
|
||||
track_changes$output <- new_edits
|
||||
if (isTRUE(info) && !isTRUE(all.equal(x, track_changes$output))) {
|
||||
if ((info == TRUE | verbose == TRUE) && !isTRUE(all.equal(x, track_changes$output))) {
|
||||
get_original_rows <- function(rowids) {
|
||||
as.integer(rownames(original_data[which(original_data$.rowid %in% rowids), , drop = FALSE]))
|
||||
}
|
||||
|
||||
25
R/like.R
25
R/like.R
@ -23,14 +23,14 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Pattern Matching with Keyboard Shortcut
|
||||
#' Vectorised Pattern Matching with Keyboard Shortcut
|
||||
#'
|
||||
#' Convenient wrapper around [grepl()] to match a pattern: `x %like% pattern`. It always returns a [`logical`] vector and is always case-insensitive (use `x %like_case% pattern` for case-sensitive matching). Also, `pattern` can be as long as `x` to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
|
||||
#' @param pattern a character string containing a regular expression (or [character] string for `fixed = TRUE`) to be matched in the given character vector. Coerced by [as.character()] to a character string if possible. If a [character] vector of length 2 or more is supplied, the first element is used with a warning.
|
||||
#' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.
|
||||
#' @return A [`logical`] vector
|
||||
#' @return A [logical] vector
|
||||
#' @name like
|
||||
#' @rdname like
|
||||
#' @export
|
||||
@ -39,10 +39,10 @@
|
||||
#' * Is case-insensitive (use `%like_case%` for case-sensitive matching)
|
||||
#' * Supports multiple patterns
|
||||
#' * Checks if `pattern` is a regular expression and sets `fixed = TRUE` if not, to greatly improve speed
|
||||
#' * Always uses compatibility with Perl
|
||||
#' * Always uses compatibility with Perl unless `fixed = TRUE`, to greatly improve speed
|
||||
#'
|
||||
#' Using RStudio? The text `%like%` can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like `Ctrl+Shift+L` or `Cmd+Shift+L` (see `Tools` > `Modify Keyboard Shortcuts...`).
|
||||
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/master/R/like.R)
|
||||
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R)
|
||||
#' @seealso [grepl()]
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
#' @examples
|
||||
@ -68,7 +68,7 @@
|
||||
#' \donttest{
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' filter(mo_name(mo) %like% "^ent")
|
||||
#' filter(mo_name() %like% "^ent")
|
||||
#' }
|
||||
#' }
|
||||
like <- function(x, pattern, ignore.case = TRUE) {
|
||||
@ -98,14 +98,17 @@ like <- function(x, pattern, ignore.case = TRUE) {
|
||||
if (length(x) == 1) {
|
||||
x <- rep(x, length(pattern))
|
||||
} else if (length(pattern) != length(x)) {
|
||||
stop_("arguments `x` and `pattern` must be of same length, or either one must be 1")
|
||||
stop_("arguments `x` and `pattern` must be of same length, or either one must be 1 ",
|
||||
"(`x` has length ", length(x), " and `pattern` has length ", length(pattern), ")")
|
||||
}
|
||||
unlist(
|
||||
Map(f = grepl,
|
||||
pattern,
|
||||
x,
|
||||
MoreArgs = list(ignore.case = FALSE, fixed = fixed, perl = !fixed)),
|
||||
use.names = FALSE)
|
||||
mapply(FUN = grepl,
|
||||
x = x,
|
||||
pattern = pattern,
|
||||
MoreArgs = list(ignore.case = FALSE, fixed = fixed, perl = !fixed),
|
||||
SIMPLIFY = FALSE,
|
||||
USE.NAMES = FALSE)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
99
R/mdro.R
99
R/mdro.R
@ -102,10 +102,22 @@
|
||||
#' The outcome of the function can be used for the `guideline` argument in the [mdro()] function:
|
||||
#'
|
||||
#' ```
|
||||
#' x <- mdro(example_isolates, guideline = custom)
|
||||
#' x <- mdro(example_isolates,
|
||||
#' guideline = custom)
|
||||
#' table(x)
|
||||
#' #> Elderly Type A Elderly Type B Negative
|
||||
#' #> 43 891 1066
|
||||
#' #> Negative Elderly Type A Elderly Type B
|
||||
#' #> 1070 198 732
|
||||
#' ```
|
||||
#'
|
||||
#' Rules can also be combined with other custom rules by using [c()]:
|
||||
#'
|
||||
#' ```
|
||||
#' x <- mdro(example_isolates,
|
||||
#' guideline = c(custom,
|
||||
#' custom_mdro_guideline(ERY == "R" & age > 50 ~ "Elderly Type C")))
|
||||
#' table(x)
|
||||
#' #> Negative Elderly Type A Elderly Type B Elderly Type C
|
||||
#' #> 961 198 732 109
|
||||
#' ```
|
||||
#'
|
||||
#' The rules set (the `custom` object in this case) could be exported to a shared file location using [saveRDS()] if you collaborate with multiple users. The custom rules set could then be imported using [readRDS()].
|
||||
@ -246,7 +258,7 @@ mdro <- function(x = NULL,
|
||||
txt <- word_wrap(txt)
|
||||
cat(txt, "\n", sep = "")
|
||||
}
|
||||
x <- run_custom_mdro_guideline(x, guideline)
|
||||
x <- run_custom_mdro_guideline(df = x, guideline = guideline, info = info)
|
||||
if (info.bak == TRUE) {
|
||||
cat(group_msg)
|
||||
if (sum(!is.na(x$MDRO)) == 0) {
|
||||
@ -1434,6 +1446,8 @@ mdro <- function(x = NULL,
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
custom_mdro_guideline <- function(..., as_factor = TRUE) {
|
||||
meet_criteria(as_factor, allow_class = "logical", has_length = 1)
|
||||
|
||||
dots <- tryCatch(list(...),
|
||||
error = function(e) "error")
|
||||
stop_if(identical(dots, "error"),
|
||||
@ -1470,11 +1484,49 @@ custom_mdro_guideline <- function(..., as_factor = TRUE) {
|
||||
|
||||
names(out) <- paste0("rule", seq_len(n_dots))
|
||||
out <- set_clean_class(out, new_class = c("custom_mdro_guideline", "list"))
|
||||
attr(out, "values") <- c("Negative", vapply(FUN.VALUE = character(1), out, function(x) x$value))
|
||||
attr(out, "values") <- unname(c("Negative", vapply(FUN.VALUE = character(1), unclass(out), function(x) x$value)))
|
||||
attr(out, "as_factor") <- as_factor
|
||||
out
|
||||
}
|
||||
|
||||
#' @method c custom_mdro_guideline
|
||||
#' @noRd
|
||||
#' @export
|
||||
c.custom_mdro_guideline <- function(x, ..., as_factor = NULL) {
|
||||
if (length(list(...)) == 0) {
|
||||
return(x)
|
||||
}
|
||||
if (!is.null(as_factor)) {
|
||||
meet_criteria(as_factor, allow_class = "logical", has_length = 1)
|
||||
} else {
|
||||
as_factor <- attributes(x)$as_factor
|
||||
}
|
||||
for (g in list(...)) {
|
||||
stop_ifnot(inherits(g, "custom_mdro_guideline"),
|
||||
"for combining custom MDRO guidelines, all rules must be created with `custom_mdro_guideline()`",
|
||||
call = FALSE)
|
||||
vals <- attributes(x)$values
|
||||
if (!all(attributes(g)$values %in% vals)) {
|
||||
vals <- unname(unique(c(vals, attributes(g)$values)))
|
||||
}
|
||||
attributes(g) <- NULL
|
||||
x <- c(unclass(x), unclass(g))
|
||||
attr(x, "values") <- vals
|
||||
}
|
||||
names(x) <- paste0("rule", seq_len(length(x)))
|
||||
x <- set_clean_class(x, new_class = c("custom_mdro_guideline", "list"))
|
||||
attr(x, "values") <- vals
|
||||
attr(x, "as_factor") <- as_factor
|
||||
x
|
||||
}
|
||||
|
||||
#' @method as.list custom_mdro_guideline
|
||||
#' @noRd
|
||||
#' @export
|
||||
as.list.custom_mdro_guideline <- function(x, ...) {
|
||||
c(x, ...)
|
||||
}
|
||||
|
||||
#' @method print custom_mdro_guideline
|
||||
#' @export
|
||||
#' @noRd
|
||||
@ -1482,23 +1534,10 @@ print.custom_mdro_guideline <- function(x, ...) {
|
||||
cat("A set of custom MDRO rules:\n")
|
||||
for (i in seq_len(length(x))) {
|
||||
rule <- x[[i]]
|
||||
rule$query <- gsub(" & ", font_black(font_italic(" and ")), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" | ", font_black(" or "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" + ", font_black(" plus "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" - ", font_black(" minus "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" / ", font_black(" divided by "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" * ", font_black(" times "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" == ", font_black(" is "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" > ", font_black(" is higher than "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" < ", font_black(" is lower than "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" >= ", font_black(" is higher than or equal to "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" <= ", font_black(" is lower than or equal to "), rule$query, fixed = TRUE)
|
||||
rule$query <- gsub(" ^ ", font_black(" to the power of "), rule$query, fixed = TRUE)
|
||||
# replace the black colour 'stops' with blue colour 'starts'
|
||||
rule$query <- gsub("\033[39m", "\033[34m", as.character(rule$query), fixed = TRUE)
|
||||
cat(" ", i, ". ", font_blue(rule$query), font_bold(" -> "), font_red(rule$value), "\n", sep = "")
|
||||
rule$query <- format_custom_query_rule(rule$query)
|
||||
cat(" ", i, ". ", font_bold("If "), font_blue(rule$query), font_bold(" then: "), font_red(rule$value), "\n", sep = "")
|
||||
}
|
||||
cat(" ", i + 1, ". Otherwise", font_bold(" -> "), font_red(paste0("Negative")), "\n", sep = "")
|
||||
cat(" ", i + 1, ". ", font_bold("Otherwise: "), font_red(paste0("Negative")), "\n", sep = "")
|
||||
cat("\nUnmatched rows will return ", font_red("NA"), ".\n", sep = "")
|
||||
if (isTRUE(attributes(x)$as_factor)) {
|
||||
cat("Results will be of class <factor>, with ordered levels: ", paste0(attributes(x)$values, collapse = " < "), "\n", sep = "")
|
||||
@ -1507,7 +1546,7 @@ print.custom_mdro_guideline <- function(x, ...) {
|
||||
}
|
||||
}
|
||||
|
||||
run_custom_mdro_guideline <- function(df, guideline) {
|
||||
run_custom_mdro_guideline <- function(df, guideline, info) {
|
||||
n_dots <- length(guideline)
|
||||
stop_if(n_dots == 0, "no custom guidelines set", call = -2)
|
||||
out <- character(length = NROW(df))
|
||||
@ -1520,7 +1559,7 @@ run_custom_mdro_guideline <- function(df, guideline) {
|
||||
})
|
||||
if (identical(qry, "error")) {
|
||||
warning_("in custom_mdro_guideline(): rule ", i,
|
||||
" (`", guideline[[i]]$query, "`) was ignored because of this error message: ",
|
||||
" (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
|
||||
pkg_env$err_msg,
|
||||
call = FALSE,
|
||||
add_fn = font_red)
|
||||
@ -1529,9 +1568,16 @@ run_custom_mdro_guideline <- function(df, guideline) {
|
||||
stop_ifnot(is.logical(qry), "in custom_mdro_guideline(): rule ", i, " (`", guideline[[i]]$query,
|
||||
"`) must return `TRUE` or `FALSE`, not ",
|
||||
format_class(class(qry), plural = FALSE), call = FALSE)
|
||||
|
||||
new_mdros <- which(qry == TRUE & out == "")
|
||||
|
||||
if (info == TRUE) {
|
||||
cat(word_wrap("- Custom MDRO rule ", i, ": `", as.character(guideline[[i]]$query),
|
||||
"` (", length(new_mdros), " rows matched)"), "\n", sep = "")
|
||||
}
|
||||
val <- guideline[[i]]$value
|
||||
out[which(qry)] <- val
|
||||
reasons[which(qry)] <- paste0("matched rule ", gsub("rule", "", names(guideline)[i]), ": ", as.character(guideline[[i]]$query))
|
||||
out[new_mdros] <- val
|
||||
reasons[new_mdros] <- paste0("matched rule ", gsub("rule", "", names(guideline)[i]), ": ", as.character(guideline[[i]]$query))
|
||||
}
|
||||
out[out == ""] <- "Negative"
|
||||
reasons[out == "Negative"] <- "no rules matched"
|
||||
@ -1540,8 +1586,7 @@ run_custom_mdro_guideline <- function(df, guideline) {
|
||||
out <- factor(out, levels = attributes(guideline)$values, ordered = TRUE)
|
||||
}
|
||||
|
||||
rsi_cols <- vapply(FUN.VALUE = logical(1), df, function(x) is.rsi(x))
|
||||
columns_nonsusceptible <- as.data.frame(t(df[, rsi_cols] == "R"))
|
||||
columns_nonsusceptible <- as.data.frame(t(df[, is.rsi(df)] == "R"))
|
||||
columns_nonsusceptible <- vapply(FUN.VALUE = character(1),
|
||||
columns_nonsusceptible,
|
||||
function(x) paste0(rownames(columns_nonsusceptible)[which(x)], collapse = " "))
|
||||
|
||||
42
R/mo.R
42
R/mo.R
@ -1659,6 +1659,24 @@ pillar_shaft.mo <- function(x, ...) {
|
||||
out[is.na(x)] <- font_na(" NA")
|
||||
out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
|
||||
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
|
||||
# markup old mo codes
|
||||
out[!x %in% MO_lookup$mo] <- font_italic(font_na(x[!x %in% MO_lookup$mo],
|
||||
collapse = NULL),
|
||||
collapse = NULL)
|
||||
# throw a warning with the affected column name
|
||||
mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
|
||||
error = function(e) NULL)
|
||||
if (!is.null(mo)) {
|
||||
col <- paste0("Column '", mo, "'")
|
||||
} else {
|
||||
col <- "The data"
|
||||
}
|
||||
warning_(col, " contains old microbial codes (from a previous AMR package version). ",
|
||||
"Please update your MO codes with `as.mo()`.",
|
||||
call = FALSE)
|
||||
}
|
||||
|
||||
# make it always fit exactly
|
||||
max_char <- max(nchar(x))
|
||||
if (is.na(max_char)) {
|
||||
@ -1753,11 +1771,16 @@ summary.mo <- function(object, ...) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
as.data.frame.mo <- function(x, ...) {
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
|
||||
warning_("The data contains old microbial codes (from a previous AMR package version). ",
|
||||
"Please update your MO codes with `as.mo()`.",
|
||||
call = FALSE)
|
||||
}
|
||||
nm <- deparse1(substitute(x))
|
||||
if (!"nm" %in% names(list(...))) {
|
||||
as.data.frame.vector(as.mo(x), ..., nm = nm)
|
||||
as.data.frame.vector(x, ..., nm = nm)
|
||||
} else {
|
||||
as.data.frame.vector(as.mo(x), ...)
|
||||
as.data.frame.vector(x, ...)
|
||||
}
|
||||
}
|
||||
|
||||
@ -1875,6 +1898,7 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
collapse = "")
|
||||
# after strwrap, make taxonomic names italic
|
||||
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates, perl = TRUE)
|
||||
candidates <- gsub(font_italic("and"), "and", candidates, fixed = TRUE)
|
||||
candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "),
|
||||
"Also matched",
|
||||
candidates, fixed = TRUE)
|
||||
@ -2028,13 +2052,15 @@ replace_old_mo_codes <- function(x, property) {
|
||||
x[which(!is.na(matched))] <- mo_new[which(!is.na(matched))]
|
||||
n_matched <- length(matched[!is.na(matched)])
|
||||
if (property != "mo") {
|
||||
message_(font_blue("The input contained old microbial codes (from previous package versions). Please update your MO codes with `as.mo()`."))
|
||||
message_(font_blue(paste0("The input contained ", n_matched,
|
||||
" old microbial code", ifelse(n_matched == 1, "", "s"),
|
||||
" (from a previous AMR package version). Please update your MO codes with `as.mo()`.")))
|
||||
} else {
|
||||
if (n_matched == 1) {
|
||||
message_(font_blue("1 old microbial code (from previous package versions) was updated to a current used MO code."))
|
||||
} else {
|
||||
message_(font_blue(n_matched, "old microbial codes (from previous package versions) were updated to current used MO codes."))
|
||||
}
|
||||
message_(font_blue(paste0(n_matched, " old microbial code", ifelse(n_matched == 1, "", "s"),
|
||||
" (from a previous AMR package version) ",
|
||||
ifelse(n_matched == 1, "was", "were"),
|
||||
" updated to ", ifelse(n_matched == 1, "a ", ""),
|
||||
"currently used MO code", ifelse(n_matched == 1, "", "s"), ".")))
|
||||
}
|
||||
}
|
||||
x
|
||||
|
||||
@ -729,14 +729,7 @@ mo_validate <- function(x, property, language, ...) {
|
||||
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
|
||||
if (is.mo(x)
|
||||
& !Becker %in% c(TRUE, "all")
|
||||
& !Lancefield %in% c(TRUE, "all")) {
|
||||
# this will not reset mo_uncertainties and mo_failures
|
||||
# because it's already a valid MO
|
||||
x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...)
|
||||
} else if (!all(x %in% MO_lookup[, property, drop = TRUE])
|
||||
| has_Becker_or_Lancefield) {
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
|
||||
x <- exec_as.mo(x, property = property, language = language, ...)
|
||||
}
|
||||
|
||||
|
||||
213
R/plot.R
213
R/plot.R
@ -93,6 +93,14 @@ plot.mic <- function(x,
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if (length(colours_RSI) == 1) {
|
||||
colours_RSI <- rep(colours_RSI, 3)
|
||||
}
|
||||
@ -142,6 +150,7 @@ plot.mic <- function(x,
|
||||
horiz = TRUE,
|
||||
cex = 0.75,
|
||||
box.lwd = 0,
|
||||
box.col = "#FFFFFF55",
|
||||
bg = "#FFFFFF55")
|
||||
}
|
||||
}
|
||||
@ -170,6 +179,14 @@ barplot.mic <- function(height,
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
main <- gsub(" +", " ", paste0(main, collapse = " "))
|
||||
|
||||
plot(x = height,
|
||||
@ -209,6 +226,14 @@ ggplot.mic <- function(data,
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if ("main" %in% names(list(...))) {
|
||||
title <- list(...)$main
|
||||
}
|
||||
@ -285,6 +310,14 @@ plot.disk <- function(x,
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if (length(colours_RSI) == 1) {
|
||||
colours_RSI <- rep(colours_RSI, 3)
|
||||
}
|
||||
@ -335,6 +368,7 @@ plot.disk <- function(x,
|
||||
horiz = TRUE,
|
||||
cex = 0.75,
|
||||
box.lwd = 0,
|
||||
box.col = "#FFFFFF55",
|
||||
bg = "#FFFFFF55")
|
||||
}
|
||||
}
|
||||
@ -363,6 +397,14 @@ barplot.disk <- function(height,
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
main <- gsub(" +", " ", paste0(main, collapse = " "))
|
||||
|
||||
plot(x = height,
|
||||
@ -402,6 +444,14 @@ ggplot.disk <- function(data,
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if ("main" %in% names(list(...))) {
|
||||
title <- list(...)$main
|
||||
}
|
||||
@ -454,79 +504,6 @@ ggplot.disk <- function(data,
|
||||
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
|
||||
}
|
||||
|
||||
plot_prepare_table <- function(x, expand) {
|
||||
if (is.mic(x)) {
|
||||
if (expand == TRUE) {
|
||||
# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
|
||||
extra_range <- max(x) / 2
|
||||
while (min(extra_range) / 2 > min(x)) {
|
||||
extra_range <- c(min(extra_range) / 2, extra_range)
|
||||
}
|
||||
nms <- extra_range
|
||||
extra_range <- rep(0, length(extra_range))
|
||||
names(extra_range) <- nms
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x)]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
}
|
||||
x <- x[order(as.double(as.mic(names(x))))]
|
||||
} else if (is.disk(x)) {
|
||||
if (expand == TRUE) {
|
||||
# expand range for disks from lowest to highest so all mm's in between also print
|
||||
extra_range <- rep(0, max(x) - min(x) - 1)
|
||||
names(extra_range) <- seq(min(x) + 1, max(x) - 1)
|
||||
x <- table(x)
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x)]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(x)
|
||||
}
|
||||
x <- x[order(as.double(names(x)))]
|
||||
}
|
||||
as.table(x)
|
||||
}
|
||||
|
||||
plot_name_of_I <- function(guideline) {
|
||||
if (!guideline %like% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
|
||||
# interpretation since 2019
|
||||
"Incr. exposure"
|
||||
} else {
|
||||
# interpretation until 2019
|
||||
"Intermediate"
|
||||
}
|
||||
}
|
||||
|
||||
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, fn, language, ...) {
|
||||
guideline <- get_guideline(guideline, AMR::rsi_translation)
|
||||
if (!is.null(mo) && !is.null(ab)) {
|
||||
# interpret and give colour based on MIC values
|
||||
mo <- as.mo(mo)
|
||||
ab <- as.ab(ab)
|
||||
rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...)))
|
||||
cols <- character(length = length(rsi))
|
||||
cols[is.na(rsi)] <- "#BEBEBE"
|
||||
cols[rsi == "R"] <- colours_RSI[1]
|
||||
cols[rsi == "S"] <- colours_RSI[2]
|
||||
cols[rsi == "I"] <- colours_RSI[3]
|
||||
moname <- mo_name(mo, language = language)
|
||||
abname <- ab_name(ab, language = language)
|
||||
if (all(cols == "#BEBEBE")) {
|
||||
message_("No ", guideline, " interpretations found for ",
|
||||
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
|
||||
guideline_txt <- ""
|
||||
} else {
|
||||
guideline_txt <- paste0("(", guideline, ")")
|
||||
}
|
||||
sub <- bquote(.(abname)~"in"~italic(.(moname))~.(guideline_txt))
|
||||
} else {
|
||||
cols <- "#BEBEBE"
|
||||
sub <- NULL
|
||||
}
|
||||
list(cols = cols, count = as.double(x), sub = sub, guideline = guideline)
|
||||
}
|
||||
|
||||
#' @method plot rsi
|
||||
#' @export
|
||||
#' @importFrom graphics plot text axis
|
||||
@ -599,6 +576,14 @@ barplot.rsi <- function(height,
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(expand, allow_class = "logical", has_length = 1)
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if (length(colours_RSI) == 1) {
|
||||
colours_RSI <- rep(colours_RSI, 3)
|
||||
}
|
||||
@ -624,6 +609,7 @@ ggplot.rsi <- function(data,
|
||||
xlab = "Antimicrobial Interpretation",
|
||||
ylab = "Frequency",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
...) {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
|
||||
@ -631,6 +617,14 @@ ggplot.rsi <- function(data,
|
||||
meet_criteria(xlab, allow_class = "character", has_length = 1)
|
||||
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
|
||||
|
||||
# translate if not specifically set
|
||||
if (missing(ylab)) {
|
||||
ylab <- translate_AMR(ylab, language = language)
|
||||
}
|
||||
if (missing(xlab)) {
|
||||
xlab <- translate_AMR(xlab, language = language)
|
||||
}
|
||||
|
||||
if ("main" %in% names(list(...))) {
|
||||
title <- list(...)$main
|
||||
}
|
||||
@ -658,3 +652,76 @@ ggplot.rsi <- function(data,
|
||||
ggplot2::labs(title = title, x = xlab, y = ylab) +
|
||||
ggplot2::theme(legend.position = "none")
|
||||
}
|
||||
|
||||
plot_prepare_table <- function(x, expand) {
|
||||
if (is.mic(x)) {
|
||||
if (expand == TRUE) {
|
||||
# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
|
||||
extra_range <- max(x) / 2
|
||||
while (min(extra_range) / 2 > min(x)) {
|
||||
extra_range <- c(min(extra_range) / 2, extra_range)
|
||||
}
|
||||
nms <- extra_range
|
||||
extra_range <- rep(0, length(extra_range))
|
||||
names(extra_range) <- nms
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x)]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(droplevels(x, as.mic = FALSE))
|
||||
}
|
||||
x <- x[order(as.double(as.mic(names(x))))]
|
||||
} else if (is.disk(x)) {
|
||||
if (expand == TRUE) {
|
||||
# expand range for disks from lowest to highest so all mm's in between also print
|
||||
extra_range <- rep(0, max(x) - min(x) - 1)
|
||||
names(extra_range) <- seq(min(x) + 1, max(x) - 1)
|
||||
x <- table(x)
|
||||
extra_range <- extra_range[!names(extra_range) %in% names(x)]
|
||||
x <- as.table(c(x, extra_range))
|
||||
} else {
|
||||
x <- table(x)
|
||||
}
|
||||
x <- x[order(as.double(names(x)))]
|
||||
}
|
||||
as.table(x)
|
||||
}
|
||||
|
||||
plot_name_of_I <- function(guideline) {
|
||||
if (!guideline %like% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
|
||||
# interpretation since 2019
|
||||
"Incr. exposure"
|
||||
} else {
|
||||
# interpretation until 2019
|
||||
"Intermediate"
|
||||
}
|
||||
}
|
||||
|
||||
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, fn, language, ...) {
|
||||
guideline <- get_guideline(guideline, AMR::rsi_translation)
|
||||
if (!is.null(mo) && !is.null(ab)) {
|
||||
# interpret and give colour based on MIC values
|
||||
mo <- as.mo(mo)
|
||||
ab <- as.ab(ab)
|
||||
rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...)))
|
||||
cols <- character(length = length(rsi))
|
||||
cols[is.na(rsi)] <- "#BEBEBE"
|
||||
cols[rsi == "R"] <- colours_RSI[1]
|
||||
cols[rsi == "S"] <- colours_RSI[2]
|
||||
cols[rsi == "I"] <- colours_RSI[3]
|
||||
moname <- mo_name(mo, language = language)
|
||||
abname <- ab_name(ab, language = language)
|
||||
if (all(cols == "#BEBEBE")) {
|
||||
message_("No ", guideline, " interpretations found for ",
|
||||
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
|
||||
guideline_txt <- ""
|
||||
} else {
|
||||
guideline_txt <- paste0("(", guideline, ")")
|
||||
}
|
||||
sub <- bquote(.(abname)~"-"~italic(.(moname))~.(guideline_txt))
|
||||
} else {
|
||||
cols <- "#BEBEBE"
|
||||
sub <- NULL
|
||||
}
|
||||
list(cols = cols, count = as.double(x), sub = sub, guideline = guideline)
|
||||
}
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@ -157,11 +157,13 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
|
||||
df_trans$regular_expr[is.na(df_trans$regular_expr)] <- FALSE
|
||||
|
||||
# check if text to look for is in one of the patterns
|
||||
any_form_in_patterns <- tryCatch(any(from_unique %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
|
||||
any_form_in_patterns <- tryCatch(
|
||||
any(from_unique %like% paste0("(", paste(gsub(" +\\(.*", "", df_trans$pattern), collapse = "|"), ")")),
|
||||
error = function(e) {
|
||||
warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call = FALSE)
|
||||
return(FALSE)
|
||||
})
|
||||
|
||||
if (NROW(df_trans) == 0 | !any_form_in_patterns) {
|
||||
return(from)
|
||||
}
|
||||
@ -170,7 +172,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
|
||||
function(i) from_unique_translated <<- gsub(pattern = df_trans$pattern[i],
|
||||
replacement = df_trans[i, language, drop = TRUE],
|
||||
x = from_unique_translated,
|
||||
ignore.case = !df_trans$case_sensitive[i],
|
||||
ignore.case = !df_trans$case_sensitive[i] & df_trans$regular_expr[i],
|
||||
fixed = !df_trans$regular_expr[i],
|
||||
perl = df_trans$regular_expr[i]))
|
||||
|
||||
|
||||
@ -143,6 +143,7 @@ reference:
|
||||
- "`as.mic`"
|
||||
- "`as.disk`"
|
||||
- "`eucast_rules`"
|
||||
- "`custom_eucast_rules`"
|
||||
|
||||
- title: "Analysing data: antimicrobial resistance"
|
||||
desc: >
|
||||
|
||||
Binary file not shown.
@ -134,7 +134,7 @@ create_intr_resistance <- function() {
|
||||
|
||||
|
||||
|
||||
# Save internal data sets to R/sysdata.rda --------------------------------
|
||||
# Save internal data to R/sysdata.rda -------------------------------------
|
||||
|
||||
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
|
||||
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
@ -188,6 +188,35 @@ AB_lookup <- create_AB_lookup()
|
||||
MO_lookup <- create_MO_lookup()
|
||||
MO.old_lookup <- create_MO.old_lookup()
|
||||
|
||||
# antibiotic groups
|
||||
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
|
||||
globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab")
|
||||
AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab)
|
||||
AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
|
||||
CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab)
|
||||
CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab)
|
||||
CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
|
||||
CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
|
||||
CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
|
||||
CEPHALOSPORINS_EXCEPT_CAZ <- CEPHALOSPORINS[CEPHALOSPORINS != "CAZ"]
|
||||
FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone") %>% pull(ab)
|
||||
LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
|
||||
GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab)
|
||||
GLYCOPEPTIDES_EXCEPT_LIPO <- GLYCOPEPTIDES[!GLYCOPEPTIDES %in% LIPOGLYCOPEPTIDES]
|
||||
LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide") %>% pull(ab) %>% c("PRL")
|
||||
MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide") %>% pull(ab)
|
||||
OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
|
||||
PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
|
||||
POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
|
||||
STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
|
||||
TETRACYCLINES <- antibiotics %>% filter(atc_group2 %like% "tetracycline") %>% pull(ab)
|
||||
TETRACYCLINES_EXCEPT_TGC <- TETRACYCLINES[TETRACYCLINES != "TGC"]
|
||||
UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
|
||||
BETALACTAMS <- c(PENICILLINS, CEPHALOSPORINS, CARBAPENEMS)
|
||||
|
||||
DEFINED_AB_GROUPS <- ls(envir = globalenv())
|
||||
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
|
||||
|
||||
# Export to package as internal data ----
|
||||
usethis::use_data(eucast_rules_file,
|
||||
translations_file,
|
||||
@ -199,6 +228,29 @@ usethis::use_data(eucast_rules_file,
|
||||
AB_lookup,
|
||||
MO_lookup,
|
||||
MO.old_lookup,
|
||||
AMINOGLYCOSIDES,
|
||||
AMINOPENICILLINS,
|
||||
CARBAPENEMS,
|
||||
CEPHALOSPORINS,
|
||||
CEPHALOSPORINS_1ST,
|
||||
CEPHALOSPORINS_2ND,
|
||||
CEPHALOSPORINS_3RD,
|
||||
CEPHALOSPORINS_EXCEPT_CAZ,
|
||||
FLUOROQUINOLONES,
|
||||
LIPOGLYCOPEPTIDES,
|
||||
GLYCOPEPTIDES,
|
||||
GLYCOPEPTIDES_EXCEPT_LIPO,
|
||||
LINCOSAMIDES,
|
||||
MACROLIDES,
|
||||
OXAZOLIDINONES,
|
||||
PENICILLINS,
|
||||
POLYMYXINS,
|
||||
STREPTOGRAMINS,
|
||||
TETRACYCLINES,
|
||||
TETRACYCLINES_EXCEPT_TGC,
|
||||
UREIDOPENICILLINS,
|
||||
BETALACTAMS,
|
||||
DEFINED_AB_GROUPS,
|
||||
internal = TRUE,
|
||||
overwrite = TRUE,
|
||||
version = 2,
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
# -------------------------------------------------------------------------------------------------------------------------------
|
||||
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
|
||||
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_3rd', 'cephalosporins_except_CAZ',
|
||||
# 'fluoroquinolones', 'glycopeptides', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins',
|
||||
# 'betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_3rd', 'cephalosporins_except_CAZ',
|
||||
# 'fluoroquinolones', 'glycopeptides', 'glycopeptides_except_lipo', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'tetracyclines_except_TGC', 'ureidopenicillins',
|
||||
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
|
||||
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
|
||||
# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
|
||||
@ -14,7 +14,7 @@ order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 10
|
||||
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 10
|
||||
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 10
|
||||
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 10
|
||||
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 10
|
||||
@ -120,7 +120,7 @@ order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 11
|
||||
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 11
|
||||
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 11
|
||||
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 11
|
||||
@ -224,7 +224,7 @@ genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei
|
||||
genus is Bacillus NOR S fluoroquinolones S Bacillus Breakpoints 11 added in 11
|
||||
genus is Bacillus NOR I fluoroquinolones I Bacillus Breakpoints 11 added in 11
|
||||
genus is Bacillus NOR R fluoroquinolones R Bacillus Breakpoints 11 added in 11
|
||||
order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
@ -232,17 +232,17 @@ genus_species is Klebsiella aerogenes aminopenicillins, AMC, CZO, FOX R Table
|
||||
genus_species is Escherichia hermannii aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Morganella morganii aminopenicillins, AMC, CZO, DOX, MNO, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus penneri aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
@ -251,9 +251,9 @@ genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, E
|
||||
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, DOX, MNO, TCY, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
|
||||
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides_except_lipo, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
|
||||
@ -279,8 +279,8 @@ genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CA
|
||||
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus one_of Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus one_of Leuconostoc, Pediococcus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus is Lactobacillus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
|
||||
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
|
||||
@ -298,7 +298,7 @@ genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules fo
|
||||
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
|
||||
order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
|
||||
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
|
||||
order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
@ -308,13 +308,13 @@ genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LE
|
||||
genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
@ -324,20 +324,20 @@ genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R Table 1:
|
||||
genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
|
||||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
|
||||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
|
||||
fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, tetracyclines, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus_species is Moraxella catarrhalis TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus is Neisseria TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
|
||||
gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
|
||||
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
|
||||
genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
|
||||
@ -372,8 +372,8 @@ fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules o
|
||||
genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.2
|
||||
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2
|
||||
genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 R all_betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 S all_betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.2 all penicillins without beta-lactamse inhibitor
|
||||
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
@ -400,7 +400,7 @@ genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Strep
|
||||
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
|
||||
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
|
||||
fullname like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae PEN S all_betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
|
||||
|
Can't render this file because it contains an unexpected character in line 6 and column 96.
|
@ -160,7 +160,7 @@ updated_microorganisms <- taxonomy %>%
|
||||
TRUE ~ "subsp."),
|
||||
ref = get_author_year(authors),
|
||||
species_id = as.character(record_no),
|
||||
source = "LSPN",
|
||||
source = "LPSN",
|
||||
prevalence = 0,
|
||||
snomed = NA)
|
||||
|
||||
|
||||
@ -39,6 +39,10 @@ antibiotic TRUE TRUE FALSE Antibiotikum antibioticum antibiótico
|
||||
Antibiotic TRUE TRUE FALSE Antibiotikum Antibioticum Antibiótico
|
||||
Drug TRUE TRUE FALSE Medikament Middel Fármaco
|
||||
drug TRUE TRUE FALSE Medikament middel fármaco
|
||||
Frequency FALSE TRUE FALSE Zahl Aantal
|
||||
Minimum Inhibitory Concentration (mg/L) FALSE FALSE FALSE Minimale Hemm-Konzentration (mg/L) Minimale inhiberende concentratie (mg/L)
|
||||
Disk diffusion diameter (mm) FALSE FALSE FALSE Durchmesser der Scheibenzone (mm) Diameter diskzone (mm)
|
||||
Antimicrobial Interpretation FALSE FALSE FALSE Antimikrobielle Auswertung Antimicrobiële interpretatie
|
||||
4-aminosalicylic acid FALSE TRUE FALSE 4-Aminosalicylsäure 4-aminosalicylzuur Ácido 4-aminosalicílico
|
||||
Adefovir dipivoxil FALSE TRUE FALSE Adefovir Dipivoxil Adefovir Adefovir dipivoxil
|
||||
Aldesulfone sodium FALSE TRUE FALSE Aldesulfon-Natrium Aldesulfon Aldesulfona sódica
|
||||
|
||||
|
Binary file not shown.
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,11 +19,10 @@
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
|
||||
<script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet">
|
||||
<script src="extra.js"></script><meta property="og:title" content="Antimicrobial Resistance Data Analysis">
|
||||
<meta property="og:description" content="Functions to simplify the analysis and prediction of Antimicrobial
|
||||
Resistance (AMR) and to work with microbial and antimicrobial properties by
|
||||
using evidence-based methods, like those defined by Leclercq et al. (2013)
|
||||
<doi:10.1111/j.1469-0691.2011.03703.x> and containing reference data such as
|
||||
LPSN <doi:10.1099/ijsem.0.004332>.">
|
||||
<meta property="og:description" content="Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
using evidence-based methods and reliable reference data such as LPSN
|
||||
<doi:10.1099/ijsem.0.004332>.">
|
||||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
|
||||
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
@ -43,7 +42,7 @@
|
||||
</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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -197,7 +196,7 @@
|
||||
<div class="page-header"><h1 class="hasAnchor">
|
||||
<a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
|
||||
</h1></div>
|
||||
<p><em>Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ are now implemented</em></p>
|
||||
<p><em>Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ are now implemented.</em></p>
|
||||
<blockquote>
|
||||
<p><span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> <strong>PLEASE TAKE PART IN OUR SURVEY!</strong><br>
|
||||
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <a href="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance! <br><a class="btn btn-info btn-amr" href="./survey.html">Take me to the 5-min survey!</a></p>
|
||||
|
||||
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -236,14 +236,32 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-160" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.6.0">
|
||||
<a href="#amr-160" class="anchor"></a>AMR 1.6.0<small> Unreleased </small>
|
||||
<div id="amr-1609000" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.6.0.9000">
|
||||
<a href="#amr-1609000" class="anchor"></a>AMR 1.6.0.9000<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-7-april-2021" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-7-april-2021" class="anchor"></a><small>Last updated: 7 April 2021</small>
|
||||
</h2>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-160" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.6.0">
|
||||
<a href="#amr-160" class="anchor"></a>AMR 1.6.0<small> 2021-03-14 </small>
|
||||
</h1>
|
||||
<div id="new-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-1" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function and in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC and disk diffusion values. This is now the default guideline in this package.</p>
|
||||
<ul>
|
||||
@ -316,11 +334,11 @@
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed" class="section level3">
|
||||
<div id="changed-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-1" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LSPN</a>)
|
||||
<li>Updated the bacterial taxonomy to 3 March 2021 (using <a href="https://lpsn.dsmz.de">LPSN</a>)
|
||||
<ul>
|
||||
<li>Added 3,372 new species and 1,523 existing species became synomyms</li>
|
||||
<li>The URL of a bacterial species (<code><a href="../reference/mo_property.html">mo_url()</a></code>) will now lead to <a href="https://lpsn.dsmz.de" class="uri">https://lpsn.dsmz.de</a>
|
||||
@ -378,9 +396,9 @@
|
||||
<h1 class="page-header" data-toc-text="1.5.0">
|
||||
<a href="#amr-150" class="anchor"></a>AMR 1.5.0<small> 2021-01-06 </small>
|
||||
</h1>
|
||||
<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>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
|
||||
@ -396,9 +414,9 @@
|
||||
<li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take microorganism names and antibiotic names as input to make generation more realistic.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-1" class="section level3">
|
||||
<div id="changed-2" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-1" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-2" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li><p>New argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to correct for AmpC de-repressed cephalosporin-resistant mutants</p></li>
|
||||
<li>
|
||||
@ -492,9 +510,9 @@
|
||||
<h1 class="page-header" data-toc-text="1.4.0">
|
||||
<a href="#amr-140" class="anchor"></a>AMR 1.4.0<small> 2020-10-08 </small>
|
||||
</h1>
|
||||
<div id="new-2" class="section level3">
|
||||
<div id="new-3" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-2" class="anchor"></a>New</h3>
|
||||
<a href="#new-3" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li><p>Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can now correct for more than 180 different antibiotics and the <code><a href="../reference/mdro.html">mdro()</a></code> function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function consequently gained the arguments <code>version_breakpoints</code> (at the moment defaults to v10.0, 2020) and <code>version_expertrules</code> (at the moment defaults to v3.2, 2020). The <code>example_isolates</code> data set now also reflects the change from v3.1 to v3.2. The <code><a href="../reference/mdro.html">mdro()</a></code> function now accepts <code>guideline == "EUCAST3.1"</code> and <code>guideline == "EUCAST3.2"</code>.</p></li>
|
||||
<li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
|
||||
@ -514,9 +532,9 @@
|
||||
<li><p>Support for skimming classes <code><rsi></code>, <code><mic></code>, <code><disk></code> and <code><mo></code> with the <code>skimr</code> package</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-2" class="section level3">
|
||||
<div id="changed-3" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-2" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-3" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li><p>Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.</p></li>
|
||||
<li>
|
||||
@ -596,9 +614,9 @@
|
||||
<h1 class="page-header" data-toc-text="1.3.0">
|
||||
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> 2020-07-31 </small>
|
||||
</h1>
|
||||
<div id="new-3" class="section level3">
|
||||
<div id="new-4" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-3" class="anchor"></a>New</h3>
|
||||
<a href="#new-4" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
|
||||
<li>
|
||||
@ -620,9 +638,9 @@
|
||||
<li><p>Added argument <code>conserve_capped_values</code> to <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “<” (but not “<=”) will always return “S” and values starting with “>” (but not “>=”) will always return “R”. The default behaviour of <code><a href="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><a href="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-3" class="section level3">
|
||||
<div id="changed-4" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-3" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-4" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><a href="../reference/as.mo.html">as.mo()</a></code>, <code><a href="../reference/mo_property.html">mo_name()</a></code>, <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, etc.</p>
|
||||
@ -696,9 +714,9 @@
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-4" class="section level3">
|
||||
<div id="changed-5" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-4" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-5" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Taxonomy:
|
||||
<ul>
|
||||
@ -743,17 +761,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="1.1.0">
|
||||
<a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> 2020-04-15 </small>
|
||||
</h1>
|
||||
<div id="new-4" class="section level3">
|
||||
<div id="new-5" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-4" class="anchor"></a>New</h3>
|
||||
<a href="#new-5" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>Support for easy principal component analysis for AMR, using the new <code><a href="../reference/pca.html">pca()</a></code> function</li>
|
||||
<li>Plotting biplots for principal component analysis using the new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-5" class="section level3">
|
||||
<div id="changed-6" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-5" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-6" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Improvements for the algorithm used by <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):
|
||||
<ul>
|
||||
@ -785,9 +803,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="1.0.1">
|
||||
<a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small>
|
||||
</h1>
|
||||
<div id="changed-6" class="section level3">
|
||||
<div id="changed-7" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-6" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-7" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
|
||||
<li>
|
||||
@ -811,9 +829,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small>
|
||||
</h1>
|
||||
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
|
||||
<div id="new-5" class="section level3">
|
||||
<div id="new-6" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-5" class="anchor"></a>New</h3>
|
||||
<a href="#new-6" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>Support for the newest <a href="https://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
|
||||
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <a href="https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
|
||||
@ -909,9 +927,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="new-6" class="section level3">
|
||||
<div id="new-7" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-6" class="anchor"></a>New</h3>
|
||||
<a href="#new-7" 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>
|
||||
@ -1029,9 +1047,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="new-7" class="section level3">
|
||||
<div id="new-8" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new-7" class="anchor"></a>New</h3>
|
||||
<a href="#new-8" 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>
|
||||
@ -1096,9 +1114,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-7" class="section level3">
|
||||
<div id="changed-8" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#changed-7" class="anchor"></a>Changed</h3>
|
||||
<a href="#changed-8" class="anchor"></a>Changed</h3>
|
||||
<ul>
|
||||
<li>Many algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
|
||||
<ul>
|
||||
@ -1163,9 +1181,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="0.7.1">
|
||||
<a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
|
||||
</h1>
|
||||
<div id="new-8" class="section level4">
|
||||
<div id="new-9" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-8" class="anchor"></a>New</h4>
|
||||
<a href="#new-9" 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>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
|
||||
@ -1209,9 +1227,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<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>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-8" class="section level4">
|
||||
<div id="changed-9" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-8" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-9" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> are now lowercase</li>
|
||||
<li>Fixed bug in translation of microorganism names</li>
|
||||
@ -1248,9 +1266,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="0.7.0">
|
||||
<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
|
||||
</h1>
|
||||
<div id="new-9" class="section level4">
|
||||
<div id="new-10" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-9" class="anchor"></a>New</h4>
|
||||
<a href="#new-10" 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>
|
||||
@ -1258,9 +1276,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-9" class="section level4">
|
||||
<div id="changed-10" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-9" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-10" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
|
||||
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
|
||||
@ -1345,9 +1363,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="0.6.1">
|
||||
<a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small>
|
||||
</h1>
|
||||
<div id="changed-10" class="section level4">
|
||||
<div id="changed-11" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-10" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-11" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed a critical bug when using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> with <code>verbose = TRUE</code>
|
||||
</li>
|
||||
@ -1365,9 +1383,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Contains the complete manual of this package and all of its functions with an explanation of their arguments</li>
|
||||
<li>Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more.</li>
|
||||
</ul>
|
||||
<div id="new-10" class="section level4">
|
||||
<div id="new-11" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-10" class="anchor"></a>New</h4>
|
||||
<a href="#new-11" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li><p><strong>BREAKING</strong>: removed deprecated functions, arguments and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</p></li>
|
||||
<li>
|
||||
@ -1465,9 +1483,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-11" class="section level4">
|
||||
<div id="changed-12" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-11" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-12" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
|
||||
<ul>
|
||||
@ -1611,9 +1629,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="0.5.0">
|
||||
<a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
|
||||
</h1>
|
||||
<div id="new-11" class="section level4">
|
||||
<div id="new-12" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-11" class="anchor"></a>New</h4>
|
||||
<a href="#new-12" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Repository moved to GitLab</li>
|
||||
<li>Function <code>count_all</code> to get all available isolates (that like all <code>portion_*</code> and <code>count_*</code> functions also supports <code>summarise</code> and <code>group_by</code>), the old <code>n_rsi</code> is now an alias of <code>count_all</code>
|
||||
@ -1624,9 +1642,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Functions <code>mo_authors</code> and <code>mo_year</code> to get specific values about the scientific reference of a taxonomic entry</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-12" class="section level4">
|
||||
<div id="changed-13" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-12" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-13" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
|
||||
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
|
||||
@ -1735,9 +1753,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="0.4.0">
|
||||
<a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
|
||||
</h1>
|
||||
<div id="new-12" class="section level4">
|
||||
<div id="new-13" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-12" class="anchor"></a>New</h4>
|
||||
<a href="#new-13" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li><p>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</p></li>
|
||||
<li>
|
||||
@ -1815,9 +1833,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Renamed <code>septic_patients$sex</code> to <code>septic_patients$gender</code></p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-13" class="section level4">
|
||||
<div id="changed-14" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-13" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-14" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
|
||||
<li>
|
||||
@ -1884,9 +1902,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="0.3.0">
|
||||
<a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
|
||||
</h1>
|
||||
<div id="new-13" class="section level4">
|
||||
<div id="new-14" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-13" class="anchor"></a>New</h4>
|
||||
<a href="#new-14" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
|
||||
@ -1957,9 +1975,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-14" class="section level4">
|
||||
<div id="changed-15" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-14" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-15" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Improvements for forecasting with <code>resistance_predict</code> and added more examples</li>
|
||||
<li>More antibiotics added as arguments for EUCAST rules</li>
|
||||
@ -2021,9 +2039,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<h1 class="page-header" data-toc-text="0.2.0">
|
||||
<a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
|
||||
</h1>
|
||||
<div id="new-14" class="section level4">
|
||||
<div id="new-15" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-14" class="anchor"></a>New</h4>
|
||||
<a href="#new-15" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Full support for Windows, Linux and macOS</li>
|
||||
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
|
||||
@ -2043,9 +2061,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed-15" class="section level4">
|
||||
<div id="changed-16" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed-15" class="anchor"></a>Changed</h4>
|
||||
<a href="#changed-16" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Fixed <code>rsi</code> class for vectors that contain only invalid antimicrobial interpretations</li>
|
||||
<li>Renamed dataset <code>ablist</code> to <code>antibiotics</code>
|
||||
|
||||
@ -12,7 +12,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2021-03-14T08:55Z
|
||||
last_built: 2021-04-07T06:37Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
||||
@ -83,7 +83,7 @@
|
||||
</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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
312
docs/reference/custom_eucast_rules.html
Normal file
312
docs/reference/custom_eucast_rules.html
Normal file
@ -0,0 +1,312 @@
|
||||
<!-- Generated by pkgdown: do not edit by hand -->
|
||||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
|
||||
<meta charset="utf-8">
|
||||
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|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Create Custom EUCAST Rules — custom_eucast_rules • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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|
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|
||||
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<!-- bootstrap-toc -->
|
||||
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||||
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|
||||
|
||||
<!-- Font Awesome icons -->
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|
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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<div class="row">
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<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Create Custom EUCAST Rules</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
|
||||
<div class="hidden name"><code>custom_eucast_rules.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>Create Custom EUCAST Rules</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>rules in formula notation, see <em>Examples</em></p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>This documentation page will be updated shortly. <strong>This function is experimental.</strong></p>
|
||||
<h2 class="hasAnchor" id="how-it-works"><a class="anchor" href="#how-it-works"></a>How it works</h2>
|
||||
|
||||
|
||||
|
||||
<p>..</p>
|
||||
<p>It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): <code>aminoglycosides</code>, <code>aminopenicillins</code>, <code>betalactams</code>, <code>carbapenems</code>, <code>cephalosporins</code>, <code>cephalosporins_1st</code>, <code>cephalosporins_2nd</code>, <code>cephalosporins_3rd</code>, <code>cephalosporins_except_caz</code>, <code>fluoroquinolones</code>, <code>glycopeptides</code>, <code>glycopeptides_except_lipo</code>, <code>lincosamides</code>, <code>lipoglycopeptides</code>, <code>macrolides</code>, <code>oxazolidinones</code>, <code>penicillins</code>, <code>polymyxins</code>, <code>streptogramins</code>, <code>tetracyclines</code>, <code>tetracyclines_except_tgc</code> and <code>ureidopenicillins</code>.</p>
|
||||
<h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental Lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='va'>x</span> <span class='op'><-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
|
||||
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>example_isolates</span>,
|
||||
rules <span class='op'>=</span> <span class='st'>"custom"</span>,
|
||||
custom_rules <span class='op'>=</span> <span class='va'>x</span>,
|
||||
info <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># combine rule sets</span>
|
||||
<span class='va'>x2</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'>x</span>,
|
||||
<span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>carbapenems</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='va'>x2</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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|
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<h2 data-toc-skip>Contents</h2>
|
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|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
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|
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|
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|
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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|
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</body>
|
||||
</html>
|
||||
|
||||
|
||||
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -254,6 +254,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
|
||||
ampc_cephalosporin_resistance <span class='op'>=</span> <span class='cn'>NA</span>,
|
||||
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
||||
custom_rules <span class='op'>=</span> <span class='cn'>NULL</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span>
|
||||
|
||||
@ -276,7 +277,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</tr>
|
||||
<tr>
|
||||
<th>rules</th>
|
||||
<td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value, e.g. using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>.</p></td>
|
||||
<td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value, e.g. using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>verbose</th>
|
||||
@ -298,6 +299,10 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
<th>only_rsi_columns</th>
|
||||
<td><p>a logical to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>custom_rules</th>
|
||||
<td><p>custom rules to apply, created with <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></td>
|
||||
@ -332,7 +337,17 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
|
||||
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
|
||||
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
|
||||
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' Rules</h3>
|
||||
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Custom Rules</h3>
|
||||
|
||||
|
||||
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre><span class='va'>x</span> <span class='op'><-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
|
||||
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>example_isolates</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>x</span><span class='op'>)</span>
|
||||
</pre>
|
||||
|
||||
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' Rules</h3>
|
||||
|
||||
|
||||
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
|
||||
|
||||
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -450,6 +450,12 @@
|
||||
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_dosage()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Apply EUCAST Rules</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Create Custom EUCAST Rules</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
@ -595,7 +601,7 @@
|
||||
<td>
|
||||
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> <code><a href="like.html">`%like_case%`</a></code> </p>
|
||||
</td>
|
||||
<td><p>Pattern Matching with Keyboard Shortcut</p></td>
|
||||
<td><p>Vectorised Pattern Matching with Keyboard Shortcut</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Pattern Matching with Keyboard Shortcut — like • AMR (for R)</title>
|
||||
<title>Vectorised Pattern Matching with Keyboard Shortcut — like • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
@ -48,7 +48,7 @@
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="Pattern Matching with Keyboard Shortcut — like" />
|
||||
<meta property="og:title" content="Vectorised Pattern Matching with Keyboard Shortcut — like" />
|
||||
<meta property="og:description" content="Convenient wrapper around grepl() to match a pattern: x %like% pattern. It always returns a logical vector and is always case-insensitive (use x %like_case% pattern for case-sensitive matching). Also, pattern can be as long as x to compare items of each index in both vectors, or they both can have the same length to iterate over all cases." />
|
||||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
|
||||
|
||||
@ -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">1.5.0.9027</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -233,7 +233,7 @@
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Pattern Matching with Keyboard Shortcut</h1>
|
||||
<h1>Vectorised Pattern Matching with Keyboard Shortcut</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/like.R'><code>R/like.R</code></a></small>
|
||||
<div class="hidden name"><code>like.Rd</code></div>
|
||||
</div>
|
||||
@ -267,17 +267,17 @@
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/master/R/like.R'><code>like</code> function from the <code>data.table</code> package</a></p>
|
||||
<p>Idea from the <a href='https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R'><code>like</code> function from the <code>data.table</code> package</a></p>
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector</p>
|
||||
<p>A <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector</p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>The <code>%like%</code> function:</p><ul>
|
||||
<li><p>Is case-insensitive (use <code>%like_case%</code> for case-sensitive matching)</p></li>
|
||||
<li><p>Supports multiple patterns</p></li>
|
||||
<li><p>Checks if <code>pattern</code> is a regular expression and sets <code>fixed = TRUE</code> if not, to greatly improve speed</p></li>
|
||||
<li><p>Always uses compatibility with Perl</p></li>
|
||||
<li><p>Always uses compatibility with Perl unless <code>fixed = TRUE</code>, to greatly improve speed</p></li>
|
||||
</ul>
|
||||
|
||||
<p>Using RStudio? The text <code>%like%</code> can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like <code>Ctrl+Shift+L</code> or <code>Cmd+Shift+L</code> (see <code>Tools</code> > <code>Modify Keyboard Shortcuts...</code>).</p>
|
||||
@ -320,7 +320,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</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='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</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='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%like%</span> <span class='st'>"^ent"</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
|
||||
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -374,10 +374,19 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
|
||||
<span class='co'>#> Unmatched rows will return NA.</span>
|
||||
</pre>
|
||||
|
||||
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p><pre><span class='va'>x</span> <span class='op'><-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>, guideline <span class='op'>=</span> <span class='va'>custom</span><span class='op'>)</span>
|
||||
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p><pre><span class='va'>x</span> <span class='op'><-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
|
||||
guideline <span class='op'>=</span> <span class='va'>custom</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
<span class='co'>#> Elderly Type A Elderly Type B Negative </span>
|
||||
<span class='co'>#> 43 891 1066 </span>
|
||||
<span class='co'>#> Negative Elderly Type A Elderly Type B</span>
|
||||
<span class='co'>#> 1070 198 732</span>
|
||||
</pre>
|
||||
|
||||
<p>Rules can also be combined with other custom rules by using <code><a href='https://rdrr.io/r/base/c.html'>c()</a></code>:</p><pre><span class='va'>x</span> <span class='op'><-</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='va'>example_isolates</span>,
|
||||
guideline <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'>custom</span>,
|
||||
<span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>ERY</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&</span> <span class='va'>age</span> <span class='op'>></span> <span class='fl'>50</span> <span class='op'>~</span> <span class='st'>"Elderly Type C"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
<span class='co'>#> Negative Elderly Type A Elderly Type B Elderly Type C </span>
|
||||
<span class='co'>#> 961 198 732 109</span>
|
||||
</pre>
|
||||
|
||||
<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href='https://rdrr.io/r/base/readRDS.html'>saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>.</p>
|
||||
|
||||
@ -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">1.5.0.9031</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -321,6 +321,7 @@
|
||||
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
|
||||
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
|
||||
colours_RSI <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'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
|
||||
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
|
||||
<span class='va'>...</span>
|
||||
<span class='op'>)</span></pre>
|
||||
|
||||
@ -407,7 +408,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_mic_values</span>, mo <span class='op'>=</span> <span class='st'>"S. aureus"</span>, ab <span class='op'>=</span> <span class='st'>"ampicillin"</span><span class='op'>)</span>
|
||||
<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_disk_values</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
|
||||
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_disk_values</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
|
||||
|
||||
@ -66,6 +66,9 @@
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/count.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/custom_eucast_rules.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/dosage.html</loc>
|
||||
</url>
|
||||
|
||||
@ -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">1.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
2
index.md
2
index.md
@ -1,6 +1,6 @@
|
||||
# `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
|
||||
|
||||
*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' are now implemented*
|
||||
*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' are now implemented.*
|
||||
|
||||
> <span class="fa fa-clipboard-list" style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span> **PLEASE TAKE PART IN OUR SURVEY!**
|
||||
> Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. **If you have a minute, please [anonymously fill in this short questionnaire](./survey.html)**. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!
|
||||
|
||||
43
man/custom_eucast_rules.Rd
Normal file
43
man/custom_eucast_rules.Rd
Normal file
@ -0,0 +1,43 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/custom_eucast_rules.R
|
||||
\name{custom_eucast_rules}
|
||||
\alias{custom_eucast_rules}
|
||||
\title{Create Custom EUCAST Rules}
|
||||
\usage{
|
||||
custom_eucast_rules(...)
|
||||
}
|
||||
\arguments{
|
||||
\item{...}{rules in formula notation, see \emph{Examples}}
|
||||
}
|
||||
\description{
|
||||
Create Custom EUCAST Rules
|
||||
}
|
||||
\details{
|
||||
This documentation page will be updated shortly. \strong{This function is experimental.}
|
||||
}
|
||||
\section{How it works}{
|
||||
|
||||
..
|
||||
|
||||
It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): \code{aminoglycosides}, \code{aminopenicillins}, \code{betalactams}, \code{carbapenems}, \code{cephalosporins}, \code{cephalosporins_1st}, \code{cephalosporins_2nd}, \code{cephalosporins_3rd}, \code{cephalosporins_except_caz}, \code{fluoroquinolones}, \code{glycopeptides}, \code{glycopeptides_except_lipo}, \code{lincosamides}, \code{lipoglycopeptides}, \code{macrolides}, \code{oxazolidinones}, \code{penicillins}, \code{polymyxins}, \code{streptogramins}, \code{tetracyclines}, \code{tetracyclines_except_tgc} and \code{ureidopenicillins}.
|
||||
}
|
||||
|
||||
\section{Experimental Lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
|
||||
}
|
||||
|
||||
\examples{
|
||||
x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
|
||||
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
|
||||
eucast_rules(example_isolates,
|
||||
rules = "custom",
|
||||
custom_rules = x,
|
||||
info = FALSE)
|
||||
|
||||
# combine rule sets
|
||||
x2 <- c(x,
|
||||
custom_eucast_rules(TZP == "R" ~ carbapenems == "R"))
|
||||
x2
|
||||
}
|
||||
@ -27,6 +27,7 @@ eucast_rules(
|
||||
version_expertrules = 3.2,
|
||||
ampc_cephalosporin_resistance = NA,
|
||||
only_rsi_columns = FALSE,
|
||||
custom_rules = NULL,
|
||||
...
|
||||
)
|
||||
|
||||
@ -39,7 +40,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
|
||||
|
||||
\item{info}{a logical to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions}
|
||||
|
||||
\item{rules}{a character vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value, e.g. using \code{options(AMR_eucastrules = "all")}.}
|
||||
\item{rules}{a character vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value, e.g. using \code{options(AMR_eucastrules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
|
||||
|
||||
\item{verbose}{a \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}
|
||||
|
||||
@ -51,6 +52,8 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
|
||||
|
||||
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
|
||||
|
||||
\item{custom_rules}{custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}}
|
||||
|
||||
\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}
|
||||
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
|
||||
@ -70,6 +73,15 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
\strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
|
||||
|
||||
The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
|
||||
\subsection{Custom Rules}{
|
||||
|
||||
Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.:\preformatted{x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
|
||||
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
|
||||
|
||||
eucast_rules(example_isolates, rules = "custom", custom_rules = x)
|
||||
}
|
||||
}
|
||||
|
||||
\subsection{'Other' Rules}{
|
||||
|
||||
Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:
|
||||
|
||||
10
man/like.Rd
10
man/like.Rd
@ -4,9 +4,9 @@
|
||||
\alias{like}
|
||||
\alias{\%like\%}
|
||||
\alias{\%like_case\%}
|
||||
\title{Pattern Matching with Keyboard Shortcut}
|
||||
\title{Vectorised Pattern Matching with Keyboard Shortcut}
|
||||
\source{
|
||||
Idea from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}
|
||||
Idea from the \href{https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R}{\code{like} function from the \code{data.table} package}
|
||||
}
|
||||
\usage{
|
||||
like(x, pattern, ignore.case = TRUE)
|
||||
@ -23,7 +23,7 @@ x \%like_case\% pattern
|
||||
\item{ignore.case}{if \code{FALSE}, the pattern matching is \emph{case sensitive} and if \code{TRUE}, case is ignored during matching.}
|
||||
}
|
||||
\value{
|
||||
A \code{\link{logical}} vector
|
||||
A \link{logical} vector
|
||||
}
|
||||
\description{
|
||||
Convenient wrapper around \code{\link[=grepl]{grepl()}} to match a pattern: \code{x \%like\% pattern}. It always returns a \code{\link{logical}} vector and is always case-insensitive (use \code{x \%like_case\% pattern} for case-sensitive matching). Also, \code{pattern} can be as long as \code{x} to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
|
||||
@ -34,7 +34,7 @@ The \verb{\%like\%} function:
|
||||
\item Is case-insensitive (use \verb{\%like_case\%} for case-sensitive matching)
|
||||
\item Supports multiple patterns
|
||||
\item Checks if \code{pattern} is a regular expression and sets \code{fixed = TRUE} if not, to greatly improve speed
|
||||
\item Always uses compatibility with Perl
|
||||
\item Always uses compatibility with Perl unless \code{fixed = TRUE}, to greatly improve speed
|
||||
}
|
||||
|
||||
Using RStudio? The text \verb{\%like\%} can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like \code{Ctrl+Shift+L} or \code{Cmd+Shift+L} (see \code{Tools} > \verb{Modify Keyboard Shortcuts...}).
|
||||
@ -75,7 +75,7 @@ a \%like\% b[1]
|
||||
\donttest{
|
||||
if (require("dplyr")) {
|
||||
example_isolates \%>\%
|
||||
filter(mo_name(mo) \%like\% "^ent")
|
||||
filter(mo_name() \%like\% "^ent")
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
15
man/mdro.Rd
15
man/mdro.Rd
@ -134,10 +134,19 @@ You can print the rules set in the console for an overview. Colours will help re
|
||||
#> Unmatched rows will return NA.
|
||||
}
|
||||
|
||||
The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:\preformatted{x <- mdro(example_isolates, guideline = custom)
|
||||
The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:\preformatted{x <- mdro(example_isolates,
|
||||
guideline = custom)
|
||||
table(x)
|
||||
#> Elderly Type A Elderly Type B Negative
|
||||
#> 43 891 1066
|
||||
#> Negative Elderly Type A Elderly Type B
|
||||
#> 1070 198 732
|
||||
}
|
||||
|
||||
Rules can also be combined with other custom rules by using \code{\link[=c]{c()}}:\preformatted{x <- mdro(example_isolates,
|
||||
guideline = c(custom,
|
||||
custom_mdro_guideline(ERY == "R" & age > 50 ~ "Elderly Type C")))
|
||||
table(x)
|
||||
#> Negative Elderly Type A Elderly Type B Elderly Type C
|
||||
#> 961 198 732 109
|
||||
}
|
||||
|
||||
The rules set (the \code{custom} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}}.
|
||||
|
||||
@ -83,6 +83,7 @@
|
||||
xlab = "Antimicrobial Interpretation",
|
||||
ylab = "Frequency",
|
||||
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
|
||||
language = get_locale(),
|
||||
...
|
||||
)
|
||||
}
|
||||
|
||||
@ -80,11 +80,10 @@ test_that("EUCAST rules work", {
|
||||
library(dplyr, warn.conflicts = FALSE)
|
||||
expect_equal(suppressWarnings(
|
||||
example_isolates %>%
|
||||
filter(mo_family(mo) == "Enterobacteriaceae") %>%
|
||||
mutate(TIC = as.rsi("R"),
|
||||
PIP = as.rsi("S")) %>%
|
||||
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
|
||||
left_join_microorganisms(by = "mo") %>%
|
||||
filter(family == "Enterobacteriaceae") %>%
|
||||
pull(PIP) %>%
|
||||
unique() %>%
|
||||
as.character()),
|
||||
@ -145,3 +144,21 @@ test_that("EUCAST rules work", {
|
||||
expect_s3_class(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame")
|
||||
|
||||
})
|
||||
|
||||
test_that("Custom EUCAST rules work", {
|
||||
|
||||
skip_on_cran()
|
||||
x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
|
||||
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
|
||||
expect_output(print(x))
|
||||
expect_output(print(c(x, x)))
|
||||
expect_output(print(as.list(x, x)))
|
||||
|
||||
# this custom rules makes 8 changes
|
||||
expect_equal(nrow(eucast_rules(example_isolates,
|
||||
rules = "custom",
|
||||
custom_rules = x,
|
||||
info = FALSE,
|
||||
verbose = TRUE)),
|
||||
8)
|
||||
})
|
||||
|
||||
@ -28,20 +28,20 @@ context("kurtosis.R")
|
||||
test_that("kurtosis works", {
|
||||
skip_on_cran()
|
||||
expect_equal(kurtosis(example_isolates$age),
|
||||
3.549319,
|
||||
5.227999,
|
||||
tolerance = 0.00001)
|
||||
|
||||
expect_equal(unname(kurtosis(data.frame(example_isolates$age))),
|
||||
3.549319,
|
||||
5.227999,
|
||||
tolerance = 0.00001)
|
||||
expect_equal(unname(kurtosis(data.frame(example_isolates$age), excess = TRUE)),
|
||||
0.549319,
|
||||
2.227999,
|
||||
tolerance = 0.00001)
|
||||
|
||||
expect_equal(kurtosis(matrix(example_isolates$age)),
|
||||
3.549319,
|
||||
5.227999,
|
||||
tolerance = 0.00001)
|
||||
expect_equal(kurtosis(matrix(example_isolates$age), excess = TRUE),
|
||||
0.549319,
|
||||
2.227999,
|
||||
tolerance = 0.00001)
|
||||
})
|
||||
|
||||
@ -228,8 +228,11 @@ test_that("mdro works", {
|
||||
"ERY == 'R' & age > 60" ~ "Elderly Type B",
|
||||
as_factor = TRUE)
|
||||
expect_output(print(custom))
|
||||
expect_output(print(c(custom, custom)))
|
||||
expect_output(print(as.list(custom, custom)))
|
||||
|
||||
expect_output(x <- mdro(example_isolates, guideline = custom, info = TRUE))
|
||||
expect_equal(as.double(table(x)), c(1066, 43, 891))
|
||||
expect_equal(as.double(table(x)), c(1070, 198, 732))
|
||||
|
||||
expect_output(print(custom_mdro_guideline(AMX == "R" ~ "test", as_factor = FALSE)))
|
||||
expect_error(custom_mdro_guideline())
|
||||
|
||||
@ -28,12 +28,12 @@ context("skewness.R")
|
||||
test_that("skewness works", {
|
||||
skip_on_cran()
|
||||
expect_equal(skewness(example_isolates$age),
|
||||
-0.8958019,
|
||||
-1.212888,
|
||||
tolerance = 0.00001)
|
||||
expect_equal(unname(skewness(data.frame(example_isolates$age))),
|
||||
-0.8958019,
|
||||
-1.212888,
|
||||
tolerance = 0.00001)
|
||||
expect_equal(skewness(matrix(example_isolates$age)),
|
||||
-0.8958019,
|
||||
-1.212888,
|
||||
tolerance = 0.00001)
|
||||
})
|
||||
|
||||
Loading…
Reference in New Issue
Block a user