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v1.8.0
...
d4e22069bc
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@ -33,3 +33,4 @@
|
||||
^vignettes/SPSS.Rmd$
|
||||
^vignettes/WHONET.Rmd$
|
||||
^logo.svg$
|
||||
^CRAN-SUBMISSION$
|
||||
|
||||
6
.github/workflows/check.yaml
vendored
6
.github/workflows/check.yaml
vendored
@ -57,8 +57,8 @@ jobs:
|
||||
- {os: macOS-latest, r: '3.6', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.5', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.4', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.3', allowfail: false}
|
||||
- {os: macOS-latest, r: '3.2', allowfail: false}
|
||||
# - {os: macOS-latest, r: '3.3', allowfail: false}
|
||||
# - {os: macOS-latest, r: '3.2', allowfail: false}
|
||||
# - {os: macOS-latest, r: '3.1', allowfail: true}
|
||||
# - {os: macOS-latest, r: '3.0', allowfail: true}
|
||||
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
|
||||
@ -77,7 +77,7 @@ jobs:
|
||||
- {os: windows-latest, r: '3.6', allowfail: false}
|
||||
- {os: windows-latest, r: '3.5', allowfail: false}
|
||||
- {os: windows-latest, r: '3.4', allowfail: false}
|
||||
- {os: windows-latest, r: '3.3', allowfail: false}
|
||||
# - {os: windows-latest, r: '3.3', allowfail: false}
|
||||
# - {os: windows-latest, r: '3.2', allowfail: true}
|
||||
# - {os: windows-latest, r: '3.1', allowfail: true}
|
||||
# - {os: windows-latest, r: '3.0', allowfail: true}
|
||||
|
||||
3
CRAN-SUBMISSION
Normal file
3
CRAN-SUBMISSION
Normal file
@ -0,0 +1,3 @@
|
||||
Version: 1.8.1
|
||||
Date: 2022-03-16 18:22:51 UTC
|
||||
SHA: 7b0f1596bd65fbb72681a7e3a6a7e4e469a891e8
|
||||
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 1.8.0
|
||||
Date: 2022-01-03
|
||||
Version: 1.8.1.9004
|
||||
Date: 2022-05-09
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
@ -9,7 +9,7 @@ Description: Functions to simplify and standardise antimicrobial resistance (AMR
|
||||
Authors@R: c(
|
||||
person(given = c("Matthijs", "S."),
|
||||
family = "Berends",
|
||||
email = "m.s.berends@umcg.nl",
|
||||
email = "m.berends@certe.nl",
|
||||
role = c("aut", "cre"),
|
||||
comment = c(ORCID = "0000-0001-7620-1800")),
|
||||
person(given = c("Christian", "F."),
|
||||
@ -71,7 +71,8 @@ Depends: R (>= 3.0.0)
|
||||
Enhances:
|
||||
cleaner,
|
||||
skimr,
|
||||
ggplot2
|
||||
ggplot2,
|
||||
tidyselect
|
||||
Suggests:
|
||||
curl,
|
||||
dplyr,
|
||||
|
||||
@ -50,7 +50,6 @@ S3method(any,mic)
|
||||
S3method(as.data.frame,ab)
|
||||
S3method(as.data.frame,mo)
|
||||
S3method(as.double,mic)
|
||||
S3method(as.integer,mic)
|
||||
S3method(as.list,custom_eucast_rules)
|
||||
S3method(as.list,custom_mdro_guideline)
|
||||
S3method(as.matrix,mic)
|
||||
|
||||
37
NEWS.md
37
NEWS.md
@ -1,8 +1,35 @@
|
||||
# `AMR` 1.8.1.9004
|
||||
## <small>Last updated: 9 May 2022</small>
|
||||
|
||||
### Changed
|
||||
* Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)
|
||||
* `droplevels()` on MIC will now return a common `factor` at default and will lose the `<mic>` class. Use `droplevels(..., as.mic = TRUE)` to keep the `<mic>` class.
|
||||
* Small fix for using `ab_from_text()`
|
||||
* Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
|
||||
|
||||
|
||||
# `AMR` 1.8.1
|
||||
|
||||
### Changed
|
||||
* Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
|
||||
* Support for antibiotic interpretations of the MIPS laboratory system: `"U"` for S ('susceptible urine'), `"D"` for I ('susceptible dose-dependent')
|
||||
* Improved algorithm of `as.mo()`, especially for ignoring non-taxonomic text, such as:
|
||||
```r
|
||||
mo_name("methicillin-resistant S. aureus (MRSA)")
|
||||
#> [1] "Staphylococcus aureus"
|
||||
```
|
||||
* More informative warning messages
|
||||
* Added 192 as valid MIC
|
||||
* Updated MIC printing in tibbles
|
||||
* Increased speed for loading the package
|
||||
|
||||
### Other
|
||||
* Fix for unit testing on R 3.3
|
||||
* Fix for size of some image elements, as requested by CRAN
|
||||
|
||||
|
||||
# `AMR` 1.8.0
|
||||
|
||||
|
||||
All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
|
||||
|
||||
### Breaking changes
|
||||
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
|
||||
* Removed the `key_antibiotics()` and `key_antibiotics_equal()` functions, which were deprecated and superseded by `key_antimicrobials()` and `antimicrobials_equal()`
|
||||
@ -256,7 +283,7 @@ All functions in this package are now all considered to be stable. Updates to th
|
||||
filter(is_new_episode(date, episode_days = 60))
|
||||
```
|
||||
* Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
|
||||
* Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on [EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) from 2020.
|
||||
* Function `mo_is_intrinsic_resistant()` to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020.
|
||||
* Functions `random_mic()`, `random_disk()` and `random_rsi()` for random value generation. The functions `random_mic()` and `random_disk()` take microorganism names and antibiotic names as input to make generation more realistic.
|
||||
|
||||
### Changed
|
||||
@ -1352,7 +1379,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
|
||||
* Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
|
||||
* Function `freq` to create **frequency tables**, with additional info in a header
|
||||
* Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
|
||||
* [Exceptional resistances defined by EUCAST](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) are also supported instead of countries alone
|
||||
* Exceptional resistances defined by EUCAST are also supported instead of countries alone
|
||||
* Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
|
||||
* New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
|
||||
* New print format for `tibble`s and `data.table`s
|
||||
|
||||
@ -36,15 +36,15 @@ EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(version_txt = "v11.0",
|
||||
EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
|
||||
year = 2016,
|
||||
title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
|
||||
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
|
||||
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"),
|
||||
"3.2" = list(version_txt = "v3.2",
|
||||
year = 2020,
|
||||
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
|
||||
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
|
||||
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"),
|
||||
"3.3" = list(version_txt = "v3.3",
|
||||
year = 2021,
|
||||
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
|
||||
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
|
||||
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"))
|
||||
|
||||
SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
|
||||
current_source = "US Edition of SNOMED CT from 1 September 2020",
|
||||
|
||||
@ -206,7 +206,7 @@ check_dataset_integrity <- function() {
|
||||
" overwritten by your global environment and prevent", plural[2],
|
||||
" the AMR package from working correctly: ",
|
||||
vector_and(overwritten, quotes = "'"),
|
||||
".\nPlease rename your object", plural[3], ".", call = FALSE)
|
||||
".\nPlease rename your object", plural[3], ".")
|
||||
}
|
||||
}
|
||||
# check if other packages did not overwrite our data sets
|
||||
@ -492,7 +492,7 @@ message_ <- function(...,
|
||||
warning_ <- function(...,
|
||||
add_fn = list(),
|
||||
immediate = FALSE,
|
||||
call = TRUE) {
|
||||
call = FALSE) {
|
||||
warning(word_wrap(...,
|
||||
add_fn = add_fn,
|
||||
as_note = FALSE),
|
||||
@ -559,7 +559,7 @@ stop_ifnot <- function(expr, ..., call = TRUE) {
|
||||
|
||||
return_after_integrity_check <- function(value, type, check_vector) {
|
||||
if (!all(value[!is.na(value)] %in% check_vector)) {
|
||||
warning_(paste0("invalid ", type, ", NA generated"), call = FALSE)
|
||||
warning_(paste0("invalid ", type, ", NA generated"))
|
||||
value[!value %in% check_vector] <- NA
|
||||
}
|
||||
value
|
||||
@ -638,7 +638,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
|
||||
if (isTRUE(initial_captital)) {
|
||||
v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
|
||||
}
|
||||
if (length(v) == 1) {
|
||||
if (length(v) <= 1) {
|
||||
return(paste0(quotes, v, quotes))
|
||||
}
|
||||
if (identical(v, c("I", "R", "S"))) {
|
||||
|
||||
10
R/ab.R
10
R/ab.R
@ -455,15 +455,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
|
||||
x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
|
||||
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
|
||||
if (length(x_unknown_ATCs) > 0 & fast_mode == FALSE) {
|
||||
warning_("These ATC codes are not (yet) in the antibiotics data set: ",
|
||||
vector_and(x_unknown_ATCs), ".",
|
||||
call = FALSE)
|
||||
warning_("in `as.ab()`: these ATC codes are not (yet) in the antibiotics data set: ",
|
||||
vector_and(x_unknown_ATCs), ".")
|
||||
}
|
||||
|
||||
if (length(x_unknown) > 0 & fast_mode == FALSE) {
|
||||
warning_("These values could not be coerced to a valid antimicrobial ID: ",
|
||||
vector_and(x_unknown), ".",
|
||||
call = FALSE)
|
||||
warning_("in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
|
||||
vector_and(x_unknown), ".")
|
||||
}
|
||||
|
||||
x_result <- x_new[match(x_bak_clean, x)]
|
||||
|
||||
@ -240,8 +240,8 @@ ab_ddd <- function(x, administration = "oral", ...) {
|
||||
units <- list(...)$units
|
||||
if (!is.null(units) && isTRUE(units)) {
|
||||
if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
|
||||
warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead. ",
|
||||
"This warning will be shown once per session.", call = FALSE)
|
||||
warning_("in `ab_ddd()`: using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead.",
|
||||
"This warning will be shown once per session.")
|
||||
}
|
||||
ddd_prop <- paste0(ddd_prop, "_units")
|
||||
} else {
|
||||
@ -250,9 +250,9 @@ ab_ddd <- function(x, administration = "oral", ...) {
|
||||
out <- ab_validate(x = x, property = ddd_prop)
|
||||
|
||||
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
|
||||
warning_("DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package. ",
|
||||
warning_("in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
|
||||
"Please refer to the WHOCC website:\n",
|
||||
"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
|
||||
"www.whocc.no/ddd/list_of_ddds_combined_products/")
|
||||
}
|
||||
out
|
||||
}
|
||||
@ -265,9 +265,9 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
|
||||
|
||||
x <- as.ab(x, ...)
|
||||
if (any(ab_name(x, language = NULL) %like% "/")) {
|
||||
warning_("DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package. ",
|
||||
warning_("in `ab_ddd_units()`: DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package.",
|
||||
"Please refer to the WHOCC website:\n",
|
||||
"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
|
||||
"www.whocc.no/ddd/list_of_ddds_combined_products/")
|
||||
}
|
||||
|
||||
ddd_prop <- paste0(administration, "_units")
|
||||
@ -311,12 +311,12 @@ ab_url <- function(x, open = FALSE, ...) {
|
||||
|
||||
NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)]
|
||||
if (length(NAs) > 0) {
|
||||
warning_("No ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
|
||||
warning_("in `ab_url()`: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
|
||||
}
|
||||
|
||||
if (open == TRUE) {
|
||||
if (length(u) > 1 & !is.na(u[1L])) {
|
||||
warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||
warning_("in `ab_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||
}
|
||||
if (!is.na(u[1L])) {
|
||||
utils::browseURL(u[1L])
|
||||
@ -385,7 +385,8 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
|
||||
},
|
||||
USE.NAMES = FALSE)
|
||||
if (any(x %in% c("", NA))) {
|
||||
warning_("No ", property, " found for column(s): ", vector_and(vars[x %in% c("", NA)], sort = FALSE), call = FALSE)
|
||||
warning_("in `set_ab_names()`: no ", property, " found for column(s): ",
|
||||
vector_and(vars[x %in% c("", NA)], sort = FALSE))
|
||||
x[x %in% c("", NA)] <- vars[x %in% c("", NA)]
|
||||
}
|
||||
|
||||
|
||||
@ -481,14 +481,13 @@ ab_select_exec <- function(function_name,
|
||||
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
|
||||
if (any(untreatable %in% names(ab_in_data))) {
|
||||
if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
|
||||
warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ",
|
||||
warning_("in `", function_name, "()`: some agents were ignored since they cannot be used for treating patients: ",
|
||||
vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
|
||||
language = NULL,
|
||||
tolower = TRUE),
|
||||
quotes = FALSE,
|
||||
sort = TRUE), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
|
||||
"This warning will be shown once per session.",
|
||||
call = FALSE)
|
||||
"This warning will be shown once per session.")
|
||||
}
|
||||
ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
|
||||
}
|
||||
|
||||
6
R/age.R
6
R/age.R
@ -95,10 +95,10 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
|
||||
|
||||
if (any(ages < 0, na.rm = TRUE)) {
|
||||
ages[!is.na(ages) & ages < 0] <- NA
|
||||
warning_("NAs introduced for ages below 0.", call = TRUE)
|
||||
warning_("in `age()`: NAs introduced for ages below 0.")
|
||||
}
|
||||
if (any(ages > 120, na.rm = TRUE)) {
|
||||
warning_("Some ages are above 120.", call = TRUE)
|
||||
warning_("in `age()`: some ages are above 120.")
|
||||
}
|
||||
|
||||
if (isTRUE(na.rm)) {
|
||||
@ -171,7 +171,7 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
|
||||
|
||||
if (any(x < 0, na.rm = TRUE)) {
|
||||
x[x < 0] <- NA
|
||||
warning_("NAs introduced for ages below 0.", call = TRUE)
|
||||
warning_("in `age_groups()`: NAs introduced for ages below 0.")
|
||||
}
|
||||
if (is.character(split_at)) {
|
||||
split_at <- split_at[1L]
|
||||
|
||||
@ -175,7 +175,7 @@ atc_online_property <- function(atc_code,
|
||||
colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
|
||||
|
||||
if (length(out) == 0) {
|
||||
warning_("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call = FALSE)
|
||||
warning_("in `atc_online_property()`: ATC not found: ", atc_code[i], ". Please check ", atc_url, ".")
|
||||
returnvalue[i] <- NA
|
||||
next
|
||||
}
|
||||
|
||||
@ -184,7 +184,7 @@ format.bug_drug_combinations <- function(x,
|
||||
|
||||
if (inherits(x, "grouped")) {
|
||||
# bug_drug_combinations() has been run on groups, so de-group here
|
||||
warning_("formatting the output of `bug_drug_combinations()` does not support grouped variables, they are ignored", call = FALSE)
|
||||
warning_("in `format()`: formatting the output of `bug_drug_combinations()` does not support grouped variables, they were ignored")
|
||||
idx <- split(seq_len(nrow(x)), paste0(x$mo, "%%", x$ab))
|
||||
x <- data.frame(mo = gsub("(.*)%%(.*)", "\\1", names(idx)),
|
||||
ab = gsub("(.*)%%(.*)", "\\2", names(idx)),
|
||||
|
||||
@ -43,7 +43,7 @@ format_included_data_number <- function(data) {
|
||||
#'
|
||||
#' This package contains the complete taxonomic tree (last updated: `r CATALOGUE_OF_LIFE$yearmonth_LPSN`) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).
|
||||
#' @section Catalogue of Life:
|
||||
#' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
#' \if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
|
||||
#' This package contains the complete taxonomic tree of almost all microorganisms (`r format_included_data_number(microorganisms)` species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/CatalogueOfLife/general) is finished, which we await.
|
||||
#'
|
||||
#' [Click here][catalogue_of_life] for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with [catalogue_of_life_version()].
|
||||
|
||||
4
R/disk.R
4
R/disk.R
@ -100,10 +100,10 @@ as.disk <- function(x, na.rm = FALSE) {
|
||||
unique() %pm>%
|
||||
sort() %pm>%
|
||||
vector_and(quotes = TRUE)
|
||||
warning_(na_after - na_before, " results truncated (",
|
||||
warning_("in `as.disk()`: ", na_after - na_before, " results truncated (",
|
||||
round(((na_after - na_before) / length(x)) * 100),
|
||||
"%) that were invalid disk zones: ",
|
||||
list_missing, call = FALSE)
|
||||
list_missing)
|
||||
}
|
||||
}
|
||||
set_clean_class(as.integer(x),
|
||||
|
||||
@ -181,8 +181,7 @@ eucast_rules <- function(x,
|
||||
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,
|
||||
warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
|
||||
immediate = TRUE)
|
||||
rules <- rules[rules != "custom"]
|
||||
if (length(rules) == 0) {
|
||||
@ -915,13 +914,12 @@ eucast_rules <- function(x,
|
||||
# take order from original data set
|
||||
warn_lacking_rsi_class <- warn_lacking_rsi_class[order(colnames(x.bak))]
|
||||
warn_lacking_rsi_class <- warn_lacking_rsi_class[!is.na(warn_lacking_rsi_class)]
|
||||
warning_("Not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
|
||||
warning_("in `eucast_rules()`: not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
|
||||
" - ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1,
|
||||
warn_lacking_rsi_class,
|
||||
paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])), ")\n",
|
||||
" - ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n",
|
||||
" - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))",
|
||||
call = FALSE)
|
||||
" - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))")
|
||||
}
|
||||
|
||||
# Return data set ---------------------------------------------------------
|
||||
@ -986,14 +984,14 @@ edit_rsi <- function(x,
|
||||
TRUE
|
||||
})
|
||||
suppressWarnings(new_edits[rows, cols] <<- to)
|
||||
warning_("Value \"", to, "\" added to the factor levels of column", ifelse(length(cols) == 1, "", "s"),
|
||||
warning_("in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
|
||||
ifelse(length(cols) == 1, "", "s"),
|
||||
" ", vector_and(cols, quotes = "`", sort = FALSE),
|
||||
" because this value was not an existing factor level.",
|
||||
call = FALSE)
|
||||
" because this value was not an existing factor level.")
|
||||
txt_warning()
|
||||
warned <- FALSE
|
||||
} else {
|
||||
warning_(w$message, call = FALSE)
|
||||
warning_("in `eucast_rules()`: ", w$message)
|
||||
txt_warning()
|
||||
}
|
||||
},
|
||||
|
||||
@ -267,7 +267,6 @@ get_column_abx <- function(x,
|
||||
", as it is already set for ",
|
||||
names(already_set_as), " (", ab_name(names(already_set_as), tolower = TRUE, language = NULL), ")"),
|
||||
add_fn = font_red,
|
||||
call = FALSE,
|
||||
immediate = verbose)
|
||||
}
|
||||
}
|
||||
@ -338,6 +337,5 @@ generate_warning_abs_missing <- function(missing, any = FALSE) {
|
||||
}
|
||||
warning_(paste0("Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ",
|
||||
vector_and(missing, quotes = FALSE)),
|
||||
immediate = TRUE,
|
||||
call = FALSE)
|
||||
immediate = TRUE)
|
||||
}
|
||||
|
||||
@ -170,7 +170,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
|
||||
}
|
||||
|
||||
if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
|
||||
warning_("The newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.", call = FALSE)
|
||||
warning_("in `", type, "_join()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
|
||||
}
|
||||
|
||||
joined
|
||||
|
||||
@ -150,7 +150,7 @@ key_antimicrobials <- function(x = NULL,
|
||||
col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
|
||||
}
|
||||
if (is.null(col_mo)) {
|
||||
warning_("No column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`", call = FALSE)
|
||||
warning_("in `key_antimicrobials()`: no column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`")
|
||||
gramstain <- NA_character_
|
||||
kingdom <- NA_character_
|
||||
} else {
|
||||
@ -172,11 +172,11 @@ key_antimicrobials <- function(x = NULL,
|
||||
if (values_new_length < values_old_length &
|
||||
any(filter, na.rm = TRUE) &
|
||||
message_not_thrown_before("key_antimicrobials", name)) {
|
||||
warning_(ifelse(values_new_length == 0,
|
||||
warning_("in `key_antimicrobials()`: ",
|
||||
ifelse(values_new_length == 0,
|
||||
"No columns available ",
|
||||
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
|
||||
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.",
|
||||
call = FALSE)
|
||||
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.")
|
||||
}
|
||||
|
||||
generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])
|
||||
@ -217,7 +217,7 @@ key_antimicrobials <- function(x = NULL,
|
||||
cols = cols)
|
||||
|
||||
if (length(unique(key_ab)) == 1) {
|
||||
warning_("No distinct key antibiotics determined.", call = FALSE)
|
||||
warning_("in `key_antimicrobials()`: no distinct key antibiotics determined.")
|
||||
}
|
||||
|
||||
key_ab
|
||||
|
||||
@ -32,23 +32,23 @@
|
||||
#' @rdname lifecycle
|
||||
#' @description Functions in this `AMR` package are categorised using [the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle](https://lifecycle.r-lib.org/articles/stages.html).
|
||||
#'
|
||||
#' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
|
||||
#' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height="200" style=margin-bottom:"5"} \cr}
|
||||
#' This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions.
|
||||
#' @section Experimental Lifecycle:
|
||||
#' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
|
||||
#' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
#' The [lifecycle][AMR::lifecycle] of this function is **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 `AMR` package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
|
||||
#' @section Maturing Lifecycle:
|
||||
#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome [to suggest changes at our repository](https://github.com/msberends/AMR/issues) or [write us an email (see section 'Contact Us')][AMR::AMR].
|
||||
#' @section Stable Lifecycle:
|
||||
#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
||||
#'
|
||||
#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
||||
#' @section Retired Lifecycle:
|
||||
#' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
|
||||
#' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
|
||||
#' @section Questioning Lifecycle:
|
||||
#' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
#' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:"5"} \cr}
|
||||
#' The [lifecycle][AMR::lifecycle] of this function is **questioning**. This function might be no longer be optimal approach, or is it questionable whether this function should be in this `AMR` package at all.
|
||||
NULL
|
||||
|
||||
12
R/mdro.R
12
R/mdro.R
@ -65,7 +65,7 @@
|
||||
#'
|
||||
#' * `guideline = "TB"`
|
||||
#'
|
||||
#' The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/tb/publications/pmdt_companionhandbook/en/))
|
||||
#' The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" ([link](https://www.who.int/publications/i/item/9789241548809))
|
||||
#'
|
||||
#' * `guideline = "MRGN"`
|
||||
#'
|
||||
@ -240,7 +240,7 @@ mdro <- function(x = NULL,
|
||||
}
|
||||
|
||||
if (!is.null(list(...)$country)) {
|
||||
warning_("Using `country` is deprecated, use `guideline` instead. See ?mdro.", call = FALSE)
|
||||
warning_("in `mdro()`: using `country` is deprecated, use `guideline` instead. See ?mdro")
|
||||
guideline <- list(...)$country
|
||||
}
|
||||
|
||||
@ -343,7 +343,7 @@ mdro <- function(x = NULL,
|
||||
guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
|
||||
guideline$author <- "WHO (World Health Organization)"
|
||||
guideline$version <- "WHO/HTM/TB/2014.11, 2014"
|
||||
guideline$source_url <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
|
||||
guideline$source_url <- "https://www.who.int/publications/i/item/9789241548809"
|
||||
guideline$type <- "MDR-TB's"
|
||||
|
||||
# support per country:
|
||||
@ -1550,8 +1550,8 @@ mdro <- function(x = NULL,
|
||||
if (guideline$code == "cmi2012") {
|
||||
if (any(x$MDRO == -1, na.rm = TRUE)) {
|
||||
if (message_not_thrown_before("mdro", "availability")) {
|
||||
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
|
||||
percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
|
||||
warning_("in `mdro()`: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
|
||||
percentage(pct_required_classes), " (set with `pct_required_classes`)")
|
||||
}
|
||||
# set these -1s to NA
|
||||
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
|
||||
@ -1709,7 +1709,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
|
||||
return("error")
|
||||
})
|
||||
if (identical(qry, "error")) {
|
||||
warning_("in custom_mdro_guideline(): rule ", i,
|
||||
warning_("in `custom_mdro_guideline()`: rule ", i,
|
||||
" (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
|
||||
pkg_env$err_msg,
|
||||
call = FALSE,
|
||||
|
||||
44
R/mic.R
44
R/mic.R
@ -37,8 +37,8 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
|
||||
function(x) paste0(x, sort(c(1:9, 1.5)))))),
|
||||
c(t(vapply(FUN.VALUE = character(45), ops,
|
||||
function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
|
||||
c(t(vapply(FUN.VALUE = character(16), ops,
|
||||
function(x) paste0(x, sort(c(2 ^ c(7:11), 80 * c(2:12))))))))
|
||||
c(t(vapply(FUN.VALUE = character(17), ops,
|
||||
function(x) paste0(x, sort(c(2 ^ c(7:11), 192, 80 * c(2:12))))))))
|
||||
|
||||
#' Transform Input to Minimum Inhibitory Concentrations (MIC)
|
||||
#'
|
||||
@ -47,7 +47,7 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
|
||||
#' @rdname as.mic
|
||||
#' @param x a [character] or [numeric] vector
|
||||
#' @param na.rm a [logical] indicating whether missing values should be removed
|
||||
#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI.
|
||||
#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
|
||||
#'
|
||||
#' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
|
||||
#'
|
||||
@ -86,6 +86,10 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
|
||||
#' ```
|
||||
#'
|
||||
#' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
|
||||
#'
|
||||
#' Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the \R convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users).
|
||||
#'
|
||||
#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `<mic>` class.
|
||||
#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
|
||||
#' @aliases mic
|
||||
#' @export
|
||||
@ -175,7 +179,7 @@ as.mic <- function(x, na.rm = FALSE) {
|
||||
unique() %pm>%
|
||||
sort() %pm>%
|
||||
vector_and(quotes = TRUE)
|
||||
warning_(na_after - na_before, " results truncated (",
|
||||
warning_("in `as.mic()`: ", na_after - na_before, " results truncated (",
|
||||
round(((na_after - na_before) / length(x)) * 100),
|
||||
"%) that were invalid MICs: ",
|
||||
list_missing, call = FALSE)
|
||||
@ -196,7 +200,8 @@ all_valid_mics <- function(x) {
|
||||
}
|
||||
|
||||
#' @rdname as.mic
|
||||
#' @details `NA_mic_` is a missing value of the new `<mic>` class.
|
||||
#' @details `NA_mic_` is a missing value of the new `<mic>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
|
||||
#' @format NULL
|
||||
#' @export
|
||||
NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
|
||||
new_class = c("mic", "ordered", "factor"))
|
||||
@ -214,13 +219,6 @@ as.double.mic <- function(x, ...) {
|
||||
as.double(gsub("[<=>]+", "", as.character(x), perl = TRUE))
|
||||
}
|
||||
|
||||
#' @method as.integer mic
|
||||
#' @export
|
||||
#' @noRd
|
||||
as.integer.mic <- function(x, ...) {
|
||||
as.integer(gsub("[<=>]+", "", as.character(x), perl = TRUE))
|
||||
}
|
||||
|
||||
#' @method as.numeric mic
|
||||
#' @export
|
||||
#' @noRd
|
||||
@ -228,10 +226,12 @@ as.numeric.mic <- function(x, ...) {
|
||||
as.numeric(gsub("[<=>]+", "", as.character(x), perl = TRUE))
|
||||
}
|
||||
|
||||
#' @rdname as.mic
|
||||
#' @method droplevels mic
|
||||
#' @param exclude factor levels which should be excluded from the result even if present, see [droplevels()][base::droplevels()]
|
||||
#' @param as.mic a [logical] to indicate whether the `<mic>` class should be kept, defaults to `FALSE`
|
||||
#' @export
|
||||
#' @noRd
|
||||
droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, as.mic = TRUE, ...) {
|
||||
droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, as.mic = FALSE, ...) {
|
||||
x <- droplevels.factor(x, exclude = exclude, ...)
|
||||
if (as.mic == TRUE) {
|
||||
class(x) <- c("mic", "ordered", "factor")
|
||||
@ -243,12 +243,12 @@ droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA,
|
||||
pillar_shaft.mic <- function(x, ...) {
|
||||
crude_numbers <- as.double(x)
|
||||
operators <- gsub("[^<=>]+", "", as.character(x))
|
||||
pasted <- trimws(paste0(operators, trimws(format(crude_numbers))))
|
||||
out <- pasted
|
||||
operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
|
||||
out <- trimws(paste0(operators, trimws(format(crude_numbers))))
|
||||
out[is.na(x)] <- font_na(NA)
|
||||
out <- gsub("(<|=|>)", font_silver("\\1"), out)
|
||||
out <- gsub("([.]?0+)$", font_white("\\1"), out)
|
||||
create_pillar_column(out, align = "right", width = max(nchar(pasted)))
|
||||
# maketrailing zeroes almost invisible
|
||||
out[out %like% "[.]"] <- gsub("([.]?0+)$", font_white("\\1"), out[out %like% "[.]"], perl = TRUE)
|
||||
create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
|
||||
}
|
||||
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
@ -260,7 +260,9 @@ type_sum.mic <- function(x, ...) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
print.mic <- function(x, ...) {
|
||||
cat("Class <mic>\n")
|
||||
cat("Class <mic>",
|
||||
ifelse(length(levels(x)) < length(valid_mic_levels), font_red(" with dropped levels"), ""),
|
||||
"\n", sep = "")
|
||||
print(as.character(x), quote = FALSE)
|
||||
att <- attributes(x)
|
||||
if ("na.action" %in% names(att)) {
|
||||
@ -358,7 +360,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
hist.mic <- function(x, ...) {
|
||||
warning_("Use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values", call = FALSE)
|
||||
warning_("in `hist()`: use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values")
|
||||
hist(log2(x))
|
||||
}
|
||||
|
||||
|
||||
117
R/mo.R
117
R/mo.R
@ -31,9 +31,9 @@
|
||||
#' @param Becker a [logical] to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
|
||||
#'
|
||||
#' This excludes *Staphylococcus aureus* at default, use `Becker = "all"` to also categorise *S. aureus* as "CoPS".
|
||||
#' @param Lancefield a [logical] to indicate whether beta-haemolytic *Streptococci* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These *Streptococci* will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L.
|
||||
#' @param Lancefield a [logical] to indicate whether a beta-haemolytic *Streptococcus* should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield (4). These streptococci will be categorised in their first group, e.g. *Streptococcus dysgalactiae* will be group C, although officially it was also categorised into groups G and L.
|
||||
#'
|
||||
#' This excludes *Enterococci* at default (who are in group D), use `Lancefield = "all"` to also categorise all *Enterococci* as group D.
|
||||
#' This excludes enterococci at default (who are in group D), use `Lancefield = "all"` to also categorise all enterococci as group D.
|
||||
#' @param allow_uncertain a number between `0` (or `"none"`) and `3` (or `"all"`), or `TRUE` (= `2`) or `FALSE` (= `0`) to indicate whether the input should be checked for less probable results, see *Details*
|
||||
#' @param reference_df a [data.frame] to be used for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
|
||||
#' @param ignore_pattern a regular expression (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the option `AMR_ignore_pattern`, e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
|
||||
@ -1003,6 +1003,35 @@ exec_as.mo <- function(x,
|
||||
}
|
||||
}
|
||||
|
||||
# try splitting of characters in the middle and then find ID based on old names ----
|
||||
# only when text length is 6 or lower
|
||||
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
|
||||
if (nchar(g.x_backup_without_spp) <= 6) {
|
||||
x_length <- nchar(g.x_backup_without_spp)
|
||||
x_split <- paste0("^",
|
||||
g.x_backup_without_spp %pm>% substr(1, x_length / 2),
|
||||
".* ",
|
||||
g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
|
||||
found <- lookup(fullname_lower %like_case% x_split,
|
||||
haystack = MO.old_lookup,
|
||||
column = NULL)
|
||||
if (!all(is.na(found))) {
|
||||
# it's an old name, so return it
|
||||
if (property == "ref") {
|
||||
x[i] <- found["ref"]
|
||||
} else {
|
||||
x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
|
||||
}
|
||||
pkg_env$mo_renamed_last_run <- found["fullname"]
|
||||
was_renamed(name_old = found["fullname"],
|
||||
name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup),
|
||||
ref_old = found["ref"],
|
||||
ref_new = lookup(fullname == found["fullname_new"], "ref", haystack = MO_lookup),
|
||||
mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup))
|
||||
return(x[i])
|
||||
}
|
||||
}
|
||||
|
||||
# try fullname without start and without nchar limit of >= 6 ----
|
||||
# like "K. pneu rhino" >> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
|
||||
found <- lookup(fullname_lower %like_case% e.x_withspaces_start_only,
|
||||
@ -1188,9 +1217,38 @@ exec_as.mo <- function(x,
|
||||
return(found)
|
||||
}
|
||||
|
||||
# (6) try to strip off half an element from end and check the remains ----
|
||||
# (6) remove non-taxonomic prefix and suffix ----
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (6) try to strip off half an element from end and check the remains\n"))
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (6) remove non-taxonomic prefix and suffix\n"))
|
||||
}
|
||||
x_without_nontax <- gsub("(^[a-zA-Z]+[./-]+[a-zA-Z]+[^a-zA-Z]* )([a-zA-Z.]+ [a-zA-Z]+.*)",
|
||||
"\\2", a.x_backup, perl = TRUE)
|
||||
x_without_nontax <- gsub("( *[(].*[)] *)[^a-zA-Z]*$", "", x_without_nontax, perl = TRUE)
|
||||
if (isTRUE(debug)) {
|
||||
message("Running '", x_without_nontax, "'")
|
||||
}
|
||||
|
||||
# first try without dyslexia mode
|
||||
found <- suppressMessages(suppressWarnings(exec_as.mo(x_without_nontax, initial_search = FALSE, dyslexia_mode = FALSE, allow_uncertain = FALSE, debug = debug, reference_data_to_use = uncertain.reference_data_to_use, actual_uncertainty = 2, actual_input = x_without_nontax)))
|
||||
if (empty_result(found)) {
|
||||
# then with dyslexia mode
|
||||
found <- suppressMessages(suppressWarnings(exec_as.mo(x_without_nontax, initial_search = FALSE, dyslexia_mode = TRUE, allow_uncertain = FALSE, debug = debug, reference_data_to_use = uncertain.reference_data_to_use, actual_uncertainty = 2, actual_input = x_without_nontax)))
|
||||
}
|
||||
if (!empty_result(found) & nchar(g.x_backup_without_spp) >= 6) {
|
||||
# we ran with actual_input = x_without_nontax, so now correct for a.x_backup:
|
||||
uncertain_df <- attr(found, which = "uncertainties", exact = TRUE)
|
||||
uncertain_df$input <- a.x_backup
|
||||
found_result <- found
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
uncertain_df,
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
|
||||
# (7) try to strip off half an element from end and check the remains ----
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (7) try to strip off half an element from end and check the remains\n"))
|
||||
}
|
||||
x_strip <- a.x_backup %pm>% strsplit("[ .]") %pm>% unlist()
|
||||
if (length(x_strip) > 1) {
|
||||
@ -1220,9 +1278,9 @@ exec_as.mo <- function(x,
|
||||
}
|
||||
}
|
||||
}
|
||||
# (7) try to strip off one element from end and check the remains ----
|
||||
# (8) try to strip off one element from end and check the remains ----
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (7) try to strip off one element from end and check the remains\n"))
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (8) try to strip off one element from end and check the remains\n"))
|
||||
}
|
||||
if (length(x_strip) > 1) {
|
||||
for (i in seq_len(length(x_strip) - 1)) {
|
||||
@ -1249,9 +1307,9 @@ exec_as.mo <- function(x,
|
||||
}
|
||||
}
|
||||
}
|
||||
# (8) check for unknown yeasts/fungi ----
|
||||
# (9) check for unknown yeasts/fungi ----
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (8) check for unknown yeasts/fungi\n"))
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (9) check for unknown yeasts/fungi\n"))
|
||||
}
|
||||
if (b.x_trimmed %like_case% "yeast") {
|
||||
found <- "F_YEAST"
|
||||
@ -1275,9 +1333,9 @@ exec_as.mo <- function(x,
|
||||
stringsAsFactors = FALSE)
|
||||
return(found)
|
||||
}
|
||||
# (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
|
||||
# (10) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n"))
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (10) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n"))
|
||||
}
|
||||
x_strip <- a.x_backup %pm>% strsplit("[ .]") %pm>% unlist()
|
||||
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
|
||||
@ -1311,9 +1369,9 @@ exec_as.mo <- function(x,
|
||||
if (uncertainty_level >= 3) {
|
||||
now_checks_for_uncertainty_level <- 3
|
||||
|
||||
# (10) try to strip off one element from start and check the remains (any text size) ----
|
||||
# (11) try to strip off one element from start and check the remains (any text size) ----
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (10) try to strip off one element from start and check the remains (any text size)\n"))
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (11) try to strip off one element from start and check the remains (any text size)\n"))
|
||||
}
|
||||
x_strip <- a.x_backup %pm>% strsplit("[ .]") %pm>% unlist()
|
||||
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
|
||||
@ -1338,10 +1396,10 @@ exec_as.mo <- function(x,
|
||||
}
|
||||
}
|
||||
}
|
||||
# (11) try to strip off one element from end and check the remains (any text size) ----
|
||||
# (12) try to strip off one element from end and check the remains (any text size) ----
|
||||
# (this is in fact 7 but without nchar limit of >=6)
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (11) try to strip off one element from end and check the remains (any text size)\n"))
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (12) try to strip off one element from end and check the remains (any text size)\n"))
|
||||
}
|
||||
if (length(x_strip) > 1) {
|
||||
for (i in seq_len(length(x_strip) - 1)) {
|
||||
@ -1366,9 +1424,9 @@ exec_as.mo <- function(x,
|
||||
}
|
||||
}
|
||||
|
||||
# (12) part of a name (very unlikely match) ----
|
||||
# (13) part of a name (very unlikely match) ----
|
||||
if (isTRUE(debug)) {
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (12) part of a name (very unlikely match)\n"))
|
||||
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (13) part of a name (very unlikely match)\n"))
|
||||
}
|
||||
if (isTRUE(debug)) {
|
||||
message("Running '", f.x_withspaces_end_only, "'")
|
||||
@ -1460,9 +1518,8 @@ exec_as.mo <- function(x,
|
||||
"You can also use your own reference data with set_mo_source() or directly, e.g.:\n",
|
||||
' as.mo("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n',
|
||||
' mo_name("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n')
|
||||
warning_(paste0("\n", msg),
|
||||
warning_(paste0("\nin `as.mo()`: ", msg),
|
||||
add_fn = font_red,
|
||||
call = FALSE,
|
||||
immediate = TRUE) # thus will always be shown, even if >= warnings
|
||||
}
|
||||
# handling uncertainties ----
|
||||
@ -1502,12 +1559,11 @@ exec_as.mo <- function(x,
|
||||
# comment below code if all staphylococcal species are categorised as CoNS/CoPS
|
||||
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
|
||||
if (message_not_thrown_before("as.mo", "becker")) {
|
||||
warning_("Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
|
||||
warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
|
||||
font_italic(paste("S.",
|
||||
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
|
||||
collapse = ", ")),
|
||||
". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
|
||||
call = FALSE,
|
||||
immediate = TRUE)
|
||||
}
|
||||
}
|
||||
@ -1680,8 +1736,7 @@ pillar_shaft.mo <- function(x, ...) {
|
||||
col <- "The data"
|
||||
}
|
||||
warning_(col, " contains old MO codes (from a previous AMR package version). ",
|
||||
"Please update your MO codes with `as.mo()`.",
|
||||
call = FALSE)
|
||||
"Please update your MO codes with `as.mo()`.")
|
||||
}
|
||||
|
||||
# make it always fit exactly
|
||||
@ -1755,8 +1810,7 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
|
||||
names(x) <- x_names
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
|
||||
warning_("Some MO codes are from a previous AMR package version. ",
|
||||
"Please update these MO codes with `as.mo()`.",
|
||||
call = FALSE)
|
||||
"Please update the MO codes with `as.mo()`.")
|
||||
}
|
||||
print.default(x, quote = FALSE)
|
||||
}
|
||||
@ -1785,8 +1839,7 @@ summary.mo <- function(object, ...) {
|
||||
as.data.frame.mo <- function(x, ...) {
|
||||
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
|
||||
warning_("The data contains old MO codes (from a previous AMR package version). ",
|
||||
"Please update your MO codes with `as.mo()`.",
|
||||
call = FALSE)
|
||||
"Please update your MO codes with `as.mo()`.")
|
||||
}
|
||||
nm <- deparse1(substitute(x))
|
||||
if (!"nm" %in% names(list(...))) {
|
||||
@ -1882,7 +1935,7 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
if (NROW(x) == 0) {
|
||||
return(NULL)
|
||||
}
|
||||
cat(word_wrap("Matching scores", ifelse(has_colour(), " (in blue)", ""), " are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.\n\n", add_fn = font_blue))
|
||||
cat(word_wrap("Matching scores", ifelse(has_colour(), " (in blue)", ""), " are based on pathogenicity in humans and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.\n\n", add_fn = font_blue))
|
||||
|
||||
txt <- ""
|
||||
for (i in seq_len(nrow(x))) {
|
||||
@ -2090,13 +2143,12 @@ replace_old_mo_codes <- function(x, property) {
|
||||
n_unique <- ""
|
||||
}
|
||||
if (property != "mo") {
|
||||
warning_(paste0("The input contained ", n_matched,
|
||||
warning_("in `mo_", property, "()`: the input contained ", n_matched,
|
||||
" old MO code", ifelse(n_matched == 1, "", "s"),
|
||||
" (", n_unique, "from a previous AMR package version). ",
|
||||
"Please update your MO codes with `as.mo()` to increase speed."),
|
||||
call = FALSE)
|
||||
"Please update your MO codes with `as.mo()` to increase speed.")
|
||||
} else {
|
||||
warning_(paste0("The input contained ", n_matched,
|
||||
warning_("in `as.mo()`: the input contained ", n_matched,
|
||||
" old MO code", ifelse(n_matched == 1, "", "s"),
|
||||
" (", n_unique, "from a previous AMR package version). ",
|
||||
n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),
|
||||
@ -2106,8 +2158,7 @@ replace_old_mo_codes <- function(x, property) {
|
||||
"currently used MO code", ifelse(n_solved == 1, "", "s"),
|
||||
ifelse(n_unsolved > 0,
|
||||
paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
|
||||
".")),
|
||||
call = FALSE)
|
||||
"."))
|
||||
}
|
||||
}
|
||||
x
|
||||
|
||||
@ -27,13 +27,13 @@
|
||||
#'
|
||||
#' This algorithm is used by [as.mo()] and all the [`mo_*`][mo_property()] functions to determine the most probable match of taxonomic records based on user input.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @author Dr. Matthijs Berends
|
||||
#' @author Dr Matthijs Berends
|
||||
#' @param x Any user input value(s)
|
||||
#' @param n A full taxonomic name, that exists in [`microorganisms$fullname`][microorganisms]
|
||||
#' @section Matching Score for Microorganisms:
|
||||
#' With ambiguous user input in [as.mo()] and all the [`mo_*`][mo_property()] functions, the returned results are chosen based on their matching score using [mo_matching_score()]. This matching score \eqn{m}, is calculated as:
|
||||
#'
|
||||
#' \ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300px" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
||||
#' \ifelse{latex}{\deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \textrm{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}}{\ifelse{html}{\figure{mo_matching_score.png}{options: width="300" alt="mo matching score"}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}}
|
||||
#'
|
||||
#' where:
|
||||
#'
|
||||
@ -49,6 +49,8 @@
|
||||
#' All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
|
||||
#'
|
||||
#' All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., `"E. coli"` will return the microbial ID of *Escherichia coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Escherichia coli"), 3)`}, a highly prevalent microorganism found in humans) and not *Entamoeba coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Entamoeba coli"), 3)`}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
|
||||
#'
|
||||
#' Since `AMR` version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: `r vector_and(pkg_env$mo_field_abbreviations, quotes = FALSE)`.
|
||||
#' @export
|
||||
#' @inheritSection AMR Reference Data Publicly Available
|
||||
#' @inheritSection AMR Read more on Our Website!
|
||||
@ -65,6 +67,13 @@ mo_matching_score <- function(x, n) {
|
||||
x <- parse_and_convert(x)
|
||||
# no dots and other non-whitespace characters
|
||||
x <- gsub("[^a-zA-Z0-9 \\(\\)]+", "", x)
|
||||
|
||||
# remove abbreviations known to the field
|
||||
x <- gsub(paste0("(^|[^a-z0-9]+)(",
|
||||
paste0(pkg_env$mo_field_abbreviations, collapse = "|"),
|
||||
")([^a-z0-9]+|$)"),
|
||||
"", x, perl = TRUE, ignore.case = TRUE)
|
||||
|
||||
# only keep one space
|
||||
x <- gsub(" +", " ", x)
|
||||
|
||||
@ -82,7 +91,7 @@ mo_matching_score <- function(x, n) {
|
||||
l_n.lev <- double(length = length(x))
|
||||
for (i in seq_len(length(x))) {
|
||||
# determine Levenshtein distance, but maximise to nchar of n
|
||||
lev[i] <- utils::adist(x[i], n[i], ignore.case = FALSE, fixed = TRUE)
|
||||
lev[i] <- utils::adist(x[i], n[i], ignore.case = FALSE, fixed = TRUE, costs = c(ins = 1, del = 1, sub = 1))
|
||||
# minimum of (l_n, Levenshtein distance)
|
||||
l_n.lev[i] <- min(l_n[i], as.double(lev[i]))
|
||||
}
|
||||
|
||||
@ -684,7 +684,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), ...) {
|
||||
|
||||
if (isTRUE(open)) {
|
||||
if (length(u) > 1) {
|
||||
warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||
warning_("in `mo_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||
}
|
||||
utils::browseURL(u[1L])
|
||||
}
|
||||
|
||||
@ -29,16 +29,16 @@
|
||||
#'
|
||||
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.
|
||||
#' @inheritSection lifecycle Stable Lifecycle
|
||||
#' @param path location of your reference file, see *Details*. Can be `""`, `NULL` or `FALSE` to delete the reference file.
|
||||
#' @param path location of your reference file, this can be any text file (comma-, tab- or pipe-separated) or an Excel file (see *Details*). Can also be `""`, `NULL` or `FALSE` to delete the reference file.
|
||||
#' @param destination destination of the compressed data file, default to the user's home directory.
|
||||
#' @rdname mo_source
|
||||
#' @name mo_source
|
||||
#' @aliases set_mo_source get_mo_source
|
||||
#' @details The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an \R object file (extension '.rds'). To use an Excel file, you will need to have the `readxl` package installed.
|
||||
#'
|
||||
#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
|
||||
#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] or [`microorganisms$fullname`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
|
||||
#'
|
||||
#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an attribute to the compressed data file.
|
||||
#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an [attribute][base::attributes()] to the compressed data file.
|
||||
#'
|
||||
#' The function [get_mo_source()] will return the data set by reading `"mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the location and timestamp of the original file), it will call [set_mo_source()] to update the data file automatically if used in an interactive session.
|
||||
#'
|
||||
@ -46,14 +46,14 @@
|
||||
#'
|
||||
#' @section How to Setup:
|
||||
#'
|
||||
#' Imagine this data on a sheet of an Excel file (mo codes were looked up in the [microorganisms] data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
|
||||
#' Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:
|
||||
#'
|
||||
#' ```
|
||||
#' | A | B |
|
||||
#' --|--------------------|--------------|
|
||||
#' --|--------------------|-----------------------|
|
||||
#' 1 | Organisation XYZ | mo |
|
||||
#' 2 | lab_mo_ecoli | B_ESCHR_COLI |
|
||||
#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
|
||||
#' 2 | lab_mo_ecoli | Escherichia coli |
|
||||
#' 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
|
||||
#' 4 | | |
|
||||
#' ```
|
||||
#'
|
||||
@ -90,11 +90,11 @@
|
||||
#'
|
||||
#' ```
|
||||
#' | A | B |
|
||||
#' --|--------------------|--------------|
|
||||
#' --|--------------------|-----------------------|
|
||||
#' 1 | Organisation XYZ | mo |
|
||||
#' 2 | lab_mo_ecoli | B_ESCHR_COLI |
|
||||
#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
|
||||
#' 4 | lab_Staph_aureus | B_STPHY_AURS |
|
||||
#' 2 | lab_mo_ecoli | Escherichia coli |
|
||||
#' 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
|
||||
#' 4 | lab_Staph_aureus | Staphylococcus aureus |
|
||||
#' 5 | | |
|
||||
#' ```
|
||||
#'
|
||||
@ -144,6 +144,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
|
||||
stop_ifnot(file.exists(path), "file not found: ", path)
|
||||
|
||||
df <- NULL
|
||||
if (path %like% "[.]rds$") {
|
||||
df <- readRDS(path)
|
||||
|
||||
@ -153,28 +154,34 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
df <- readxl::read_excel(path)
|
||||
|
||||
} else if (path %like% "[.]tsv$") {
|
||||
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
|
||||
|
||||
} else if (path %like% "[.]csv$") {
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = ",", stringsAsFactors = FALSE)
|
||||
|
||||
} else {
|
||||
# try comma first
|
||||
try(
|
||||
df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = ",", stringsAsFactors = FALSE),
|
||||
silent = TRUE)
|
||||
if (!check_validity_mo_source(df, stop_on_error = FALSE)) {
|
||||
# try tab
|
||||
try(
|
||||
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = "\t", stringsAsFactors = FALSE),
|
||||
silent = TRUE)
|
||||
}
|
||||
if (!check_validity_mo_source(df, stop_on_error = FALSE)) {
|
||||
# try pipe
|
||||
try(
|
||||
df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
|
||||
df <- utils::read.table(file = path, header = TRUE, sep = "|", stringsAsFactors = FALSE),
|
||||
silent = TRUE)
|
||||
}
|
||||
}
|
||||
|
||||
# check integrity
|
||||
if (is.null(df)) {
|
||||
stop_("the path '", path, "' could not be imported as a dataset.")
|
||||
}
|
||||
check_validity_mo_source(df)
|
||||
|
||||
df <- subset(df, !is.na(mo))
|
||||
@ -187,7 +194,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
}
|
||||
|
||||
df <- as.data.frame(df, stringAsFactors = FALSE)
|
||||
df[, "mo"] <- set_clean_class(df[, "mo", drop = TRUE], c("mo", "character"))
|
||||
df[, "mo"] <- as.mo(df[, "mo", drop = TRUE])
|
||||
|
||||
# success
|
||||
if (file.exists(mo_source_destination)) {
|
||||
@ -275,9 +282,9 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
|
||||
return(FALSE)
|
||||
}
|
||||
}
|
||||
if (!all(x$mo %in% c("", microorganisms$mo), na.rm = TRUE)) {
|
||||
if (!all(x$mo %in% c("", microorganisms$mo, microorganisms$fullname), na.rm = TRUE)) {
|
||||
if (stop_on_error == TRUE) {
|
||||
invalid <- x[which(!x$mo %in% c("", microorganisms$mo)), , drop = FALSE]
|
||||
invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms$fullname)), , drop = FALSE]
|
||||
if (nrow(invalid) > 1) {
|
||||
plural <- "s"
|
||||
} else {
|
||||
|
||||
2
R/pca.R
2
R/pca.R
@ -98,7 +98,7 @@ pca <- function(x,
|
||||
|
||||
x <- as.data.frame(new_list, stringsAsFactors = FALSE)
|
||||
if (any(vapply(FUN.VALUE = logical(1), x, function(y) !is.numeric(y)))) {
|
||||
warning_("Be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with [numeric] variables only. See Examples in ?pca.", call = FALSE)
|
||||
warning_("in `pca()`: be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. See Examples in ?pca.", call = FALSE)
|
||||
}
|
||||
|
||||
# set column names
|
||||
|
||||
@ -106,7 +106,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
|
||||
if (nrow(df_new) > 0) {
|
||||
df <- df_new
|
||||
} else {
|
||||
warning_("No rows found that match mo '", mo, "', ignoring argument `mo`", call = FALSE)
|
||||
warning_("in `random_", tolower(type), "()`: no rows found that match mo '", mo, "', ignoring argument `mo`")
|
||||
}
|
||||
}
|
||||
|
||||
@ -117,7 +117,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
|
||||
if (nrow(df_new) > 0) {
|
||||
df <- df_new
|
||||
} else {
|
||||
warning_("No rows found that match ab '", ab, "', ignoring argument `ab`", call = FALSE)
|
||||
warning_("in `random_", tolower(type), "()`: no rows found that match ab '", ab, "', ignoring argument `ab`")
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -153,7 +153,7 @@ resistance_predict <- function(x,
|
||||
x <- dots[which(dots.names == "tbl")]
|
||||
}
|
||||
if ("I_as_R" %in% dots.names) {
|
||||
warning_("`I_as_R is deprecated - use I_as_S instead.", call = FALSE)
|
||||
warning_("in `resistance_predict()`: I_as_R is deprecated - use I_as_S instead.")
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
353
R/rsi.R
353
R/rsi.R
@ -33,7 +33,7 @@
|
||||
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
|
||||
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
|
||||
#' @inheritParams first_isolate
|
||||
#' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options
|
||||
#' @param guideline defaults to the latest included EUCAST guideline, supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`), see *Details*
|
||||
#' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
|
||||
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
|
||||
#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
|
||||
@ -67,7 +67,7 @@
|
||||
#'
|
||||
#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
|
||||
#'
|
||||
#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
|
||||
#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
|
||||
#'
|
||||
#' ## After Interpretation
|
||||
#'
|
||||
@ -179,7 +179,7 @@
|
||||
#' example_isolates %>%
|
||||
#' mutate_if(is.rsi.eligible, as.rsi)
|
||||
#'
|
||||
#' # note: from dplyr 1.0.0 on, this will be:
|
||||
#' # since dplyr 1.0.0, this can also be:
|
||||
#' # example_isolates %>%
|
||||
#' # mutate(across(where(is.rsi.eligible), as.rsi))
|
||||
#' }
|
||||
@ -189,7 +189,7 @@ as.rsi <- function(x, ...) {
|
||||
}
|
||||
|
||||
#' @rdname as.rsi
|
||||
#' @details `NA_rsi_` is a missing value of the new `<rsi>` class.
|
||||
#' @details `NA_rsi_` is a missing value of the new `<rsi>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
|
||||
#' @export
|
||||
NA_rsi_ <- set_clean_class(factor(NA, levels = c("S", "I", "R"), ordered = TRUE),
|
||||
new_class = c("rsi", "ordered", "factor"))
|
||||
@ -233,9 +233,9 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
|
||||
} else if (!any(c("R", "S", "I") %in% x, na.rm = TRUE) & !all(is.na(x))) {
|
||||
return(FALSE)
|
||||
} else {
|
||||
x <- x[!is.na(x) & !is.null(x) & x != ""]
|
||||
x <- x[!is.na(x) & !is.null(x) & !x %in% c("", "-", "NULL")]
|
||||
if (length(x) == 0) {
|
||||
# no other values than NA or ""
|
||||
# no other values than empty
|
||||
cur_col <- get_current_column()
|
||||
if (!is.null(cur_col)) {
|
||||
ab <- suppressWarnings(as.ab(cur_col, fast_mode = TRUE, info = FALSE))
|
||||
@ -257,7 +257,7 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
|
||||
}
|
||||
|
||||
#' @export
|
||||
# extra param: warn (never throw warning)
|
||||
# extra param: warn (logical, to never throw a warning)
|
||||
as.rsi.default <- function(x, ...) {
|
||||
if (is.rsi(x)) {
|
||||
return(x)
|
||||
@ -284,16 +284,17 @@ as.rsi.default <- function(x, ...) {
|
||||
if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
|
||||
# check if they are actually MICs or disks
|
||||
if (all_valid_mics(x)) {
|
||||
warning_("The input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.", call = FALSE)
|
||||
warning_("in `as.rsi()`: the input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.")
|
||||
} else if (all_valid_disks(x)) {
|
||||
warning_("The input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.", call = FALSE)
|
||||
warning_("in `as.rsi()`: the input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.")
|
||||
}
|
||||
}
|
||||
|
||||
# trim leading and trailing spaces, new lines, etc.
|
||||
x <- trimws2(as.character(unlist(x)))
|
||||
x[x %in% c(NA, "", "-", "NULL")] <- NA_character_
|
||||
x.bak <- x
|
||||
na_before <- length(x[is.na(x) | x == ""])
|
||||
na_before <- length(x[is.na(x)])
|
||||
|
||||
# correct for translations
|
||||
trans_R <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
|
||||
@ -310,11 +311,15 @@ as.rsi.default <- function(x, ...) {
|
||||
x[x %like% "([^a-z]|^)sus(cep(tible)?)?"] <- "S"
|
||||
x[x %like% "([^a-z]|^)int(er(mediate)?)?|incr.*exp"] <- "I"
|
||||
# remove other invalid characters
|
||||
x <- gsub("[^rsiRSIHi]+", "", x, perl = TRUE)
|
||||
# some labs now report "H" instead of "I" to not interfere with EUCAST prior to 2019
|
||||
x <- gsub("H", "I", x, ignore.case = TRUE)
|
||||
# set to capitals
|
||||
x <- toupper(x)
|
||||
x <- gsub("[^RSIHDU]+", "", x, perl = TRUE)
|
||||
# some labs now report "H" instead of "I" to not interfere with EUCAST prior to 2019
|
||||
x <- gsub("^H$", "I", x, perl = TRUE)
|
||||
# and MIPS uses D for Dose-dependent (which is I, but it will throw a note)
|
||||
x <- gsub("^D$", "I", x, perl = TRUE)
|
||||
# and MIPS uses U for "susceptible urine"
|
||||
x <- gsub("^U$", "S", x, perl = TRUE)
|
||||
# in cases of "S;S" keep S, but in case of "S;I" make it NA
|
||||
x <- gsub("^S+$", "S", x)
|
||||
x <- gsub("^I+$", "I", x)
|
||||
@ -328,11 +333,20 @@ as.rsi.default <- function(x, ...) {
|
||||
unique() %pm>%
|
||||
sort() %pm>%
|
||||
vector_and(quotes = TRUE)
|
||||
warning_(na_after - na_before, " results truncated (",
|
||||
warning_("in `as.rsi()`: ", na_after - na_before, " results truncated (",
|
||||
round(((na_after - na_before) / length(x)) * 100),
|
||||
"%) that were invalid antimicrobial interpretations: ",
|
||||
list_missing, call = FALSE)
|
||||
}
|
||||
if (any(toupper(x.bak[!is.na(x.bak)]) == "U") && message_not_thrown_before("as.rsi", "U")) {
|
||||
warning_("in `as.rsi()`: 'U' was interpreted as 'S', following some laboratory systems")
|
||||
}
|
||||
if (any(toupper(x.bak[!is.na(x.bak)]) == "D") && message_not_thrown_before("as.rsi", "D")) {
|
||||
warning_("in `as.rsi()`: 'D' (dose-dependent) was interpreted as 'I', following some laboratory systems")
|
||||
}
|
||||
if (any(toupper(x.bak[!is.na(x.bak)]) == "H") && message_not_thrown_before("as.rsi", "H")) {
|
||||
warning_("in `as.rsi()`: 'H' was interpreted as 'I', following some laboratory systems")
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -351,89 +365,17 @@ as.rsi.mic <- function(x,
|
||||
add_intrinsic_resistance = FALSE,
|
||||
reference_data = AMR::rsi_translation,
|
||||
...) {
|
||||
meet_criteria(x)
|
||||
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
|
||||
meet_criteria(ab, allow_class = c("ab", "character"))
|
||||
meet_criteria(guideline, allow_class = "character", has_length = 1)
|
||||
meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
|
||||
meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(reference_data, allow_class = "data.frame")
|
||||
check_reference_data(reference_data)
|
||||
|
||||
# for dplyr's across()
|
||||
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
|
||||
# try to get current column, which will only be available when in across()
|
||||
ab <- tryCatch(cur_column_dplyr(),
|
||||
error = function(e) ab)
|
||||
}
|
||||
|
||||
# for auto-determining mo
|
||||
mo_var_found <- ""
|
||||
if (is.null(mo)) {
|
||||
tryCatch({
|
||||
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
|
||||
mo <- NULL
|
||||
try({
|
||||
mo <- suppressMessages(search_type_in_df(df, "mo"))
|
||||
}, silent = TRUE)
|
||||
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
|
||||
mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
|
||||
mo <- df[, mo, drop = TRUE]
|
||||
}
|
||||
}, error = function(e)
|
||||
stop_('No information was supplied about the microorganisms (missing argument `mo`). See ?as.rsi.\n\n',
|
||||
"To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
|
||||
"To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
|
||||
)
|
||||
}
|
||||
if (length(ab) == 1 && ab %like% "as.mic") {
|
||||
stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
|
||||
}
|
||||
|
||||
ab_coerced <- suppressWarnings(as.ab(ab))
|
||||
mo_coerced <- suppressWarnings(as.mo(mo))
|
||||
guideline_coerced <- get_guideline(guideline, reference_data)
|
||||
if (is.na(ab_coerced)) {
|
||||
message_("Returning NAs for unknown drug: '", font_bold(ab),
|
||||
"'. Rename this column to a drug name or code, and check the output with `as.ab()`.",
|
||||
add_fn = font_red,
|
||||
as_note = FALSE)
|
||||
return(as.rsi(rep(NA, length(x))))
|
||||
}
|
||||
if (length(mo_coerced) == 1) {
|
||||
mo_coerced <- rep(mo_coerced, length(x))
|
||||
}
|
||||
if (length(uti) == 1) {
|
||||
uti <- rep(uti, length(x))
|
||||
}
|
||||
|
||||
agent_formatted <- paste0("'", font_bold(ab), "'")
|
||||
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
|
||||
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
|
||||
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
|
||||
}
|
||||
message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
|
||||
agent_formatted,
|
||||
mo_var_found,
|
||||
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
|
||||
font_bold(guideline_coerced),
|
||||
"manually defined 'reference_data'"),
|
||||
"... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE)
|
||||
|
||||
result <- exec_as.rsi(method = "mic",
|
||||
as_rsi_method(method_short = "mic",
|
||||
method_long = "MIC values",
|
||||
x = x,
|
||||
mo = mo_coerced,
|
||||
ab = ab_coerced,
|
||||
guideline = guideline_coerced,
|
||||
mo = mo,
|
||||
ab = ab,
|
||||
guideline = guideline,
|
||||
uti = uti,
|
||||
conserve_capped_values = conserve_capped_values,
|
||||
add_intrinsic_resistance = add_intrinsic_resistance,
|
||||
reference_data = reference_data) # exec_as.rsi will return message 'OK'
|
||||
result
|
||||
reference_data = reference_data,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname as.rsi
|
||||
@ -446,88 +388,17 @@ as.rsi.disk <- function(x,
|
||||
add_intrinsic_resistance = FALSE,
|
||||
reference_data = AMR::rsi_translation,
|
||||
...) {
|
||||
meet_criteria(x)
|
||||
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
|
||||
meet_criteria(ab, allow_class = c("ab", "character"))
|
||||
meet_criteria(guideline, allow_class = "character", has_length = 1)
|
||||
meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
|
||||
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(reference_data, allow_class = "data.frame")
|
||||
check_reference_data(reference_data)
|
||||
|
||||
# for dplyr's across()
|
||||
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
|
||||
# try to get current column, which will only be available when in across()
|
||||
ab <- tryCatch(cur_column_dplyr(),
|
||||
error = function(e) ab)
|
||||
}
|
||||
|
||||
# for auto-determining mo
|
||||
mo_var_found <- ""
|
||||
if (is.null(mo)) {
|
||||
tryCatch({
|
||||
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
|
||||
mo <- NULL
|
||||
try({
|
||||
mo <- suppressMessages(search_type_in_df(df, "mo"))
|
||||
}, silent = TRUE)
|
||||
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
|
||||
mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
|
||||
mo <- df[, mo, drop = TRUE]
|
||||
}
|
||||
}, error = function(e)
|
||||
stop_('No information was supplied about the microorganisms (missing argument `mo`). See ?as.rsi.\n\n',
|
||||
"To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
|
||||
"To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
|
||||
)
|
||||
}
|
||||
if (length(ab) == 1 && ab %like% "as.disk") {
|
||||
stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
|
||||
}
|
||||
|
||||
ab_coerced <- suppressWarnings(as.ab(ab))
|
||||
mo_coerced <- suppressWarnings(as.mo(mo))
|
||||
guideline_coerced <- get_guideline(guideline, reference_data)
|
||||
if (is.na(ab_coerced)) {
|
||||
message_("Returning NAs for unknown drug: '", font_bold(ab),
|
||||
"'. Rename this column to a drug name or code, and check the output with `as.ab()`.",
|
||||
add_fn = font_red,
|
||||
as_note = FALSE)
|
||||
return(as.rsi(rep(NA, length(x))))
|
||||
}
|
||||
if (length(mo_coerced) == 1) {
|
||||
mo_coerced <- rep(mo_coerced, length(x))
|
||||
}
|
||||
if (length(uti) == 1) {
|
||||
uti <- rep(uti, length(x))
|
||||
}
|
||||
|
||||
agent_formatted <- paste0("'", font_bold(ab), "'")
|
||||
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
|
||||
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
|
||||
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
|
||||
}
|
||||
message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
|
||||
agent_formatted,
|
||||
mo_var_found,
|
||||
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
|
||||
font_bold(guideline_coerced),
|
||||
"manually defined 'reference_data'"),
|
||||
"... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE)
|
||||
|
||||
result <- exec_as.rsi(method = "disk",
|
||||
as_rsi_method(method_short = "disk",
|
||||
method_long = "disk diffusion zones",
|
||||
x = x,
|
||||
mo = mo_coerced,
|
||||
ab = ab_coerced,
|
||||
guideline = guideline_coerced,
|
||||
mo = mo,
|
||||
ab = ab,
|
||||
guideline = guideline,
|
||||
uti = uti,
|
||||
conserve_capped_values = FALSE,
|
||||
add_intrinsic_resistance = add_intrinsic_resistance,
|
||||
reference_data = reference_data) # exec_as.rsi will return message 'OK'
|
||||
result
|
||||
reference_data = reference_data,
|
||||
...)
|
||||
}
|
||||
|
||||
#' @rdname as.rsi
|
||||
@ -732,6 +603,105 @@ get_guideline <- function(guideline, reference_data) {
|
||||
guideline_param
|
||||
}
|
||||
|
||||
as_rsi_method <- function(method_short = "mic",
|
||||
method_long = "MIC values",
|
||||
x = x,
|
||||
mo = NULL,
|
||||
ab = deparse(substitute(x)),
|
||||
guideline = "EUCAST",
|
||||
uti = FALSE,
|
||||
conserve_capped_values = FALSE,
|
||||
add_intrinsic_resistance = FALSE,
|
||||
reference_data = AMR::rsi_translation,
|
||||
...) {
|
||||
meet_criteria(x)
|
||||
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
|
||||
meet_criteria(ab, allow_class = c("ab", "character"))
|
||||
meet_criteria(guideline, allow_class = "character", has_length = 1)
|
||||
meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
|
||||
meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(reference_data, allow_class = "data.frame")
|
||||
check_reference_data(reference_data)
|
||||
|
||||
# for dplyr's across()
|
||||
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
|
||||
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
|
||||
# try to get current column, which will only be available when in across()
|
||||
ab <- tryCatch(cur_column_dplyr(),
|
||||
error = function(e) ab)
|
||||
}
|
||||
|
||||
# for auto-determining mo
|
||||
mo_var_found <- ""
|
||||
if (is.null(mo)) {
|
||||
tryCatch({
|
||||
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
|
||||
mo <- NULL
|
||||
try({
|
||||
mo <- suppressMessages(search_type_in_df(df, "mo"))
|
||||
}, silent = TRUE)
|
||||
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
|
||||
mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
|
||||
mo <- df[, mo, drop = TRUE]
|
||||
}
|
||||
}, error = function(e) {
|
||||
mo <- NULL
|
||||
})
|
||||
}
|
||||
if (is.null(mo)) {
|
||||
stop_("No information was supplied about the microorganisms (missing argument `mo` and no column of class <mo> found). See ?as.rsi.\n\n",
|
||||
"To transform certain columns with e.g. mutate(), use `data %>% mutate(across(..., as.rsi, mo = x))`, where x is your column with microorganisms.\n",
|
||||
"To tranform all ", method_long, " in a data set, use `data %>% as.rsi()` or `data %>% mutate(across(where(is.", method_short, "), as.rsi))`.", call = FALSE)
|
||||
}
|
||||
|
||||
if (length(ab) == 1 && ab %like% paste0("as.", method_short)) {
|
||||
stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
|
||||
}
|
||||
|
||||
ab_coerced <- suppressWarnings(as.ab(ab))
|
||||
mo_coerced <- suppressWarnings(as.mo(mo))
|
||||
guideline_coerced <- get_guideline(guideline, reference_data)
|
||||
if (is.na(ab_coerced)) {
|
||||
message_("Returning NAs for unknown drug: '", font_bold(ab),
|
||||
"'. Rename this column to a drug name or code, and check the output with `as.ab()`.",
|
||||
add_fn = font_red,
|
||||
as_note = FALSE)
|
||||
return(as.rsi(rep(NA, length(x))))
|
||||
}
|
||||
if (length(mo_coerced) == 1) {
|
||||
mo_coerced <- rep(mo_coerced, length(x))
|
||||
}
|
||||
if (length(uti) == 1) {
|
||||
uti <- rep(uti, length(x))
|
||||
}
|
||||
|
||||
agent_formatted <- paste0("'", font_bold(ab), "'")
|
||||
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
|
||||
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
|
||||
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
|
||||
}
|
||||
message_("=> Interpreting ", method_long, " of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
|
||||
agent_formatted,
|
||||
mo_var_found,
|
||||
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
|
||||
font_bold(guideline_coerced),
|
||||
"manually defined 'reference_data'"),
|
||||
"... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE)
|
||||
result <- exec_as.rsi(method = method_short,
|
||||
x = x,
|
||||
mo = mo_coerced,
|
||||
ab = ab_coerced,
|
||||
guideline = guideline_coerced,
|
||||
uti = uti,
|
||||
conserve_capped_values = conserve_capped_values,
|
||||
add_intrinsic_resistance = add_intrinsic_resistance,
|
||||
reference_data = reference_data) # exec_as.rsi will return message 'OK'
|
||||
result
|
||||
}
|
||||
|
||||
exec_as.rsi <- function(method,
|
||||
x,
|
||||
mo,
|
||||
@ -744,7 +714,7 @@ exec_as.rsi <- function(method,
|
||||
metadata_mo <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
x_bak <- data.frame(x_mo = paste0(x, mo), stringsAsFactors = FALSE)
|
||||
df <- unique(data.frame(x, mo), stringsAsFactors = FALSE)
|
||||
df <- unique(data.frame(x, mo, x_mo = paste0(x, mo), stringsAsFactors = FALSE))
|
||||
x <- df$x
|
||||
mo <- df$mo
|
||||
|
||||
@ -754,7 +724,7 @@ exec_as.rsi <- function(method,
|
||||
x <- as.disk(x) # when as.rsi.disk is called directly
|
||||
}
|
||||
|
||||
warned <- FALSE
|
||||
rise_warning <- FALSE
|
||||
method_param <- toupper(method)
|
||||
|
||||
genera <- mo_genus(mo, language = NULL)
|
||||
@ -799,13 +769,6 @@ exec_as.rsi <- function(method,
|
||||
lookup_lancefield <- paste(mo_lancefield, ab)
|
||||
lookup_other <- paste(mo_other, ab)
|
||||
|
||||
if (length(unique(paste(trans$mo, trans$ab))) == length(unique(paste(trans$mo, trans$ab, trans$uti))) &&
|
||||
any(trans$uti == TRUE, na.rm = TRUE) && all(uti == FALSE)) {
|
||||
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
|
||||
warning_("Introducing NA: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " for some microorganisms is only available for (uncomplicated) urinary tract infections (UTI). Use argument `uti` to set which isolates are from urine. See ?as.rsi.", call = FALSE)
|
||||
warned <- TRUE
|
||||
}
|
||||
|
||||
any_is_intrinsic_resistant <- FALSE
|
||||
|
||||
for (i in seq_len(length(x))) {
|
||||
@ -815,7 +778,7 @@ exec_as.rsi <- function(method,
|
||||
if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
|
||||
if (guideline_coerced %unlike% "EUCAST") {
|
||||
if (message_not_thrown_before("as.rsi", "msg2")) {
|
||||
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
|
||||
warning_("in `as.rsi()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
|
||||
}
|
||||
} else {
|
||||
new_rsi[i] <- "R"
|
||||
@ -824,7 +787,7 @@ exec_as.rsi <- function(method,
|
||||
}
|
||||
|
||||
get_record <- trans %pm>%
|
||||
# no subsetting to UTI for now
|
||||
# no subsetting to UTI here
|
||||
subset(lookup %in% c(lookup_mo[i],
|
||||
lookup_genus[i],
|
||||
lookup_family[i],
|
||||
@ -833,6 +796,11 @@ exec_as.rsi <- function(method,
|
||||
lookup_lancefield[i],
|
||||
lookup_other[i]))
|
||||
|
||||
if (any(get_record$uti == TRUE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "msg3", ab)) {
|
||||
warning_("in `as.rsi()`: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use argument `uti` to set which isolates are from urine. See ?as.rsi.")
|
||||
rise_warning <- TRUE
|
||||
}
|
||||
|
||||
if (isTRUE(uti[i])) {
|
||||
get_record <- get_record %pm>%
|
||||
# be as specific as possible (i.e. prefer species over genus):
|
||||
@ -872,20 +840,21 @@ exec_as.rsi <- function(method,
|
||||
|
||||
if (any_is_intrinsic_resistant & guideline_coerced %like% "EUCAST" & !isTRUE(add_intrinsic_resistance)) {
|
||||
# found some intrinsic resistance, but was not applied
|
||||
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
|
||||
if (message_not_thrown_before("as.rsi", "msg3")) {
|
||||
warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE)
|
||||
if (message_not_thrown_before("as.rsi", "msg4")) {
|
||||
warning_("in `as.rsi()`: found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.")
|
||||
}
|
||||
warned <- TRUE
|
||||
rise_warning <- TRUE
|
||||
}
|
||||
|
||||
new_rsi <- x_bak %pm>%
|
||||
pm_left_join(data.frame(x_mo = paste0(df$x, df$mo), new_rsi,
|
||||
pm_left_join(data.frame(x_mo = paste0(x, mo), new_rsi,
|
||||
stringsAsFactors = FALSE),
|
||||
by = "x_mo") %pm>%
|
||||
pm_pull(new_rsi)
|
||||
|
||||
if (warned == FALSE) {
|
||||
if (isTRUE(rise_warning)) {
|
||||
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
|
||||
} else {
|
||||
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
|
||||
}
|
||||
|
||||
@ -937,13 +906,13 @@ freq.rsi <- function(x, ...) {
|
||||
.add_header = list(
|
||||
Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", paste(ab_atc(ab), collapse = "/"), ")"),
|
||||
`Drug group` = ab_group(ab, language = NULL),
|
||||
`%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
|
||||
digits = digits)))
|
||||
`%SI` = trimws(percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
|
||||
digits = digits))))
|
||||
} else {
|
||||
cleaner::freq.default(x = x, ...,
|
||||
.add_header = list(
|
||||
`%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
|
||||
digits = digits)))
|
||||
`%SI` = trimws(percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
|
||||
digits = digits))))
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -95,7 +95,7 @@ rsi_calc <- function(...,
|
||||
}
|
||||
|
||||
if (is.null(x)) {
|
||||
warning_("argument is NULL (check if columns exist): returning NA", call = FALSE)
|
||||
warning_("argument is NULL (check if columns exist): returning NA")
|
||||
if (as_percent == TRUE) {
|
||||
return(NA_character_)
|
||||
} else {
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@ -193,7 +193,7 @@ translate_AMR <- function(from,
|
||||
any_form_in_patterns <- tryCatch(
|
||||
any(from_unique %like% paste0("(", paste(gsub(" +\\(.*", "", df_trans$pattern), collapse = "|"), ")")),
|
||||
error = function(e) {
|
||||
warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call = FALSE)
|
||||
warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).")
|
||||
return(FALSE)
|
||||
})
|
||||
|
||||
|
||||
@ -27,7 +27,7 @@
|
||||
#'
|
||||
#' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
|
||||
#' @section WHOCC:
|
||||
#' \if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
|
||||
#' \if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr}
|
||||
#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>).
|
||||
#'
|
||||
#' These have become the gold standard for international drug utilisation monitoring and research.
|
||||
|
||||
28
R/zzz.R
28
R/zzz.R
@ -26,6 +26,11 @@
|
||||
# set up package environment, used by numerous AMR functions
|
||||
pkg_env <- new.env(hash = FALSE)
|
||||
pkg_env$mo_failed <- character(0)
|
||||
pkg_env$mo_field_abbreviations <- c("AIEC", "ATEC", "BORSA", "CRSM", "DAEC", "EAEC",
|
||||
"EHEC", "EIEC", "EPEC", "ETEC", "GISA", "MRPA",
|
||||
"MRSA", "MRSE", "MSSA", "MSSE", "NMEC", "PISP",
|
||||
"PRSP", "STEC", "UPEC", "VISA", "VISP", "VRE",
|
||||
"VRSA", "VRSP")
|
||||
|
||||
# determine info icon for messages
|
||||
utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
|
||||
@ -111,21 +116,7 @@ if (utf8_supported && !is_latex) {
|
||||
# Helper functions --------------------------------------------------------
|
||||
|
||||
create_AB_lookup <- function() {
|
||||
AB_lookup <- AMR::antibiotics
|
||||
AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
|
||||
AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[,
|
||||
c("ab", "atc", "cid", "name",
|
||||
colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
|
||||
drop = FALSE]),
|
||||
stringsAsFactors = FALSE)),
|
||||
function(x) {
|
||||
x <- generalise_antibiotic_name(unname(unlist(x)))
|
||||
x[x != ""]
|
||||
}))
|
||||
AB_lookup
|
||||
cbind(AMR::antibiotics, AB_LOOKUP)
|
||||
}
|
||||
|
||||
create_MO_lookup <- function() {
|
||||
@ -140,12 +131,7 @@ create_MO_lookup <- function() {
|
||||
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
|
||||
|
||||
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
|
||||
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
|
||||
MO_lookup$species,
|
||||
MO_lookup$subspecies)))
|
||||
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
|
||||
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
|
||||
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
|
||||
MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
|
||||
|
||||
# add a column with only "e coli" like combinations
|
||||
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
|
||||
|
||||
@ -1 +1,2 @@
|
||||
* This package has a data folder size of ~1.7 MB, which might return a NOTE on some R CMD CHECKs. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, as it has been in the 16 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.
|
||||
Extra release for fixing image options, as requested by CRAN team on 17 February 2022 (Kurt Hornik).
|
||||
|
||||
|
||||
Binary file not shown.
@ -122,9 +122,21 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
|
||||
"mo", drop = TRUE]
|
||||
}
|
||||
}
|
||||
create_MO_fullname_lower <- function() {
|
||||
MO_lookup <- AMR::microorganisms
|
||||
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
|
||||
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
|
||||
MO_lookup$species,
|
||||
MO_lookup$subspecies)))
|
||||
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
|
||||
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
|
||||
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
|
||||
MO_lookup$fullname_lower
|
||||
}
|
||||
MO_CONS <- create_species_cons_cops("CoNS")
|
||||
MO_COPS <- create_species_cons_cops("CoPS")
|
||||
MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
|
||||
MO_FULLNAME_LOWER <- create_MO_fullname_lower()
|
||||
|
||||
# antibiotic groups
|
||||
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
|
||||
@ -160,6 +172,24 @@ AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
|
||||
# this will be used for documentation:
|
||||
DEFINED_AB_GROUPS <- ls(envir = globalenv())
|
||||
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
|
||||
create_AB_lookup <- function() {
|
||||
AB_lookup <- AMR::antibiotics
|
||||
AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)
|
||||
AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name)
|
||||
AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[,
|
||||
c("ab", "atc", "cid", "name",
|
||||
colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]),
|
||||
drop = FALSE]),
|
||||
stringsAsFactors = FALSE)),
|
||||
function(x) {
|
||||
x <- generalise_antibiotic_name(unname(unlist(x)))
|
||||
x[x != ""]
|
||||
}))
|
||||
AB_lookup[, colnames(AB_lookup)[colnames(AB_lookup) %like% "^generalised"]]
|
||||
}
|
||||
AB_LOOKUP <- create_AB_lookup()
|
||||
|
||||
# Export to package as internal data ----
|
||||
usethis::use_data(EUCAST_RULES_DF,
|
||||
@ -169,6 +199,8 @@ usethis::use_data(EUCAST_RULES_DF,
|
||||
MO_CONS,
|
||||
MO_COPS,
|
||||
MO_STREP_ABCG,
|
||||
MO_FULLNAME_LOWER,
|
||||
AB_LOOKUP,
|
||||
AB_AMINOGLYCOSIDES,
|
||||
AB_AMINOPENICILLINS,
|
||||
AB_ANTIFUNGALS,
|
||||
|
||||
@ -26,8 +26,8 @@
|
||||
# Reproduction of the `microorganisms` data set
|
||||
|
||||
# Data retrieved from the Catalogue of Life (CoL):
|
||||
# https://download.catalogueoflife.org/col/monthly/life/
|
||||
# (download latest dwca, such as https://download.catalogueoflife.org/col/monthly/2020-12-01_dwca.zip)
|
||||
# https://download.catalogueoflife.org/col/monthly/
|
||||
# (download latest dwca, such as https://download.catalogueoflife.org/col/monthly/2022-01-14_dwca.zip)
|
||||
# Data retrieved from the Global Biodiversity Information Facility (GBIF):
|
||||
# https://doi.org/10.15468/rffz4x
|
||||
#
|
||||
|
||||
@ -43,7 +43,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -57,7 +57,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="https://msberends.github.io/AMR/#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="https://msberends.github.io/AMR/#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -210,7 +210,7 @@ Content not found. Please use links in the navbar.
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -420,7 +420,7 @@ END OF TERMS AND CONDITIONS
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 40 KiB After Width: | Height: | Size: 38 KiB |
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|
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|
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|
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|
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|
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|
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|
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|
Before Width: | Height: | Size: 69 KiB After Width: | Height: | Size: 76 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 46 KiB After Width: | Height: | Size: 49 KiB |
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to apply EUCAST rules</h1>
|
||||
@ -402,7 +402,7 @@
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
|
||||
@ -295,8 +295,8 @@
|
||||
<span class="co"># Table 3 - Enterobacteriaceae... OK.</span>
|
||||
<span class="co"># Table 4 - Pseudomonas aeruginosa... OK.</span>
|
||||
<span class="co"># Table 5 - Acinetobacter spp.... OK.</span>
|
||||
<span class="co"># Warning: NA introduced for isolates where the available percentage of antimicrobial</span>
|
||||
<span class="co"># classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
|
||||
<span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span>
|
||||
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
|
||||
<p>Only results with ‘R’ are considered as resistance. Use <code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
|
||||
<p>Determining multidrug-resistant organisms (MDRO), according to: Guideline: Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Author(s): Magiorakos AP, Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x</p>
|
||||
<p>(16 isolates had no test results)</p>
|
||||
@ -320,17 +320,17 @@ Unique: 2</p>
|
||||
<td align="left">1</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">1601</td>
|
||||
<td align="right">92.60%</td>
|
||||
<td align="right">92.6%</td>
|
||||
<td align="right">1601</td>
|
||||
<td align="right">92.60%</td>
|
||||
<td align="right">92.6%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Multi-drug-resistant (MDR)</td>
|
||||
<td align="right">128</td>
|
||||
<td align="right">7.40%</td>
|
||||
<td align="right">7.4%</td>
|
||||
<td align="right">1729</td>
|
||||
<td align="right">100.00%</td>
|
||||
<td align="right">100.0%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -358,19 +358,19 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||
<span class="co"># 1 I R I S R S</span>
|
||||
<span class="co"># 2 I S R R S R</span>
|
||||
<span class="co"># 3 R I S I R S</span>
|
||||
<span class="co"># 4 S S I R I S</span>
|
||||
<span class="co"># 5 S R S S S I</span>
|
||||
<span class="co"># 6 S R R S R I</span>
|
||||
<span class="co"># 1 S R S I R S</span>
|
||||
<span class="co"># 2 I I S S I I</span>
|
||||
<span class="co"># 3 I S R R R S</span>
|
||||
<span class="co"># 4 S S I S R S</span>
|
||||
<span class="co"># 5 R R S I R I</span>
|
||||
<span class="co"># 6 R S R S S I</span>
|
||||
<span class="co"># kanamycin</span>
|
||||
<span class="co"># 1 S</span>
|
||||
<span class="co"># 2 I</span>
|
||||
<span class="co"># 3 R</span>
|
||||
<span class="co"># 4 R</span>
|
||||
<span class="co"># 1 I</span>
|
||||
<span class="co"># 2 S</span>
|
||||
<span class="co"># 3 S</span>
|
||||
<span class="co"># 4 I</span>
|
||||
<span class="co"># 5 I</span>
|
||||
<span class="co"># 6 R</span></code></pre></div>
|
||||
<span class="co"># 6 I</span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
|
||||
@ -390,7 +390,7 @@ Unique: 2</p>
|
||||
<span class="co"># management of drug-resistant tuberculosis</span>
|
||||
<span class="co"># Author(s): WHO (World Health Organization)</span>
|
||||
<span class="co"># Version: WHO/HTM/TB/2014.11, 2014</span>
|
||||
<span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></code></pre></div>
|
||||
<span class="co"># Source: https://www.who.int/publications/i/item/9789241548809</span></code></pre></div>
|
||||
<p>Create a frequency table of the results:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></code></pre></div>
|
||||
@ -398,7 +398,7 @@ Unique: 2</p>
|
||||
<p>Class: factor > ordered (numeric)<br>
|
||||
Length: 5,000<br>
|
||||
Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant <…<br>
|
||||
Available: 5,000 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Available: 5,000 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 5</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
@ -413,40 +413,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3250</td>
|
||||
<td align="right">65.00%</td>
|
||||
<td align="right">3250</td>
|
||||
<td align="right">65.00%</td>
|
||||
<td align="right">3244</td>
|
||||
<td align="right">64.88%</td>
|
||||
<td align="right">3244</td>
|
||||
<td align="right">64.88%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">975</td>
|
||||
<td align="right">19.50%</td>
|
||||
<td align="right">4225</td>
|
||||
<td align="right">84.50%</td>
|
||||
<td align="right">990</td>
|
||||
<td align="right">19.80%</td>
|
||||
<td align="right">4234</td>
|
||||
<td align="right">84.68%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">474</td>
|
||||
<td align="right">9.48%</td>
|
||||
<td align="right">4699</td>
|
||||
<td align="right">93.98%</td>
|
||||
<td align="right">417</td>
|
||||
<td align="right">8.34%</td>
|
||||
<td align="right">4651</td>
|
||||
<td align="right">93.02%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">203</td>
|
||||
<td align="right">4.06%</td>
|
||||
<td align="right">4902</td>
|
||||
<td align="right">98.04%</td>
|
||||
<td align="right">248</td>
|
||||
<td align="right">4.96%</td>
|
||||
<td align="right">4899</td>
|
||||
<td align="right">97.98%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">98</td>
|
||||
<td align="right">1.96%</td>
|
||||
<td align="right">101</td>
|
||||
<td align="right">2.02%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@ -470,7 +470,7 @@ Unique: 5</p>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="PCA_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
|
||||
@ -199,18 +199,18 @@
|
||||
|
||||
|
||||
<p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
|
||||
<div class="section level1">
|
||||
<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h1>
|
||||
<div class="section level2">
|
||||
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h2>
|
||||
</div>
|
||||
<div class="section level1">
|
||||
<h1 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
|
||||
</h1>
|
||||
<div class="section level2">
|
||||
<h2 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
|
||||
</h2>
|
||||
<p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></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/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||||
<span class="co"># Rows: 2,000</span>
|
||||
<span class="co"># Columns: 49</span>
|
||||
<span class="co"># $ date <span style="color: #949494; font-style: italic;"><date></span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
|
||||
@ -283,9 +283,9 @@
|
||||
<span class="co"># <span style="color: #BCBCBC;">5</span> Caryophanales Gemella <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="co"># <span style="color: #BCBCBC;">6</span> Caryophanales Listeria <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span></code></pre></div>
|
||||
</div>
|
||||
<div class="section level1">
|
||||
<h1 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
|
||||
</h1>
|
||||
<div class="section level2">
|
||||
<h2 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
|
||||
</h2>
|
||||
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">pca_result</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
|
||||
@ -305,9 +305,9 @@
|
||||
<span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></code></pre>
|
||||
<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
|
||||
</div>
|
||||
<div class="section level1">
|
||||
<h1 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
|
||||
</h1>
|
||||
<div class="section level2">
|
||||
<h2 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
|
||||
</h2>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
|
||||
@ -340,7 +340,7 @@
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
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|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
if (linkList[j].innerHTML === "") {
|
||||
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|
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||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
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}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,13 +185,13 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
|
||||
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
||||
|
||||
<h4 data-toc-skip class="date">23 December 2021</h4>
|
||||
<h4 data-toc-skip class="date">27 March 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>SPSS.Rmd</code></div>
|
||||
@ -226,7 +226,7 @@
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R has a huge community.</strong></p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">430,288 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">440,893 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
||||
@ -241,7 +241,7 @@
|
||||
<li>
|
||||
<p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
|
||||
<p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/" class="external-link">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
|
||||
<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2021, I don’t see any reason why SPSS would be of any better use than R.</p>
|
||||
<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2022, I don’t see any reason why SPSS would be of any better use than R.</p>
|
||||
</li>
|
||||
</ul>
|
||||
<p>To demonstrate the first point:</p>
|
||||
@ -414,7 +414,7 @@
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="WHONET_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to work with WHONET data</h1>
|
||||
@ -215,7 +215,7 @@
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span> <span class="co"># this package</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span> <span class="co"># this package</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
|
||||
<p>We will have to transform some variables to simplify and automate the analysis:</p>
|
||||
<ul>
|
||||
@ -238,7 +238,7 @@
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 500<br>
|
||||
Available: 500 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Available: 500 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 37</p>
|
||||
<p>Shortest: 11<br>
|
||||
Longest: 40</p>
|
||||
@ -334,7 +334,7 @@ Longest: 40</p>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>(omitted 27 entries, n = 56 [11.20%])</p>
|
||||
<p>(omitted 27 entries, n = 56 [11.2%])</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># our transformed antibiotic columns</span>
|
||||
<span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span>
|
||||
@ -413,7 +413,7 @@ Drug group: Beta-lactams/penicillins<br>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
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|
||||
}
|
||||
}
|
||||
});
|
||||
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|
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|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Benchmarks</h1>
|
||||
@ -202,7 +202,7 @@
|
||||
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/" class="external-link">microbenchmark</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
|
||||
<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
|
||||
<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, its taxonomic kingdom).</p>
|
||||
@ -222,23 +222,23 @@
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
|
||||
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 10.0 12.0 20.0 12.0 15.0 53 25</span>
|
||||
<span class="co"># as.mo("stau") 49.0 54.0 72.0 58.0 91.0 97 25</span>
|
||||
<span class="co"># as.mo("STAU") 50.0 54.0 71.0 57.0 90.0 110 25</span>
|
||||
<span class="co"># as.mo("staaur") 10.0 12.0 17.0 12.0 14.0 51 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 10.0 12.0 17.0 12.0 14.0 54 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 26.0 27.0 40.0 31.0 56.0 74 25</span>
|
||||
<span class="co"># as.mo("S aureus") 26.0 27.0 39.0 29.0 58.0 68 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 3.5 3.9 6.6 4.1 4.8 38 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 230.0 240.0 250.0 240.0 250.0 280 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 180.0 190.0 200.0 190.0 200.0 290 25</span>
|
||||
<span class="co"># as.mo("MRSA") 11.0 12.0 19.0 13.0 14.0 50 25</span>
|
||||
<span class="co"># as.mo("VISA") 21.0 22.0 32.0 25.0 50.0 60 25</span></code></pre></div>
|
||||
<span class="co"># as.mo("sau") 19.0 20.0 25.0 20.0 26.0 55 25</span>
|
||||
<span class="co"># as.mo("stau") 94.0 95.0 110.0 100.0 130.0 140 25</span>
|
||||
<span class="co"># as.mo("STAU") 92.0 97.0 110.0 110.0 120.0 140 25</span>
|
||||
<span class="co"># as.mo("staaur") 19.0 19.0 24.0 20.0 21.0 56 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 19.0 20.0 21.0 20.0 20.0 49 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 54.0 57.0 72.0 64.0 86.0 96 25</span>
|
||||
<span class="co"># as.mo("S aureus") 55.0 55.0 72.0 57.0 90.0 100 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 5.6 5.7 8.5 5.8 6.2 40 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 360.0 370.0 400.0 400.0 420.0 550 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 280.0 290.0 300.0 300.0 320.0 350 25</span>
|
||||
<span class="co"># as.mo("MRSA") 19.0 20.0 24.0 20.0 21.0 51 25</span>
|
||||
<span class="co"># as.mo("VISA") 34.0 34.0 48.0 36.0 65.0 73 25</span></code></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 47 times slower to determine.</p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 69 times slower to determine.</p>
|
||||
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
|
||||
@ -258,8 +258,8 @@
|
||||
<span class="co"># what do these values look like? They are of class <mo>:</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="co"># Class <mo></span>
|
||||
<span class="co"># [1] B_STPHY_AURS B_STRPT_EQNS B_KLBSL_PNMN B_STPHY_EPDR B_STPHY_AURS</span>
|
||||
<span class="co"># [6] B_CRYNB_STRT</span>
|
||||
<span class="co"># [1] B_ENTRBC_CLOC B_ESCHR_COLI B_STRPT_PYGN B_STPHY_AURS B_ESCHR_COLI </span>
|
||||
<span class="co"># [6] B_STRPT_PNMN</span>
|
||||
|
||||
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
@ -272,11 +272,11 @@
|
||||
<span class="co"># now let's see:</span>
|
||||
<span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 196 209 274 223 364 388 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.223 seconds. That is 112 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
<span class="co"># mo_name(x) 259 264 357 299 451 509 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.299 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
|
||||
@ -287,13 +287,13 @@
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
|
||||
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 8.00 9.16 9.19 9.28 9.46 9.73 10</span>
|
||||
<span class="co"># B 23.40 27.20 32.60 27.90 28.10 80.20 10</span>
|
||||
<span class="co"># C 1.85 2.25 2.40 2.47 2.62 2.90 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0025 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<span class="co"># A 11.90 12.10 13.0 13.50 13.70 13.80 10</span>
|
||||
<span class="co"># B 60.90 61.20 67.7 66.20 66.90 99.70 10</span>
|
||||
<span class="co"># C 2.91 2.94 3.2 3.32 3.38 3.46 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0033 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
|
||||
@ -304,17 +304,17 @@
|
||||
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
|
||||
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.76 1.80 2.07 1.95 2.26 2.90 10</span>
|
||||
<span class="co"># B 1.69 1.73 1.90 1.81 2.03 2.48 10</span>
|
||||
<span class="co"># C 1.71 1.77 1.92 1.91 2.05 2.17 10</span>
|
||||
<span class="co"># D 1.68 1.71 1.76 1.76 1.82 1.88 10</span>
|
||||
<span class="co"># E 1.68 1.70 1.89 1.89 2.04 2.26 10</span>
|
||||
<span class="co"># F 1.67 1.75 1.93 1.89 2.11 2.35 10</span>
|
||||
<span class="co"># G 1.70 1.76 1.97 1.88 2.12 2.43 10</span>
|
||||
<span class="co"># H 1.67 1.71 1.83 1.75 1.98 2.14 10</span></code></pre></div>
|
||||
<span class="co"># A 2.92 2.93 3.02 2.94 3.02 3.40 10</span>
|
||||
<span class="co"># B 2.87 2.90 3.14 3.09 3.32 3.71 10</span>
|
||||
<span class="co"># C 2.91 2.94 3.15 3.12 3.33 3.46 10</span>
|
||||
<span class="co"># D 2.86 2.90 3.05 2.96 3.27 3.30 10</span>
|
||||
<span class="co"># E 2.87 2.88 3.03 2.96 3.16 3.29 10</span>
|
||||
<span class="co"># F 2.92 2.95 3.08 2.98 3.29 3.35 10</span>
|
||||
<span class="co"># G 2.89 2.96 3.04 2.99 3.11 3.29 10</span>
|
||||
<span class="co"># H 2.85 2.95 3.11 3.08 3.31 3.38 10</span></code></pre></div>
|
||||
<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
@ -347,19 +347,19 @@
|
||||
ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
|
||||
sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
|
||||
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># da 1.9470 2.0220 2.190 2.0720 2.358 3.234 100</span>
|
||||
<span class="co"># de 1.9560 2.0330 3.649 2.1610 2.401 50.670 100</span>
|
||||
<span class="co"># en 0.8937 0.9124 1.022 0.9776 1.120 1.748 100</span>
|
||||
<span class="co"># es 1.9710 2.0290 2.216 2.1000 2.391 3.109 100</span>
|
||||
<span class="co"># fr 1.8280 1.8960 3.214 1.9420 2.237 71.550 100</span>
|
||||
<span class="co"># it 1.9370 1.9970 2.163 2.0610 2.339 3.210 100</span>
|
||||
<span class="co"># nl 1.9710 2.0280 2.698 2.1110 2.421 49.340 100</span>
|
||||
<span class="co"># pt 1.8920 1.9600 2.119 2.0200 2.261 3.265 100</span>
|
||||
<span class="co"># ru 1.8630 1.9420 2.779 2.0270 2.335 66.660 100</span>
|
||||
<span class="co"># sv 1.8680 1.9190 4.062 1.9890 2.263 78.870 100</span></code></pre></div>
|
||||
<span class="co"># da 3.546 3.643 4.072 3.704 3.832 35.930 100</span>
|
||||
<span class="co"># de 3.597 3.659 4.422 3.734 3.839 36.400 100</span>
|
||||
<span class="co"># en 1.672 1.726 1.804 1.767 1.794 2.259 100</span>
|
||||
<span class="co"># es 3.609 3.685 4.496 3.760 3.843 36.540 100</span>
|
||||
<span class="co"># fr 3.484 3.567 3.725 3.654 3.713 6.281 100</span>
|
||||
<span class="co"># it 3.523 3.615 4.419 3.720 3.787 36.720 100</span>
|
||||
<span class="co"># nl 3.614 3.676 3.805 3.732 3.838 4.703 100</span>
|
||||
<span class="co"># pt 3.512 3.595 4.077 3.659 3.789 37.310 100</span>
|
||||
<span class="co"># ru 3.556 3.647 4.057 3.680 3.812 35.230 100</span>
|
||||
<span class="co"># sv 3.540 3.642 4.093 3.732 3.803 36.340 100</span></code></pre></div>
|
||||
<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
|
||||
</div>
|
||||
</div>
|
||||
@ -379,7 +379,7 @@
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
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const codeList = document.getElementsByClassName("sourceCode");
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|
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|
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if (linkList[j].innerHTML === "") {
|
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linkList[j].setAttribute('aria-hidden', 'true');
|
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|
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|
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|
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});
|
||||
Binary file not shown.
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@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -58,7 +58,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -190,7 +190,7 @@
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">23 December 2021</h4>
|
||||
<h4 data-toc-skip class="date">09 May 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||
@ -199,42 +199,71 @@
|
||||
|
||||
|
||||
|
||||
<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
|
||||
<p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
|
||||
<p>All reference data (about microorganisms, antibiotics, R/SI
|
||||
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
|
||||
reliable, up-to-date and freely available. We continually export our
|
||||
data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also
|
||||
supply tab separated files that are machine-readable and suitable for
|
||||
input in any software program, such as laboratory information
|
||||
systems.</p>
|
||||
<p>On this page, we explain how to download them and how the structure
|
||||
of the data sets look like.</p>
|
||||
<p class="dataset-within-r">
|
||||
If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.
|
||||
If you are reading this page from within R, please
|
||||
<a href="https://msberends.github.io/AMR/articles/datasets.html">visit
|
||||
our website</a>, which is automatically updated with every code change.
|
||||
</p>
|
||||
<div class="section level2">
|
||||
<h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a>
|
||||
</h2>
|
||||
<p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p>A data set with 70,760 rows and 16 columns, containing the following
|
||||
column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>,
|
||||
<em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>,
|
||||
<em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>,
|
||||
<em>species_id</em>, <em>source</em>, <em>prevalence</em> and
|
||||
<em>snomed</em>.</p>
|
||||
<p>This data set is in R available as <code>microorganisms</code>, after
|
||||
you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R
|
||||
file</a> (1.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel
|
||||
file</a> (6.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (13.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain
|
||||
text file</a> (13.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (30.7 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS
|
||||
file</a> (30.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (16.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS
|
||||
file</a> (16.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (27.5 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
|
||||
file</a> (27.5 MB)</li>
|
||||
</ul>
|
||||
<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
|
||||
<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not
|
||||
contain SNOMED codes, as their file size would exceed 100 MB; the file
|
||||
size limit of GitHub.</strong> Advice? Use R instead.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
|
||||
</h3>
|
||||
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
|
||||
<p>Our full taxonomy of microorganisms is based on the authoritative and
|
||||
comprehensive:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a>
|
||||
(included version: 2019)</li>
|
||||
<li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
|
||||
Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public
|
||||
Health Information Network Vocabulary Access and Distribution System
|
||||
(PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
@ -427,40 +456,64 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<div class="section level2">
|
||||
<h2 id="microorganisms-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-previously-accepted-names"></a>
|
||||
</h2>
|
||||
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
|
||||
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
|
||||
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p>A data set with 14,338 rows and 4 columns, containing the following
|
||||
column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and
|
||||
<em>prevalence</em>.</p>
|
||||
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the
|
||||
scientific reference to the old taxonomic entries, i.e. of column
|
||||
<em>‘fullname’</em>. For the scientific reference of the new names,
|
||||
i.e. of column <em>‘fullname_new’</em>, see the
|
||||
<code>microorganisms</code> data set.</p>
|
||||
<p>This data set is in R available as <code>microorganisms.old</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R
|
||||
file</a> (0.2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel
|
||||
file</a> (0.5 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain
|
||||
text file</a> (1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS
|
||||
file</a> (2.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (1.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS
|
||||
file</a> (1.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata
|
||||
file</a> (2 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
|
||||
</h3>
|
||||
<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
|
||||
<p>This data set contains old, previously accepted taxonomic names. The
|
||||
data sources are the same as the <code>microorganisms</code> data
|
||||
set:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
|
||||
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a>
|
||||
(included version: 2019)</li>
|
||||
<li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
|
||||
Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
|
||||
</h3>
|
||||
<p>Example rows when filtering on <em>Escherichia</em>:</p>
|
||||
<table class="table">
|
||||
<table style="width:100%;" class="table">
|
||||
<colgroup>
|
||||
<col width="31%">
|
||||
<col width="30%">
|
||||
<col width="24%">
|
||||
<col width="13%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">fullname</th>
|
||||
<th align="center">fullname_new</th>
|
||||
@ -493,31 +546,50 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<div class="section level2">
|
||||
<h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
|
||||
</h2>
|
||||
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
|
||||
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>A data set with 464 rows and 14 columns, containing the following
|
||||
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
|
||||
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
|
||||
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
|
||||
<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
|
||||
<p>This data set is in R available as <code>antibiotics</code>, after
|
||||
you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R
|
||||
file</a> (33 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel
|
||||
file</a> (65 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain
|
||||
text file</a> (0.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS
|
||||
file</a> (1.8 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS
|
||||
file</a> (0.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
|
||||
file</a> (0.3 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
|
||||
</h3>
|
||||
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||||
<p>This data set contains all EARS-Net and ATC codes gathered from WHO
|
||||
and WHONET, and all compound IDs from PubChem. It also contains all
|
||||
brand names (synonyms) as found on PubChem and Defined Daily Doses
|
||||
(DDDs) for oral and parenteral administration.</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
|
||||
Collaborating Centre for Drug Statistics Methodology</a> (note: this may
|
||||
not be used for commercial purposes, but is freely available from the
|
||||
WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
|
||||
National Library of Medicine</a></li>
|
||||
<li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
@ -597,7 +669,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">Beta-lactams/penicillins</td>
|
||||
<td align="center">J01CR02</td>
|
||||
<td align="center">Beta-lactam antibacterials, penicillins</td>
|
||||
<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
|
||||
<td align="center">Combinations of penicillins, incl. beta-lactamase
|
||||
inhibitors</td>
|
||||
<td align="center">a/c, amcl, aml, …</td>
|
||||
<td align="center">amocla, amoclan, amoclav, …</td>
|
||||
<td align="center">1.5</td>
|
||||
@ -661,31 +734,49 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<div class="section level2">
|
||||
<h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a>
|
||||
</h2>
|
||||
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
|
||||
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p>A data set with 102 rows and 9 columns, containing the following
|
||||
column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
|
||||
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
|
||||
<em>iv_ddd</em> and <em>iv_units</em>.</p>
|
||||
<p>This data set is in R available as <code>antivirals</code>, after you
|
||||
load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R
|
||||
file</a> (5 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel
|
||||
file</a> (14 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain
|
||||
text file</a> (16 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS
|
||||
file</a> (80 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS
|
||||
file</a> (68 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata
|
||||
file</a> (67 kB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
|
||||
</h3>
|
||||
<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
|
||||
<p>This data set contains all ATC codes gathered from WHO and all
|
||||
compound IDs from PubChem. It also contains all brand names (synonyms)
|
||||
as found on PubChem and Defined Daily Doses (DDDs) for oral and
|
||||
parenteral administration.</p>
|
||||
<ul>
|
||||
<li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
|
||||
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
|
||||
Collaborating Centre for Drug Statistics Methodology</a> (note: this may
|
||||
not be used for commercial purposes, but is freely available from the
|
||||
WHO CC website for personal use)</li>
|
||||
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
|
||||
National Library of Medicine</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
@ -719,7 +810,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">J05AF06</td>
|
||||
<td align="center">441300</td>
|
||||
<td align="center">Abacavir</td>
|
||||
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
|
||||
<td align="center">Nucleoside and nucleotide reverse transcriptase
|
||||
inhibitors</td>
|
||||
<td align="center">Abacavir, Abacavir sulfate, Ziagen</td>
|
||||
<td align="center">0.6</td>
|
||||
<td align="center">g</td>
|
||||
@ -730,7 +822,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">J05AB01</td>
|
||||
<td align="center">135398513</td>
|
||||
<td align="center">Aciclovir</td>
|
||||
<td align="center">Nucleosides and nucleotides excl. reverse transcriptase inhibitors</td>
|
||||
<td align="center">Nucleosides and nucleotides excl. reverse
|
||||
transcriptase inhibitors</td>
|
||||
<td align="center">Acicloftal, Aciclovier, Aciclovir, …</td>
|
||||
<td align="center">4.0</td>
|
||||
<td align="center">g</td>
|
||||
@ -741,8 +834,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">J05AF08</td>
|
||||
<td align="center">60871</td>
|
||||
<td align="center">Adefovir dipivoxil</td>
|
||||
<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
|
||||
<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, …</td>
|
||||
<td align="center">Nucleoside and nucleotide reverse transcriptase
|
||||
inhibitors</td>
|
||||
<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir
|
||||
Dipivoxil, …</td>
|
||||
<td align="center">10.0</td>
|
||||
<td align="center">mg</td>
|
||||
<td align="center"></td>
|
||||
@ -788,27 +883,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<div class="section level2">
|
||||
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
|
||||
</h2>
|
||||
<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
|
||||
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p>A data set with 134,956 rows and 2 columns, containing the following
|
||||
column names:<br><em>mo</em> and <em>ab</em>.</p>
|
||||
<p>This data set is in R available as <code>intrinsic_resistant</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R
|
||||
file</a> (78 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel
|
||||
file</a> (0.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (5.1 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain
|
||||
text file</a> (5.1 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (10.4 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS
|
||||
file</a> (10.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (7.4 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS
|
||||
file</a> (7.4 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (10.2 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
|
||||
file</a> (10.2 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
|
||||
</h3>
|
||||
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
|
||||
<p>This data set contains all defined intrinsic resistance by EUCAST of
|
||||
all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">‘EUCAST
|
||||
Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’
|
||||
v3.3</a> (2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
|
||||
@ -1055,27 +1162,40 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<div class="section level2">
|
||||
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
|
||||
</h2>
|
||||
<p>A data set with 20,318 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p>A data set with 20,318 rows and 11 columns, containing the following
|
||||
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
|
||||
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
|
||||
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (39 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
|
||||
file</a> (39 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
|
||||
file</a> (0.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.7 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
|
||||
text file</a> (1.7 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.6 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
|
||||
file</a> (3.6 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
|
||||
file</a> (2.2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.4 MB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
|
||||
file</a> (3.4 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
|
||||
</h3>
|
||||
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST (2011-2021).</p>
|
||||
<p>This data set contains interpretation rules for MIC values and disk
|
||||
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
|
||||
(2011-2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
|
||||
@ -1193,33 +1313,57 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<div class="section level2">
|
||||
<h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a>
|
||||
</h2>
|
||||
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
|
||||
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p>A data set with 169 rows and 9 columns, containing the following
|
||||
column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
|
||||
<em>dose_times</em>, <em>administration</em>, <em>notes</em>,
|
||||
<em>original_txt</em> and <em>eucast_version</em>.</p>
|
||||
<p>This data set is in R available as <code>dosage</code>, after you
|
||||
load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R
|
||||
file</a> (3 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel
|
||||
file</a> (14 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain
|
||||
text file</a> (15 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS
|
||||
file</a> (52 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS
|
||||
file</a> (45 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata
|
||||
file</a> (44 kB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
|
||||
</h3>
|
||||
<p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
|
||||
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
|
||||
<p>EUCAST breakpoints used in this package are based on the dosages in
|
||||
this data set.</p>
|
||||
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
|
||||
Breakpoint Tables’ v11.0</a> (2021).</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
|
||||
</h3>
|
||||
<table class="table">
|
||||
<colgroup>
|
||||
<col width="4%">
|
||||
<col width="10%">
|
||||
<col width="15%">
|
||||
<col width="10%">
|
||||
<col width="9%">
|
||||
<col width="13%">
|
||||
<col width="5%">
|
||||
<col width="16%">
|
||||
<col width="13%">
|
||||
</colgroup>
|
||||
<thead><tr class="header">
|
||||
<th align="center">ab</th>
|
||||
<th align="center">name</th>
|
||||
@ -1321,7 +1465,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
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const codeList = document.getElementsByClassName("sourceCode");
|
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for (var i = 0; i < codeList.length; i++) {
|
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var linkList = codeList[i].getElementsByTagName('a');
|
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for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -17,7 +17,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -189,7 +189,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
|
||||
@ -206,7 +206,7 @@
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
|
||||
<span class="co"># (if not yet installed, install with:)</span>
|
||||
<span class="co"># install.packages(c("tidyverse", "AMR"))</span></code></pre></div>
|
||||
@ -216,18 +216,18 @@
|
||||
</h2>
|
||||
<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR data analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
|
||||
<p>It is basically as easy as:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># or:</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>example_isolates <span class="sc">%>%</span> </span>
|
||||
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> model <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
|
||||
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>predict_TZP <span class="ot"><-</span> example_isolates <span class="sc">%>%</span> </span>
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
|
||||
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true"></a><span class="kw">resistance_predict</span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true"></a></span>
|
||||
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true"></a><span class="co"># or:</span></span>
|
||||
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true"></a>example_isolates <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true"></a> model <span class="st">"binomial"</span>)</span>
|
||||
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true"></a></span>
|
||||
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
|
||||
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true"></a>predict_TZP <-<span class="st"> </span>example_isolates <span class="op">%>%</span><span class="st"> </span></span>
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true"></a> <span class="dt">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
|
||||
<pre><code><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre>
|
||||
@ -264,7 +264,8 @@
|
||||
<span class="co"># 27 2028 0.43730688 0.3418075 0.5328063 NA NA 0.43730688</span>
|
||||
<span class="co"># 28 2029 0.46175755 0.3597639 0.5637512 NA NA 0.46175755</span>
|
||||
<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span>
|
||||
<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span></code></pre></div>
|
||||
<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span>
|
||||
<span class="co"># 31 2032 0.53574417 0.4169574 0.6545309 NA NA 0.53574417</span></code></pre></div>
|
||||
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
|
||||
@ -371,7 +372,7 @@
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
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@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
|
||||
</header><div class="row">
|
||||
</header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
|
||||
@ -242,7 +242,7 @@
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@ -0,0 +1,15 @@
|
||||
// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
|
||||
// v0.0.1
|
||||
// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
|
||||
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
const codeList = document.getElementsByClassName("sourceCode");
|
||||
for (var i = 0; i < codeList.length; i++) {
|
||||
var linkList = codeList[i].getElementsByTagName('a');
|
||||
for (var j = 0; j < linkList.length; j++) {
|
||||
if (linkList[j].innerHTML === "") {
|
||||
linkList[j].setAttribute('aria-hidden', 'true');
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -1,12 +0,0 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
@ -17,7 +17,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -30,7 +30,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
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|
||||
How to
|
||||
@ -218,7 +218,7 @@
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-427" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-4277" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
</ul></div>
|
||||
@ -273,7 +273,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer></div>
|
||||
|
||||
@ -47,7 +47,7 @@
|
||||
</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="Released version">1.8.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -61,7 +61,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
@ -195,7 +195,7 @@
|
||||
<code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
|
||||
</h1></div>
|
||||
<blockquote>
|
||||
<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST guideline for intrinsic resistance</a> (v3.3, October 2021) is now supported, the CLSI 2021 interpretation guideline is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).</p>
|
||||
<p>Update March 2022: All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
|
||||
</blockquote>
|
||||
<div class="section level3">
|
||||
<h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
|
||||
@ -214,7 +214,7 @@
|
||||
</h5>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
|
||||
|
||||
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
@ -340,7 +340,7 @@
|
||||
</h4>
|
||||
<p>The development of this package is part of, related to, or made possible by:</p>
|
||||
<div align="center">
|
||||
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
|
||||
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
@ -414,13 +414,13 @@
|
||||
<div class="section level4">
|
||||
<h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
|
||||
</h4>
|
||||
<p>This package contains the complete taxonomic tree of almost all ~70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
|
||||
<p>This package contains the complete taxonomic tree of almost all ~71,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
|
||||
<p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
|
||||
</div>
|
||||
<div class="section level4">
|
||||
<h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
|
||||
</h4>
|
||||
<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
|
||||
<p>This package contains <strong>all ~570 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
|
||||
<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
|
||||
</div>
|
||||
@ -561,7 +561,7 @@
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
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