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(v1.7.1.9022) rely on vctrs for ab selectors

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dr. M.S. (Matthijs) Berends
2021-07-23 21:42:11 +02:00
parent 0ec81cc12e
commit 4e1efd902c
130 changed files with 3785 additions and 2960 deletions
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5
DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9021
Date: 2021-07-12
Version: 1.7.1.9022
Date: 2021-07-23
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@@ -57,6 +57,7 @@ Suggests:
skimr,
tidyr,
tinytest,
vctrs,
xml2
VignetteBuilder: knitr,rmarkdown
URL: https://github.com/msberends/AMR, https://msberends.github.io/AMR

53
NEWS.md
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@@ -1,8 +1,8 @@
# `AMR` 1.7.1.9021
## <small>Last updated: 12 July 2021</small>
# `AMR` 1.7.1.9022
## <small>Last updated: 23 July 2021</small>
### Changed
* Previously implemented `ggplot2::gggplot()` generics for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>` did not follow the `ggplot2` logic, and were replaced with `autoplot()` generics.
* Previously implemented `ggplot2::ggplot()` generics for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>` did not follow the `ggplot2` logic, and were replaced with `autoplot()` generics.
* Antibiotic class selectors (see `ab_class()`)
* They now also work in R-3.0 and R-3.1, supporting every version of R since 2013
* Added more selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()`
@@ -17,12 +17,13 @@
* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish
* When warnings are thrown because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
* `ab_name()` gained argument `snake_case`, which is useful for column renaming
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is bug ggplot2#4511, soon to be fixed)
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)
* Fix for minor translation errors
* Fix for the MIC interpretation of *Morganellaceae* (such as *Morganella* and *Proteus*) when using the EUCAST 2021 guideline
* Improved algorithm for generating random MICs with `random_mic()`
* Improved plot legends for MICs and disk diffusion values
# `AMR` 1.7.1
# AMR 1.7.1
### Breaking change
* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
@@ -96,7 +97,7 @@
* All unit tests are now processed by the `tinytest` package, instead of the `testthat` package. The `testthat` package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the `tinytest` package is very lightweight and dependency-free.
# `AMR` 1.6.0
# AMR 1.6.0
### New
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@@ -190,7 +191,7 @@
* Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)
# `AMR` 1.5.0
# AMR 1.5.0
### New
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
@@ -267,7 +268,7 @@
* Added CodeFactor as a continuous code review to this package: <https://www.codefactor.io/repository/github/msberends/amr/>
* Added Dr. Rogier Schade as contributor
# `AMR` 1.4.0
# AMR 1.4.0
### New
* Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the arguments `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`.
@@ -339,7 +340,7 @@
* Removed unnecessary references to the `base` package
* Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file
# `AMR` 1.3.0
# AMR 1.3.0
### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@@ -392,7 +393,7 @@
### Other
* Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
# `AMR` 1.2.0
# AMR 1.2.0
### Breaking
* Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
@@ -430,7 +431,7 @@
* Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`
* Removed function `read.4d()`, that was only useful for reading data from an old test database.
# `AMR` 1.1.0
# AMR 1.1.0
### New
* Support for easy principal component analysis for AMR, using the new `pca()` function
@@ -452,7 +453,7 @@
* Support for the upcoming `dplyr` version 1.0.0
* More robust assigning for classes `rsi` and `mic`
# `AMR` 1.0.1
# AMR 1.0.1
### Changed
* Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
@@ -468,7 +469,7 @@
* Added `uti` (as abbreviation of urinary tract infections) as argument to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
* Info printing in functions `eucast_rules()`, `first_isolate()`, `mdro()` and `resistance_predict()` will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)
# `AMR` 1.0.0
# AMR 1.0.0
This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
@@ -516,7 +517,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Full support for the upcoming R 4.0
* Removed unnecessary `AMR::` calls
# `AMR` 0.9.0
# AMR 0.9.0
### Breaking
* Adopted Adeolu *et al.* (2016), [PMID 27620848](https:/pubmed.ncbi.nlm.nih.gov/27620848/) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
@@ -582,7 +583,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request
* Added Dr. Sofia Ny as contributor
# `AMR` 0.8.0
# AMR 0.8.0
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new argument `include_unknown`:
@@ -711,7 +712,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
* Cleaned the coding style of every single syntax line in this package with the help of the `lintr` package
# `AMR` 0.7.1
# AMR 0.7.1
#### New
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
@@ -772,7 +773,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
#### Other
* Fixed a note thrown by CRAN tests
# `AMR` 0.7.0
# AMR 0.7.0
#### New
* Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
@@ -830,13 +831,13 @@ This software is now out of beta and considered stable. Nonetheless, this packag
#### Other
* Support for R 3.6.0 and later by providing support for [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html)
# `AMR` 0.6.1
# AMR 0.6.1
#### Changed
* Fixed a critical bug when using `eucast_rules()` with `verbose = TRUE`
* Coercion of microbial IDs are now written to the package namespace instead of the user's home folder, to comply with the CRAN policy
# `AMR` 0.6.0
# AMR 0.6.0
**New website!**
@@ -1029,7 +1030,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
#### Other
* Updated licence text to emphasise GPL 2.0 and that this is an R package.
# `AMR` 0.5.0
# AMR 0.5.0
#### New
* Repository moved to GitLab
@@ -1112,7 +1113,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Updated vignettes to comply with README
# `AMR` 0.4.0
# AMR 0.4.0
#### New
* The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms.
@@ -1223,7 +1224,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
#### Other
* More unit tests to ensure better integrity of functions
# `AMR` 0.3.0
# AMR 0.3.0
#### New
* **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated.
@@ -1293,7 +1294,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Windows: https://ci.appveyor.com/project/msberends/amr
* Added thesis advisors to DESCRIPTION file
# `AMR` 0.2.0
# AMR 0.2.0
#### New
* Full support for Windows, Linux and macOS
@@ -1328,7 +1329,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
# `AMR` 0.1.1
# AMR 0.1.1
* `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
* Edited column names to comply with GLIMS, the laboratory information system
@@ -1336,6 +1337,6 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
* Added barplots for `rsi` and `mic` classes
# `AMR` 0.1.0
# AMR 0.1.0
* First submission to CRAN.

23
R/aa_helper_functions.R
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@@ -135,7 +135,6 @@ check_dataset_integrity <- function() {
" the AMR package from working correctly: ",
vector_and(overwritten, quotes = "'"),
".\nPlease rename your object", plural[3], ".", call = FALSE)
remember_thrown_message("dataset_overwritten")
}
}
# check if other packages did not overwrite our data sets
@@ -258,7 +257,6 @@ search_type_in_df <- function(x, type, info = TRUE) {
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
}
message_(msg)
remember_thrown_message(fn = paste0("search_", type))
}
}
found
@@ -771,10 +769,11 @@ get_current_data <- function(arg_name, call) {
} else {
examples <- ""
}
stop_("this function must be used inside valid dplyr selection verbs or inside a data.frame call",
stop_("this function must be used inside a `dplyr` verb or `data.frame` call",
examples,
call = call)
} else {
# mimic a base R error that the argument is missing
stop_("argument `", arg_name, "` is missing with no default", call = call)
}
}
@@ -840,16 +839,18 @@ unique_call_id <- function(entire_session = FALSE) {
}
}
remember_thrown_message <- function(fn, entire_session = FALSE) {
message_not_thrown_before <- function(fn, entire_session = FALSE) {
# this is to prevent that messages/notes will be printed for every dplyr group
# e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative())
assign(x = paste0("thrown_msg.", fn),
value = unique_call_id(entire_session = entire_session),
envir = pkg_env)
}
message_not_thrown_before <- function(fn, entire_session = FALSE) {
is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session))
test_out <- is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]],
unique_call_id(entire_session = entire_session))
if (isTRUE(test_out)) {
# message was not thrown before - remember this so on the next run it will return FALSE:
assign(x = paste0("thrown_msg.", fn),
value = unique_call_id(entire_session = entire_session),
envir = pkg_env)
}
test_out
}
has_colour <- function() {

25
R/ab_class_selectors.R
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@@ -33,7 +33,7 @@
#' @details
#' These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but also work in base \R and not only in `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
#'
#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the [ab_class()] function to filter/select on a manually defined antibiotic class.
#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the [ab_class()] function to filter/select on a manually defined antibiotic class.
#'
#' @section Full list of supported agents:
#'
@@ -312,7 +312,6 @@ ab_selector <- function(function_name,
sort = TRUE), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
"This warning will be shown once per session.",
call = FALSE)
remember_thrown_message(paste0("ab_class.untreatable.", function_name), entire_session = TRUE)
}
ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
}
@@ -343,8 +342,8 @@ ab_selector <- function(function_name,
# get the columns with a group names in the chosen ab class
agents <- ab_in_data[names(ab_in_data) %in% abx]
if (message_not_thrown_before(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))) {
if (message_not_thrown_before(paste0(function_name, ".", paste(sort(agents), collapse = "|")))) {
if (length(agents) == 0) {
message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
} else {
@@ -360,21 +359,10 @@ ab_selector <- function(function_name,
ifelse(length(agents) == 1, "column ", "columns "),
vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
}
remember_thrown_message(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))
}
if (!is.null(attributes(vars_df)$type) &&
attributes(vars_df)$type %in% c("dplyr_cur_data_all", "base_R") &&
!any(as.character(sys.calls()) %like% paste0("(across|if_any|if_all)\\((c\\()?[a-z(), ]*", function_name))) {
structure(unname(agents),
class = c("ab_selector", "character"))
} else {
# don't return with "ab_selector" class if method is a dplyr selector,
# dplyr::select() will complain:
# > Subscript has the wrong type `ab_selector`.
# > It must be numeric or character.
unname(agents)
}
structure(unname(agents),
class = c("ab_selector", "character"))
}
#' @method c ab_selector
@@ -412,7 +400,6 @@ all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
#' @export
#' @noRd
all.ab_selector <- function(..., na.rm = FALSE) {
# this is all() for
all_any_ab_selector("all", ..., na.rm = na.rm)
}
@@ -458,7 +445,6 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
`==.ab_selector` <- function(e1, e2) {
calls <- as.character(match.call())
fn_name <- calls[2]
# keep only the ... in c(...)
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
if (is_any(fn_name)) {
type <- "any"
@@ -481,7 +467,6 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
`!=.ab_selector` <- function(e1, e2) {
calls <- as.character(match.call())
fn_name <- calls[2]
# keep only the ... in c(...)
fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
if (is_any(fn_name)) {
type <- "any"

2
R/count.R
View File

@@ -149,7 +149,6 @@ count_R <- function(..., only_all_tested = FALSE) {
count_IR <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" being resistant. This note will be shown once for this session.", as_note = FALSE)
remember_thrown_message("count_IR")
}
tryCatch(
rsi_calc(...,
@@ -186,7 +185,6 @@ count_SI <- function(..., only_all_tested = FALSE) {
count_S <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_S", entire_session = TRUE)) {
message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
remember_thrown_message("count_S")
}
tryCatch(
rsi_calc(...,

1
R/eucast_rules.R
View File

@@ -1072,7 +1072,6 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0)
message_("Dosages for antimicrobial drugs, as meant for ",
format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ",
font_red("This note will be shown once per session."))
remember_thrown_message(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE)
}
ab <- as.ab(ab)

4
R/first_isolate.R
View File

@@ -264,7 +264,6 @@ first_isolate <- function(x = NULL,
"")),
as_note = FALSE,
add_fn = font_black)
remember_thrown_message("first_isolate.method")
}
# try to find columns based on type
@@ -364,7 +363,6 @@ first_isolate <- function(x = NULL,
message_("Excluding test codes: ", toString(paste0("'", testcodes_exclude, "'")),
add_fn = font_black,
as_note = FALSE)
remember_thrown_message("first_isolate.excludingtestcodes")
}
if (is.null(col_specimen)) {
@@ -378,7 +376,6 @@ first_isolate <- function(x = NULL,
message_("Excluding other than specimen group '", specimen_group, "'",
add_fn = font_black,
as_note = FALSE)
remember_thrown_message("first_isolate.excludingspecimen")
}
}
if (!is.null(col_keyantimicrobials)) {
@@ -474,7 +471,6 @@ first_isolate <- function(x = NULL,
add_fn = font_black,
as_note = FALSE)
}
remember_thrown_message("first_isolate.type")
}
type_param <- type

5
R/ggplot_rsi.R
View File

@@ -389,10 +389,11 @@ scale_rsi_colours <- function(...,
names_susceptible <- c("S", "SI", "IS", "S+I", "I+S", "susceptible", "Susceptible",
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
"replacement", drop = TRUE]))
names_incr_exposure <- c("I", "intermediate", "increased exposure", "incr. exposure", "Increased exposure", "Incr. exposure",
names_incr_exposure <- c("I", "intermediate", "increased exposure", "incr. exposure",
"Increased exposure", "Incr. exposure", "Susceptible, incr. exp.",
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Intermediate"),
"replacement", drop = TRUE]),
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Incr. exposure"),
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible, incr. exp."),
"replacement", drop = TRUE]))
names_resistant <- c("R", "IR", "RI", "R+I", "I+R", "resistant", "Resistant",
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),

2
R/guess_ab_col.R
View File

@@ -121,7 +121,7 @@ get_column_abx <- function(x,
# these columns did not exist in the last call, so add them
new_cols_rsi <- get_column_abx(x[, new_cols, drop = FALSE], reuse_previous_result = FALSE, info = FALSE, sort = FALSE)
current <- c(current, new_cols_rsi)
# order according to data in current call
# order according to columns in current call
current <- current[match(colnames(x)[colnames(x) %in% current], current)]
}

6
R/italicise_taxonomy.R
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@@ -44,11 +44,11 @@
#' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
#'
#' # since ggplot2 supports no markdown (yet), use
#' # italicise_taxonomy() and the `ggtext` pkg for titles:
#' # italicise_taxonomy() and the `ggtext` package for titles:
#' \donttest{
#' if (require("ggplot2") && require("ggtext")) {
#' ggplot(example_isolates$AMC,
#' title = italicise_taxonomy("Amoxi/clav in E. coli")) +
#' autoplot(example_isolates$AMC,
#' title = italicise_taxonomy("Amoxi/clav in E. coli")) +
#' theme(plot.title = ggtext::element_markdown())
#' }
#' }

1
R/key_antimicrobials.R
View File

@@ -177,7 +177,6 @@ key_antimicrobials <- function(x = NULL,
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.",
call = FALSE)
remember_thrown_message(paste0("key_antimicrobials.", name))
}
generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])

11
R/mdro.R
View File

@@ -187,13 +187,9 @@ mdro <- function(x = NULL,
check_dataset_integrity()
info.bak <- info
if (message_not_thrown_before("mdro")) {
remember_thrown_message("mdro")
} else {
# don't thrown info's more than once per call
info <- FALSE
}
# don't thrown info's more than once per call
info <- message_not_thrown_before("mdro")
if (interactive() & verbose == TRUE & info == TRUE) {
txt <- paste0("WARNING: In Verbose mode, the mdro() function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.",
"\n\nThis may overwrite your existing data if you use e.g.:",
@@ -1416,7 +1412,6 @@ mdro <- function(x = NULL,
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)
remember_thrown_message("mdro.availability")
}
# set these -1s to NA
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_

2
R/mo_property.R
View File

@@ -481,7 +481,6 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
message_("Determining intrinsic resistance based on ",
format_eucast_version_nr(3.2, markdown = FALSE), ". ",
font_red("This note will be shown once per session."))
remember_thrown_message("intrinsic_resistant_version", entire_session = TRUE)
}
# runs against internal vector: INTRINSIC_R (see zzz.R)
@@ -758,7 +757,6 @@ find_mo_col <- function(fn) {
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
if (message_not_thrown_before(fn = fn)) {
message_("Using column '", font_bold(mo), "' as input for `", fn, "()`")
remember_thrown_message(fn = fn)
}
return(df[, mo, drop = TRUE])
} else {

6
R/plot.R
View File

@@ -265,7 +265,7 @@ autoplot.mic <- function(object,
if (any(colours_RSI %in% cols_sub$cols)) {
vals <- c("Resistant" = colours_RSI[1],
"Susceptible" = colours_RSI[2],
"Incr. exposure" = colours_RSI[3],
"Susceptible, incr. exp." = colours_RSI[3],
"Intermediate" = colours_RSI[3])
names(vals) <- translate_AMR(names(vals), language = language)
p <- p +
@@ -482,7 +482,7 @@ autoplot.disk <- function(object,
if (any(colours_RSI %in% cols_sub$cols)) {
vals <- c("Resistant" = colours_RSI[1],
"Susceptible" = colours_RSI[2],
"Incr. exposure" = colours_RSI[3],
"Susceptible, incr. exp." = colours_RSI[3],
"Intermediate" = colours_RSI[3])
names(vals) <- translate_AMR(names(vals), language = language)
p <- p +
@@ -686,7 +686,7 @@ plot_prepare_table <- function(x, expand) {
plot_name_of_I <- function(guideline) {
if (guideline %unlike% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
# interpretation since 2019
"Incr. exposure"
"Susceptible, incr. exp."
} else {
# interpretation until 2019
"Intermediate"

52
R/random.R
View File

@@ -27,7 +27,7 @@
#'
#' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.
#' @inheritSection lifecycle Stable Lifecycle
#' @param size desired size of the returned vector
#' @param size desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank.
#' @param mo any [character] that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any [character] that can be coerced to a valid antimicrobial agent code with [as.ab()]
#' @param prob_RSI a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)
@@ -55,27 +55,36 @@
#' random_disk(100, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#' random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#' }
random_mic <- function(size, mo = NULL, ab = NULL, ...) {
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
random_mic <- function(size = NULL, mo = NULL, ab = NULL, ...) {
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
if (is.null(size)) {
size <- NROW(get_current_data(arg_name = "size", call = -3))
}
random_exec("MIC", size = size, mo = mo, ab = ab)
}
#' @rdname random
#' @export
random_disk <- function(size, mo = NULL, ab = NULL, ...) {
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
random_disk <- function(size = NULL, mo = NULL, ab = NULL, ...) {
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
if (is.null(size)) {
size <- NROW(get_current_data(arg_name = "size", call = -3))
}
random_exec("DISK", size = size, mo = mo, ab = ab)
}
#' @rdname random
#' @export
random_rsi <- function(size, prob_RSI = c(0.33, 0.33, 0.33), ...) {
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
random_rsi <- function(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) {
meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
meet_criteria(prob_RSI, allow_class = c("numeric", "integer"), has_length = 3)
if (is.null(size)) {
size <- NROW(get_current_data(arg_name = "size", call = -3))
}
sample(as.rsi(c("R", "S", "I")), size = size, replace = TRUE, prob = prob_RSI)
}
@@ -111,23 +120,22 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
warning_("No rows found that match ab '", ab, "', ignoring argument `ab`", call = FALSE)
}
}
if (type == "MIC") {
# all valid MIC levels
valid_range <- as.mic(levels(as.mic(1)))
set_range_max <- max(df$breakpoint_R)
if (log(set_range_max, 2) %% 1 == 0) {
# return powers of 2
valid_range <- unique(as.double(valid_range))
# add 1-3 higher MIC levels to set_range_max
set_range_max <- 2 ^ (log(set_range_max, 2) + sample(c(1:3), 1))
set_range <- as.mic(valid_range[log(valid_range, 2) %% 1 == 0 & valid_range <= set_range_max])
} else {
# no power of 2, return factors of 2 to left and right side
valid_mics <- suppressWarnings(as.mic(set_range_max / (2 ^ c(-3:3))))
set_range <- valid_mics[!is.na(valid_mics)]
# set range
mic_range <- c(0.001, 0.002, 0.005, 0.010, 0.025, 0.0625, 0.125, 0.250, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256)
# get highest/lowest +/- random 1 to 3 higher factors of two
max_range <- mic_range[min(length(mic_range),
which(mic_range == max(df$breakpoint_R)) + sample(c(1:3), 1))]
min_range <- mic_range[max(1,
which(mic_range == min(df$breakpoint_S)) - sample(c(1:3), 1))]
mic_range_new <- mic_range[mic_range <= max_range & mic_range >= min_range]
if (length(mic_range_new) == 0) {
mic_range_new <- mic_range
}
out <- as.mic(sample(set_range, size = size, replace = TRUE))
out <- as.mic(sample(mic_range_new, size = size, replace = TRUE))
# 50% chance that lowest will get <= and highest will get >=
if (stats::runif(1) > 0.5) {
out[out == min(out)] <- paste0("<=", out[out == min(out)])

12
R/rsi.R
View File

@@ -294,16 +294,15 @@ as.rsi.default <- function(x, ...) {
LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
trans_S <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
trans_I <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern %in% c("Incr. exposure", "Intermediate")),
trans_I <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern %in% c("Incr. exposure", "Susceptible, incr. exp.", "Intermediate")),
LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
x <- gsub(paste0(unique(trans_R[!is.na(trans_R)]), collapse = "|"), "R", x, ignore.case = TRUE)
x <- gsub(paste0(unique(trans_S[!is.na(trans_S)]), collapse = "|"), "S", x, ignore.case = TRUE)
x <- gsub(paste0(unique(trans_I[!is.na(trans_I)]), collapse = "|"), "I", x, ignore.case = TRUE)
# replace all English textual input
x <- gsub("res(is(tant)?)?", "R", x, ignore.case = TRUE)
x <- gsub("sus(cep(tible)?)?", "S", x, ignore.case = TRUE)
x <- gsub("int(er(mediate)?)?", "I", x, ignore.case = TRUE)
x <- gsub("inc(r(eased)?)? exp[a-z]*", "I", x, ignore.case = TRUE)
x[x %like% "([^a-z]|^)res(is(tant)?)?"] <- "R"
x[x %like% "([^a-z]|^)sus(cep(tible)?)?"] <- "S"
x[x %like% "([^a-z]|^)int(er(mediate)?)?|incr.*exp"] <- "I"
# remove all spaces
x <- gsub(" +", "", x)
# remove all MIC-like values: numbers, operators and periods
@@ -776,7 +775,6 @@ exec_as.rsi <- function(method,
if (guideline_coerced != guideline) {
if (message_not_thrown_before("as.rsi")) {
message_("Using guideline ", font_bold(guideline_coerced), " as input for `guideline`.")
remember_thrown_message("as.rsi")
}
}
@@ -815,7 +813,6 @@ exec_as.rsi <- function(method,
if (guideline_coerced %unlike% "EUCAST") {
if (message_not_thrown_before("as.rsi2")) {
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
remember_thrown_message("as.rsi2")
}
} else {
new_rsi[i] <- "R"
@@ -880,7 +877,6 @@ exec_as.rsi <- function(method,
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
if (message_not_thrown_before("as.rsi3")) {
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)
remember_thrown_message("as.rsi3")
}
warned <- TRUE
}

1
R/rsi_calc.R
View File

@@ -152,7 +152,6 @@ rsi_calc <- function(...,
" your_data %>% mutate_if(is.rsi.eligible, as.rsi)\n",
" your_data %>% mutate(across(where(is.rsi.eligible), as.rsi))",
call = FALSE)
remember_thrown_message("rsi_calc")
}
}

BIN
R/sysdata.rda
View File

Binary file not shown.

74
R/vctrs.R Normal file
View File

@@ -0,0 +1,74 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# These are all S3 implementations for the vctrs package,
# that is used internally by tidyverse packages such as dplyr.
# They are to convert AMR-specific classes to bare characters and integers.
# All of them will be exported using s3_register() in R/zzz.R when loading the package.
# S3: ab
vec_ptype2.character.ab <- function(x, y, ...) {
x
}
vec_ptype2.ab.character <- function(x, y, ...) {
y
}
vec_cast.character.ab <- function(x, to, ...) {
unclass(x)
}
# S3: mo
vec_ptype2.character.mo <- function(x, y, ...) {
x
}
vec_ptype2.mo.character <- function(x, y, ...) {
y
}
vec_cast.character.mo <- function(x, to, ...) {
unclass(x)
}
# S3: disk
vec_ptype2.integer.disk <- function(x, y, ...) {
x
}
vec_ptype2.disk.integer <- function(x, y, ...) {
y
}
vec_cast.integer.disk <- function(x, to, ...) {
unclass(x)
}
# S3: ab_selector
# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
vec_ptype2.character.ab_selector <- function(x, y, ...) {
x
}
vec_ptype2.ab_selector.character <- function(x, y, ...) {
y
}
vec_cast.character.ab_selector <- function(x, to, ...) {
unclass(x)
}

17
R/zzz.R
View File

@@ -56,15 +56,29 @@ if (utf8_supported && !is_latex) {
# Support for frequency tables from the cleaner package
s3_register("cleaner::freq", "mo")
s3_register("cleaner::freq", "rsi")
# Support from skim() from the skimr package
# Support for skim() from the skimr package
s3_register("skimr::get_skimmers", "mo")
s3_register("skimr::get_skimmers", "rsi")
s3_register("skimr::get_skimmers", "mic")
s3_register("skimr::get_skimmers", "disk")
# Support for autoplot() from the ggplot2 package
s3_register("ggplot2::autoplot", "rsi")
s3_register("ggplot2::autoplot", "mic")
s3_register("ggplot2::autoplot", "disk")
s3_register("ggplot2::autoplot", "resistance_predict")
# Support vctrs package for use in e.g. dplyr verbs
s3_register("vctrs::vec_ptype2", "ab.character")
s3_register("vctrs::vec_ptype2", "character.ab")
s3_register("vctrs::vec_cast", "character.ab")
s3_register("vctrs::vec_ptype2", "mo.character")
s3_register("vctrs::vec_ptype2", "character.mo")
s3_register("vctrs::vec_cast", "character.mo")
s3_register("vctrs::vec_ptype2", "ab_selector.character")
s3_register("vctrs::vec_ptype2", "character.ab_selector")
s3_register("vctrs::vec_cast", "character.ab_selector")
s3_register("vctrs::vec_ptype2", "disk.integer")
s3_register("vctrs::vec_ptype2", "integer.disk")
s3_register("vctrs::vec_cast", "integer.disk")
# if mo source exists, fire it up (see mo_source())
try({
@@ -75,6 +89,7 @@ if (utf8_supported && !is_latex) {
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
# they can't be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR"))

1
_pkgdown.yml
View File

@@ -32,6 +32,7 @@ development:
news:
one_page: true
cran_dates: true
navbar:
title: "AMR (for R)"

BIN
data-raw/AMR_latest.tar.gz
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Binary file not shown.

4
data-raw/translations.tsv
View File

@@ -32,8 +32,10 @@ vegetative TRUE TRUE FALSE FALSE vegetativ vegetatief vegetativo vegetativo vég
([([ ]*?)Group TRUE TRUE FALSE FALSE \\1Gruppe \\1Groep \\1Grupo \\1Gruppo \\1Groupe \\1Grupo
no .*growth TRUE FALSE FALSE FALSE keine? .*wachstum geen .*groei no .*crecimientonon sem .*crescimento pas .*croissance sem .*crescimento
no|not TRUE FALSE FALSE FALSE keine? geen|niet no|sin sem non sem
Susceptible TRUE FALSE FALSE FALSE Empfindlich Gevoelig Susceptible
Intermediate TRUE FALSE FALSE FALSE Mittlere Intermediair Intermedio
Susceptible, incr. exp. FALSE TRUE FALSE FALSE Empfindlich, erh Belastung Gevoelig, hoge dosis
susceptible, incr. exp. FALSE TRUE FALSE FALSE empfindlich, erh Belastung gevoelig, hoge dosis
Susceptible TRUE FALSE FALSE FALSE Empfindlich Gevoelig Susceptible
Incr. exposure TRUE FALSE FALSE FALSE Empfindlich, erh Belastung 'Incr. exposure' 'Incr. exposure'
Resistant TRUE FALSE FALSE FALSE Resistent Resistent Resistente
antibiotic TRUE TRUE FALSE FALSE Antibiotikum antibioticum antibiótico
1 pattern regular_expr case_sensitive affect_ab_name affect_mo_name de nl es it fr pt
32 ([([ ]*?)Group TRUE TRUE FALSE FALSE \\1Gruppe \\1Groep \\1Grupo \\1Gruppo \\1Groupe \\1Grupo
33 no .*growth TRUE FALSE FALSE FALSE keine? .*wachstum geen .*groei no .*crecimientonon sem .*crescimento pas .*croissance sem .*crescimento
34 no|not TRUE FALSE FALSE FALSE keine? geen|niet no|sin sem non sem
Susceptible TRUE FALSE FALSE FALSE Empfindlich Gevoelig Susceptible
35 Intermediate TRUE FALSE FALSE FALSE Mittlere Intermediair Intermedio
36 Susceptible, incr. exp. FALSE TRUE FALSE FALSE Empfindlich, erh Belastung Gevoelig, hoge dosis
37 susceptible, incr. exp. FALSE TRUE FALSE FALSE empfindlich, erh Belastung gevoelig, hoge dosis
38 Susceptible TRUE FALSE FALSE FALSE Empfindlich Gevoelig Susceptible
39 Incr. exposure TRUE FALSE FALSE FALSE Empfindlich, erh Belastung 'Incr. exposure' 'Incr. exposure'
40 Resistant TRUE FALSE FALSE FALSE Resistent Resistent Resistente
41 antibiotic TRUE TRUE FALSE FALSE Antibiotikum antibioticum antibiótico

167
docs/404.html
View File

@@ -1,76 +1,35 @@
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<head>
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@@ -187,13 +189,13 @@
</header><script src="EUCAST_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
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<h1 data-toc-skip>How to apply EUCAST rules</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
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@@ -202,21 +204,21 @@
<div id="introduction" class="section level2">
<h2 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h2>
<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">on their website</a>:</p>
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h2>
<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">on their website</a>:</p>
<blockquote>
<p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
</blockquote>
<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and unusual phenotypes (v3.2, 2020).</p>
<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and unusual phenotypes (v3.2, 2020).</p>
<p>Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
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<h2 class="hasAnchor">
<a href="#examples" class="anchor"></a>Examples</h2>
<a href="#examples" class="anchor" aria-hidden="true"></a>Examples</h2>
<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
<code class="sourceCode R"><span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
<span class="st">"Escherichia"</span><span class="op">)</span>,
ampicillin <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span>
<span class="va">oops</span>
@@ -230,16 +232,16 @@
<span class="co"># 2 Escherichia S</span></code></pre></div>
<p>A more convenient function is <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
<span class="st">"ampicillin"</span><span class="op">)</span>
<span class="co"># [1] TRUE FALSE</span>
<span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
<span class="co"># [1] TRUE FALSE</span></code></pre></div>
<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,
<code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,
<span class="st">"Enterococcus faecalis"</span>,
<span class="st">"Escherichia coli"</span>,
<span class="st">"Klebsiella pneumoniae"</span>,
@@ -398,11 +400,13 @@
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@@ -411,5 +415,7 @@
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12
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@@ -0,0 +1,12 @@
// 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++) {
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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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View File

@@ -27,6 +27,8 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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@@ -39,7 +41,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
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@@ -47,14 +49,14 @@
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@@ -63,77 +65,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
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Conduct AMR analysis
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<li>
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Get properties of an antibiotic
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Other: benchmarks
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@@ -142,14 +144,14 @@
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@@ -164,7 +166,7 @@
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@@ -172,7 +174,7 @@
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@@ -187,13 +189,13 @@
</header><script src="MDR_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
</header><script src="MDR_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
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<div class="page-header toc-ignore">
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
<div class="hidden name"><code>MDR.Rmd</code></div>
</div>
@@ -203,50 +205,50 @@
<p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine which micro-organisms are multi-drug resistant organisms (MDRO).</p>
<div id="type-of-input" class="section level3">
<h3 class="hasAnchor">
<a href="#type-of-input" class="anchor"></a>Type of input</h3>
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a regular <code>data.frame</code>. It tries to automatically determine the right columns for info about your isolates, like the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
<a href="#type-of-input" class="anchor" aria-hidden="true"></a>Type of input</h3>
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a regular <code>data.frame</code>. It tries to automatically determine the right columns for info about your isolates, such as the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
<p>For WHONET data (and most other data), all settings are automatically set correctly.</p>
</div>
<div id="guidelines" class="section level3">
<h3 class="hasAnchor">
<a href="#guidelines" class="anchor"></a>Guidelines</h3>
<p>The function support multiple guidelines. You can select a guideline with the <code>guideline</code> parameter. Currently supported guidelines are (case-insensitive):</p>
<a href="#guidelines" class="anchor" aria-hidden="true"></a>Guidelines</h3>
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function support multiple guidelines. You can select a guideline with the <code>guideline</code> parameter. Currently supported guidelines are (case-insensitive):</p>
<ul>
<li>
<p><code>guideline = "CMI2012"</code> (default)</p>
<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext">link</a>)</p>
<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext" class="external-link">link</a>)</p>
</li>
<li>
<p><code>guideline = "EUCAST3.2"</code> (or simply <code>guideline = "EUCAST"</code>)</p>
<p>The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf">link</a>)</p>
<p>The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">link</a>)</p>
</li>
<li>
<p><code>guideline = "EUCAST3.1"</code></p>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</p>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">link</a>)</p>
</li>
<li>
<p><code>guideline = "TB"</code></p>
<p>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” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/">link</a>)</p>
<p>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” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/" class="external-link">link</a>)</p>
</li>
<li>
<p><code>guideline = "MRGN"</code></p>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p>
<p>The German national guideline - Mueller <em>et al.</em> (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p>
</li>
<li>
<p><code>guideline = "BRMO"</code></p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh">link</a>)</p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh" class="external-link">link</a>)</p>
</li>
</ul>
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="uri">https://github.com/msberends/AMR/issues/new</a>.</p>
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link uri">https://github.com/msberends/AMR/issues/new</a>.</p>
<div id="custom-guidelines" class="section level4">
<h4 class="hasAnchor">
<a href="#custom-guidelines" class="anchor"></a>Custom Guidelines</h4>
<a href="#custom-guidelines" class="anchor" aria-hidden="true"></a>Custom Guidelines</h4>
<p>You can also use your own custom guideline. Custom guidelines can be set with the <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html">case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what considers to be the ‘formula notation’:</p>
<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what R considers to be the ‘formula notation’:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">custom</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span><span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,
<span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span><span class="op">)</span></code></pre></div>
<p>If a row/an isolate matches the first rule, the value after the first <code><a href="https://rdrr.io/r/base/tilde.html">~</a></code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.</p>
<p>If a row/an isolate matches the first rule, the value after the first <code><a href="https://rdrr.io/r/base/tilde.html" class="external-link">~</a></code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The maximum number of rules is unlimited.</p>
<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">custom</span>
@@ -257,30 +259,50 @@
<span class="co"># </span>
<span class="co"># Unmatched rows will return NA.</span>
<span class="co"># Results will be of class &lt;factor&gt;, with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></code></pre></div>
<p>The outcome of the function can be used for the <code>guideline</code> argument in the [mdro()] function:</p>
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/table.html">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co"># Determining MDROs based on custom rules, resulting in [factor] levels:</span>
<span class="co"># Negative &lt; Elderly Type A &lt; Elderly Type B.</span>
<span class="co"># - Custom MDRO rule 1: `CIP == "R" &amp; age &gt; 60` (198 rows matched)</span>
<span class="co"># - Custom MDRO rule 2: `ERY == "R" &amp; age &gt; 60` (732 rows matched)</span>
<span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co"># x</span>
<span class="co"># Negative Elderly Type A Elderly Type B </span>
<span class="co"># 1070 198 732</span></code></pre></div>
<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html">readRDS()</a></code>.</p>
<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
</div>
</div>
<div id="examples" class="section level3">
<h3 class="hasAnchor">
<a href="#examples" class="anchor"></a>Examples</h3>
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
<a href="#examples" class="anchor" aria-hidden="true"></a>Examples</h3>
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code> for predefined guidelines. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains full antibiograms of 2,000 microbial isolates. It reflects reality and can be used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span> <span class="co"># to support pipes: %&gt;%</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
<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"># to support pipes: %&gt;%</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>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
<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="op">)</span> <span class="co"># show frequency table of the result</span>
<span class="co"># ℹ Using column 'mo' as input for `col_mo`.</span>
<span class="co"># Auto-guessing columns suitable for analysis... OK.</span>
<span class="co"># ℹ Reliability would be improved if these antimicrobial results would be</span>
<span class="co"># available too: ampicillin/sulbactam (SAM), aztreonam (ATM), cefotetan</span>
<span class="co"># (CTT), ceftaroline (CPT), daptomycin (DAP), doripenem (DOR), ertapenem</span>
<span class="co"># (ETP), fusidic acid (FUS), gentamicin-high (GEH), levofloxacin (LVX),</span>
<span class="co"># minocycline (MNO), netilmicin (NET), polymyxin B (PLB),</span>
<span class="co"># quinupristin/dalfopristin (QDA), streptomycin-high (STH), telavancin (TLV)</span>
<span class="co"># and ticarcillin/clavulanic acid (TCC)</span>
<span class="co"># Table 1 - Staphylococcus aureus... OK.</span>
<span class="co"># Table 2 - Enterococcus spp.... OK.</span>
<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>
<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><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 2,000<br>
@@ -319,16 +341,16 @@ Unique: 2</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># random_rsi() is a helper function to generate</span>
<span class="co"># a random vector with values S, I and R</span>
<span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
<span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
@@ -337,21 +359,21 @@ Unique: 2</p>
KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>The data set now looks like this:</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">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
<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 S I R R R S</span>
<span class="co"># 2 I R R R R R</span>
<span class="co"># 3 S S S R I R</span>
<span class="co"># 4 R I R R S S</span>
<span class="co"># 5 I R S S R I</span>
<span class="co"># 6 I S S R R R</span>
<span class="co"># 1 I S S R I S</span>
<span class="co"># 2 R R R R S R</span>
<span class="co"># 3 R R R I S S</span>
<span class="co"># 4 R S I R R R</span>
<span class="co"># 5 R S S S I R</span>
<span class="co"># 6 S I S S S I</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 R</span>
<span class="co"># 5 S</span>
<span class="co"># 6 S</span></code></pre></div>
<span class="co"># 1 S</span>
<span class="co"># 2 S</span>
<span class="co"># 3 I</span>
<span class="co"># 4 S</span>
<span class="co"># 5 I</span>
<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>
@@ -359,10 +381,22 @@ Unique: 2</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
<span class="co"># ℹ No column found as input for `col_mo`, assuming all rows contain</span>
<span class="co"># Mycobacterium tuberculosis.</span></code></pre></div>
<span class="co"># Mycobacterium tuberculosis.</span>
<span class="co"># Auto-guessing columns suitable for analysis... OK.</span>
<span class="co"># ℹ Reliability would be improved if these antimicrobial results would be</span>
<span class="co"># available too: capreomycin (CAP), rifabutin (RIB) and rifapentine (RFP)</span>
<span class="co"># </span>
<span class="co"># Only results with 'R' are considered as resistance. Use `combine_SI = FALSE` to also consider 'I' as resistance.</span>
<span class="co"># </span>
<span class="co"># Determining multidrug-resistant organisms (MDRO), according to:</span>
<span class="co"># Guideline: Companion handbook to the WHO guidelines for the programmatic</span>
<span class="co"># management of drug-resistant tuberculosis</span>
<span class="co"># Author(s): WHO (World Health Organization)</span>
<span class="co"># Version: WHO/HTM/TB/2014.11, 2014</span>
<span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></code></pre></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></code></pre></div>
<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>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 5,000<br>
@@ -382,40 +416,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
<td align="right">3187</td>
<td align="right">63.74%</td>
<td align="right">3175</td>
<td align="right">63.50%</td>
<td align="right">3175</td>
<td align="right">63.50%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1027</td>
<td align="right">20.54%</td>
<td align="right">4214</td>
<td align="right">84.28%</td>
<td align="right">1014</td>
<td align="right">20.28%</td>
<td align="right">4189</td>
<td align="right">83.78%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">430</td>
<td align="right">8.60%</td>
<td align="right">4644</td>
<td align="right">92.88%</td>
<td align="right">445</td>
<td align="right">8.90%</td>
<td align="right">4634</td>
<td align="right">92.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">245</td>
<td align="right">4.90%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
<td align="right">272</td>
<td align="right">5.44%</td>
<td align="right">4906</td>
<td align="right">98.12%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">111</td>
<td align="right">2.22%</td>
<td align="right">94</td>
<td align="right">1.88%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
@@ -433,11 +467,13 @@ Unique: 5</p>
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
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@@ -446,5 +482,7 @@ Unique: 5</p>
</body>
</html>

12
docs/articles/MDR_files/header-attrs-2.9/header-attrs.js Normal file
View File

@@ -0,0 +1,12 @@
// 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);
}
});

82
docs/articles/PCA.html
View File

@@ -27,6 +27,8 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
@@ -39,7 +41,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -47,14 +49,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
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<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -63,77 +65,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
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<a href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
Predict antimicrobial resistance
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<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
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</li>
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<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
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<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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@@ -142,14 +144,14 @@
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@@ -164,7 +166,7 @@
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<a href="https://github.com/msberends/AMR" class="external-link">
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@@ -172,7 +174,7 @@
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<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
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@@ -187,13 +189,13 @@
</header><script src="PCA_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
</header><script src="PCA_files/header-attrs-2.9/header-attrs.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>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
<div class="hidden name"><code>PCA.Rmd</code></div>
</div>
@@ -203,16 +205,16 @@
<p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
</div>
<div id="transforming" class="section level1">
<h1 class="hasAnchor">
<a href="#transforming" class="anchor"></a>Transforming</h1>
<a href="#transforming" class="anchor" aria-hidden="true"></a>Transforming</h1>
<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">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">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</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://github.com/msberends/AMR" class="external-link">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="co"># Rows: 2,000</span>
<span class="co"># Columns: 49</span>
<span class="co"># $ date &lt;date&gt; 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
@@ -267,13 +269,13 @@
<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">resistance_data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span>
genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="co"># and genus as we do here</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="co"># then get resistance of all drugs</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="co"># then get resistance of all drugs</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,
<span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span><span class="op">)</span> <span class="co"># and select only relevant columns</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</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">resistance_data</span><span class="op">)</span>
<span class="co"># # A tibble: 6 x 10</span>
<span class="co"># # Groups: order [5]</span>
<span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span>
@@ -287,15 +289,15 @@
</div>
<div id="perform-principal-component-analysis" class="section level1">
<h1 class="hasAnchor">
<a href="#perform-principal-component-analysis" class="anchor"></a>Perform principal component analysis</h1>
<a href="#perform-principal-component-analysis" class="anchor" aria-hidden="true"></a>Perform principal component analysis</h1>
<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">&lt;-</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>
<span class="co"># ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
<span class="co"># and "TOB". Total observations available: 7.</span></code></pre></div>
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span>
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span>
<span class="co"># Groups (n=4, named as 'order'):</span>
<span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span>
<span class="co"># Importance of components:</span>
@@ -305,13 +307,13 @@
<span class="co"># Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></code></pre></div>
<pre><code># Groups (n=4, named as 'order'):
# [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</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">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
<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 id="plotting-the-results" class="section level1">
<h1 class="hasAnchor">
<a href="#plotting-the-results" class="anchor"></a>Plotting the results</h1>
<a href="#plotting-the-results" class="anchor" aria-hidden="true"></a>Plotting the results</h1>
<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">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
<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>
<p>But we can’t see the explanation of the points. Perhaps this works better with our new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
@@ -320,7 +322,7 @@
<p>You can also print an ellipse per group, and edit the appearance:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span>, ellipse <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">+</span>
<span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"An AMR/PCA biplot!"</span><span class="op">)</span></code></pre></div>
<span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"An AMR/PCA biplot!"</span><span class="op">)</span></code></pre></div>
<p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
</div>
</div>
@@ -336,11 +338,13 @@
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<p></p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
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</footer>
@@ -349,5 +353,7 @@
</body>
</html>

12
docs/articles/PCA_files/header-attrs-2.9/header-attrs.js Normal file
View File

@@ -0,0 +1,12 @@
// 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);
}
});

124
docs/articles/SPSS.html
View File

@@ -27,6 +27,8 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
@@ -39,7 +41,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -47,14 +49,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -63,77 +65,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
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<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
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Get properties of a microorganism
</a>
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<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
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<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -142,14 +144,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
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Manual
</a>
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<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -164,7 +166,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<a href="https://github.com/msberends/AMR" class="external-link">
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Source Code
@@ -172,7 +174,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -187,15 +189,15 @@
</header><script src="SPSS_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
</header><script src="SPSS_files/header-attrs-2.9/header-attrs.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 class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 class="date">03 June 2021</h4>
<h4 data-toc-skip class="date">23 July 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
</div>
@@ -204,17 +206,17 @@
<div id="spss-sas-stata" class="section level2">
<h2 class="hasAnchor">
<a href="#spss-sas-stata" class="anchor"></a>SPSS / SAS / Stata</h2>
<a href="#spss-sas-stata" class="anchor" aria-hidden="true"></a>SPSS / SAS / Stata</h2>
<p>SPSS (Statistical Package for the Social Sciences) is probably the most well-known software package for statistical analysis. SPSS is easier to learn than R, because in SPSS you only have to click a menu to run parts of your analysis. Because of its user-friendliness, it is taught at universities and particularly useful for students who are new to statistics. From my experience, I would guess that pretty much all (bio)medical students know it at the time they graduate. SAS and Stata are comparable statistical packages popular in big industries.</p>
</div>
<div id="compared-to-r" class="section level2">
<h2 class="hasAnchor">
<a href="#compared-to-r" class="anchor"></a>Compared to R</h2>
<a href="#compared-to-r" class="anchor" aria-hidden="true"></a>Compared to R</h2>
<p>As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major downsides when comparing it with R:</p>
<ul>
<li>
<p><strong>R is highly modular.</strong></p>
<p>The <a href="https://cran.r-project.org/">official R network (CRAN)</a> features more than 16,000 packages at the time of writing, our <code>AMR</code> package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there.</p>
<p>The <a href="https://cran.r-project.org/" class="external-link">official R network (CRAN)</a> features more than 16,000 packages at the time of writing, our <code>AMR</code> package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there.</p>
<p>Bottom line is, you can really extend it yourself or ask somebody to do this for you. Take for example our <code>AMR</code> package. Among other things, it adds reliable reference data to R to help you with the data cleaning and analysis. SPSS, SAS and Stata will never know what a valid MIC value is or what the Gram stain of <em>E. coli</em> is. Or that all species of <em>Klebiella</em> are resistant to amoxicillin and that Floxapen<sup>®</sup> is a trade name of flucloxacillin. These facts and properties are often needed to clean existing data, which would be very inconvenient in a software package without reliable reference data. See below for a demonstration.</p>
</li>
<li>
@@ -223,27 +225,27 @@
</li>
<li>
<p><strong>R can be easily automated.</strong></p>
<p>Over the last years, <a href="https://rmarkdown.rstudio.com/">R Markdown</a> has really made an interesting development. With R Markdown, you can very easily produce reports, whether the format has to be Word, PowerPoint, a website, a PDF document or just the raw data to Excel. It even allows the use of a reference file containing the layout style (e.g. fonts and colours) of your organisation. I use this a lot to generate weekly and monthly reports automatically. Just write the code once and enjoy the automatically updated reports at any interval you like.</p>
<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/">Shiny apps</a>: live manipulation of data using a custom made website. The webdesign knowledge needed (JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
<p>Over the last years, <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a> has really made an interesting development. With R Markdown, you can very easily produce reports, whether the format has to be Word, PowerPoint, a website, a PDF document or just the raw data to Excel. It even allows the use of a reference file containing the layout style (e.g. fonts and colours) of your organisation. I use this a lot to generate weekly and monthly reports automatically. Just write the code once and enjoy the automatically updated reports at any interval you like.</p>
<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/" class="external-link">Shiny apps</a>: live manipulation of data using a custom made website. The webdesign knowledge needed (JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
</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">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">404,559 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">411,199 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>
<p>And that’s not vice versa I’m afraid. You can import data from any source into R. For example from SPSS, SAS and Stata (<a href="https://haven.tidyverse.org/">link</a>), from Minitab, Epi Info and EpiData (<a href="https://cran.r-project.org/package=foreign">link</a>), from Excel (<a href="https://readxl.tidyverse.org/">link</a>), from flat files like CSV, TXT or TSV (<a href="https://readr.tidyverse.org/">link</a>), or directly from databases and datawarehouses from anywhere on the world (<a href="https://dbplyr.tidyverse.org/">link</a>). You can even scrape websites to download tables that are live on the internet (<a href="https://github.com/hadley/rvest">link</a>) or get the results of an API call and transform it into data in only one command (<a href="https://github.com/Rdatatable/data.table/wiki/Convenience-features-of-fread">link</a>).</p>
<p>And that’s not vice versa I’m afraid. You can import data from any source into R. For example from SPSS, SAS and Stata (<a href="https://haven.tidyverse.org/" class="external-link">link</a>), from Minitab, Epi Info and EpiData (<a href="https://cran.r-project.org/package=foreign" class="external-link">link</a>), from Excel (<a href="https://readxl.tidyverse.org/" class="external-link">link</a>), from flat files like CSV, TXT or TSV (<a href="https://readr.tidyverse.org/" class="external-link">link</a>), or directly from databases and datawarehouses from anywhere on the world (<a href="https://dbplyr.tidyverse.org/" class="external-link">link</a>). You can even scrape websites to download tables that are live on the internet (<a href="https://github.com/hadley/rvest" class="external-link">link</a>) or get the results of an API call and transform it into data in only one command (<a href="https://github.com/Rdatatable/data.table/wiki/Convenience-features-of-fread" class="external-link">link</a>).</p>
<p>And the best part - you can export from R to most data formats as well. So you can import an SPSS file, do your analysis neatly in R and export the resulting tables to Excel files for sharing.</p>
</li>
<li>
<p><strong>R is completely free and open-source.</strong></p>
<p>No strings attached. It was created and is being maintained by volunteers who believe that (data) science should be open and publicly available to everybody. SPSS, SAS and Stata are quite expensive. IBM SPSS Staticstics only comes with subscriptions nowadays, varying <a href="https://www.ibm.com/products/spss-statistics/pricing">between USD 1,300 and USD 8,500</a> per user <em>per year</em>. SAS Analytics Pro costs <a href="https://www.sas.com/store/products-solutions/sas-analytics-pro/prodPERSANL.html">around USD 10,000</a> per computer. Stata also has a business model with subscription fees, varying <a href="https://www.stata.com/order/new/bus/single-user-licenses/dl/">between USD 600 and USD 2,800</a> per computer per year, but lower prices come with a limitation of the number of variables you can work with. And still they do not offer the above benefits of R.</p>
<p>No strings attached. It was created and is being maintained by volunteers who believe that (data) science should be open and publicly available to everybody. SPSS, SAS and Stata are quite expensive. IBM SPSS Staticstics only comes with subscriptions nowadays, varying <a href="https://www.ibm.com/products/spss-statistics/pricing" class="external-link">between USD 1,300 and USD 8,500</a> per user <em>per year</em>. SAS Analytics Pro costs <a href="https://www.sas.com/store/products-solutions/sas-analytics-pro/prodPERSANL.html" class="external-link">around USD 10,000</a> per computer. Stata also has a business model with subscription fees, varying <a href="https://www.stata.com/order/new/bus/single-user-licenses/dl/" class="external-link">between USD 600 and USD 2,800</a> per computer per year, but lower prices come with a limitation of the number of variables you can work with. And still they do not offer the above benefits of R.</p>
<p>If you are working at a midsized or small company, you can save it tens of thousands of dollars by using R instead of e.g. SPSS - gaining even more functions and flexibility. And all R enthousiasts can do as much PR as they want (like I do here), because nobody is officially associated with or affiliated by R. It is really free.</p>
</li>
<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/">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/">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>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>
</li>
</ul>
<p>To demonstrate the first point:</p>
@@ -261,7 +263,7 @@
<span class="co"># [1] "Gram-negative"</span>
<span class="co"># Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST:</span>
<span class="va">klebsiella_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"klebsiella"</span>,
<span class="va">klebsiella_test</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"klebsiella"</span>,
amox <span class="op">=</span> <span class="st">"S"</span>,
stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="va">klebsiella_test</span> <span class="co"># (our original data)</span>
@@ -283,17 +285,17 @@
</div>
<div id="import-data-from-spsssasstata" class="section level2">
<h2 class="hasAnchor">
<a href="#import-data-from-spsssasstata" class="anchor"></a>Import data from SPSS/SAS/Stata</h2>
<a href="#import-data-from-spsssasstata" class="anchor" aria-hidden="true"></a>Import data from SPSS/SAS/Stata</h2>
<div id="rstudio" class="section level3">
<h3 class="hasAnchor">
<a href="#rstudio" class="anchor"></a>RStudio</h3>
<p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/">RStudio</a>. It is an open-source and free desktop environment which not only allows you to run R code, but also supports project management, version management, package management and convenient import menus to work with other data sources. You can also install <a href="https://www.rstudio.com/products/rstudio/">RStudio Server</a> on a private or corporate server, which brings nothing less than the complete RStudio software to you as a website (at home or at work).</p>
<a href="#rstudio" class="anchor" aria-hidden="true"></a>RStudio</h3>
<p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio</a>. It is an open-source and free desktop environment which not only allows you to run R code, but also supports project management, version management, package management and convenient import menus to work with other data sources. You can also install <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio Server</a> on a private or corporate server, which brings nothing less than the complete RStudio software to you as a website (at home or at work).</p>
<p>To import a data file, just click <em>Import Dataset</em> in the Environment tab:</p>
<p><img src="https://github.com/msberends/AMR/raw/master/docs/import1.png"></p>
<p>If additional packages are needed, RStudio will ask you if they should be installed on beforehand.</p>
<p>In the the window that opens, you can define all options (parameters) that should be used for import and you’re ready to go:</p>
<p><img src="https://github.com/msberends/AMR/raw/master/docs/import2.png"></p>
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>.</p>
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>.</p>
<p>The difference is this:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">SPSS_data</span>
@@ -330,70 +332,70 @@
</div>
<div id="base-r" class="section level3">
<h3 class="hasAnchor">
<a href="#base-r" class="anchor"></a>Base R</h3>
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/">great <code>haven</code> package</a> yourself:</p>
<a href="#base-r" class="anchor" aria-hidden="true"></a>Base R</h3>
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/" class="external-link">great <code>haven</code> package</a> yourself:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># download and install the latest version:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"haven"</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"haven"</span><span class="op">)</span>
<span class="co"># load the package you just installed:</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://haven.tidyverse.org">haven</a></span><span class="op">)</span> </code></pre></div>
<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://haven.tidyverse.org" class="external-link">haven</a></span><span class="op">)</span> </code></pre></div>
<p>You can now import files as follows:</p>
<div id="spss" class="section level4">
<h4 class="hasAnchor">
<a href="#spss" class="anchor"></a>SPSS</h4>
<a href="#spss" class="anchor" aria-hidden="true"></a>SPSS</h4>
<p>To read files from SPSS into R:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># read any SPSS file based on file extension (best way):</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_spss</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="co"># read .sav or .zsav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_sav</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="co"># read .por file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>, as mentioned above.</p>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_por</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>, as mentioned above.</p>
<p>To export your R objects to the SPSS file format:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># save as .sav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="co"># save as compressed .zsav file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
</div>
<div id="sas" class="section level4">
<h4 class="hasAnchor">
<a href="#sas" class="anchor"></a>SAS</h4>
<a href="#sas" class="anchor" aria-hidden="true"></a>SAS</h4>
<p>To read files from SAS into R:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># read .sas7bdat + .sas7bcat files:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span><span class="op">(</span>data_file <span class="op">=</span> <span class="st">"path/to/file"</span>, catalog_file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html" class="external-link">read_sas</a></span><span class="op">(</span>data_file <span class="op">=</span> <span class="st">"path/to/file"</span>, catalog_file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
<span class="co"># read SAS transport files (version 5 and version 8):</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html" class="external-link">read_xpt</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
<p>To export your R objects to the SAS file format:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># save as regular SAS file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html" class="external-link">write_sas</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
<span class="co"># the SAS transport format is an open format </span>
<span class="co"># (required for submission of the data to the FDA)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></code></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html" class="external-link">write_xpt</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></code></pre></div>
</div>
<div id="stata" class="section level4">
<h4 class="hasAnchor">
<a href="#stata" class="anchor"></a>Stata</h4>
<a href="#stata" class="anchor" aria-hidden="true"></a>Stata</h4>
<p>To read files from Stata into R:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># read .dta file:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">read_stata</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span>
<span class="co"># works exactly the same:</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></code></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">read_dta</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></code></pre></div>
<p>To export your R objects to the Stata file format:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># save as .dta file, Stata version 14:</span>
<span class="co"># (supports Stata v8 until v15 at the time of writing)</span>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></code></pre></div>
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">write_dta</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></code></pre></div>
</div>
</div>
</div>
@@ -410,11 +412,13 @@
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<p></p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
</div>
</footer>
@@ -423,5 +427,7 @@
</body>
</html>

12
docs/articles/SPSS_files/header-attrs-2.9/header-attrs.js Normal file
View File

@@ -0,0 +1,12 @@
// 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);
}
});

86
docs/articles/WHONET.html
View File

@@ -27,6 +27,8 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
@@ -39,7 +41,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -187,13 +189,13 @@
</header><script src="WHONET_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
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<h1 data-toc-skip>How to work with WHONET data</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
<div class="hidden name"><code>WHONET.Rmd</code></div>
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@@ -202,23 +204,23 @@
<div id="import-of-data" class="section level3">
<h3 class="hasAnchor">
<a href="#import-of-data" class="anchor"></a>Import of data</h3>
<p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
<a href="#import-of-data" class="anchor" aria-hidden="true"></a>Import of data</h3>
<p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/" class="external-link"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
<p>An example syntax could look like this:</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">library</a></span><span class="op">(</span><span class="va"><a href="https://readxl.tidyverse.org">readxl</a></span><span class="op">)</span>
<span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span><span class="op">(</span>path <span class="op">=</span> <span class="st">"path/to/your/file.xlsx"</span><span class="op">)</span></code></pre></div>
<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://readxl.tidyverse.org" class="external-link">readxl</a></span><span class="op">)</span>
<span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html" class="external-link">read_excel</a></span><span class="op">(</span>path <span class="op">=</span> <span class="st">"path/to/your/file.xlsx"</span><span class="op">)</span></code></pre></div>
<p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
</div>
<div id="preparation" class="section level3">
<h3 class="hasAnchor">
<a href="#preparation" class="anchor"></a>Preparation</h3>
<p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="uri">https://www.tidyverse.org/</a>.</p>
<a href="#preparation" class="anchor" aria-hidden="true"></a>Preparation</h3>
<p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="external-link uri">https://www.tidyverse.org/</a>.</p>
<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">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org">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">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">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
<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://github.com/msberends/AMR" class="external-link">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>
<li>Microorganisms should be transformed to our own microorganism codes (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
@@ -228,15 +230,15 @@
<code class="sourceCode R"><span class="co"># transform variables</span>
<span class="va">data</span> <span class="op">&lt;-</span> <span class="va">WHONET</span> <span class="op">%&gt;%</span>
<span class="co"># get microbial ID based on given organism</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></code></pre></div>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></code></pre></div>
<p>No errors or warnings, so all values are transformed succesfully.</p>
<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. Its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function can be used to create frequency tables.</p>
<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. Its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function can be used to create frequency tables.</p>
<p>So let’s check our data, with a couple of frequency tables:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
<span class="va">data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, nmax <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></code></pre></div>
<span class="va">data</span> <span class="op">%&gt;%</span> <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="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, nmax <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 500<br>
@@ -340,7 +342,7 @@ Longest: 40</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>
<span class="va">data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></code></pre></div>
<span class="va">data</span> <span class="op">%&gt;%</span> <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">AMC_ND2</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 500<br>
@@ -389,12 +391,12 @@ Drug group: Beta-lactams/penicillins<br>
</div>
<div id="a-first-glimpse-at-results" class="section level3">
<h3 class="hasAnchor">
<a href="#a-first-glimpse-at-results" class="anchor"></a>A first glimpse at results</h3>
<a href="#a-first-glimpse-at-results" class="anchor" aria-hidden="true"></a>A first glimpse at results</h3>
<p>An easy <code>ggplot</code> will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">Country</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">Country</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">'ab'</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
</div>
@@ -409,11 +411,13 @@ Drug group: Beta-lactams/penicillins<br>
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
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@@ -422,5 +426,7 @@ Drug group: Beta-lactams/penicillins<br>
</body>
</html>

12
docs/articles/WHONET_files/header-attrs-2.9/header-attrs.js Normal file
View File

@@ -0,0 +1,12 @@
// 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);
}
});

172
docs/articles/benchmarks.html
View File

@@ -27,6 +27,8 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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@@ -39,7 +41,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -47,14 +49,14 @@
<ul class="nav navbar-nav">
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@@ -63,77 +65,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
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Predict antimicrobial resistance
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Data sets for download / own use
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<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
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Conduct principal component analysis for AMR
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<a href="../articles/MDR.html">
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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@@ -142,14 +144,14 @@
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Manual
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@@ -164,7 +166,7 @@
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@@ -172,7 +174,7 @@
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@@ -187,30 +189,30 @@
</header><script src="benchmarks_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
</header><script src="benchmarks_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Benchmarks</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd" class="external-link"><code>vignettes/benchmarks.Rmd</code></a></small>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
</div>
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://www.catalogueoflife.org">Catalogue of Life</a> (CoL) and the <a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN). We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the microbial taxonomy.</p>
<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">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (CoL) and the <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN). We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the microbial taxonomy.</p>
<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">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/">microbenchmark</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span></code></pre></div>
<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://github.com/msberends/AMR" class="external-link">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>
<p>But the calculation time differs a lot:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">S.aureus</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>
<code class="sourceCode R"><span class="va">S.aureus</span> <span class="op">&lt;-</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/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"sau"</span><span class="op">)</span>, <span class="co"># WHONET code</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"stau"</span><span class="op">)</span>,
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"STAU"</span><span class="op">)</span>,
@@ -224,80 +226,80 @@
<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">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://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="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 13.0 13.0 16.0 15.0 16.0 44 25</span>
<span class="co"># as.mo("stau") 55.0 58.0 75.0 62.0 94.0 110 25</span>
<span class="co"># as.mo("STAU") 55.0 59.0 77.0 89.0 94.0 100 25</span>
<span class="co"># as.mo("staaur") 11.0 13.0 20.0 14.0 16.0 48 25</span>
<span class="co"># as.mo("STAAUR") 11.0 13.0 17.0 15.0 16.0 49 25</span>
<span class="co"># as.mo("S. aureus") 26.0 30.0 41.0 32.0 60.0 68 25</span>
<span class="co"># as.mo("S aureus") 27.0 29.0 44.0 32.0 58.0 160 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.3 3.9 5.5 4.2 4.7 37 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 280.0 280.0 290.0 320 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 170.0 200.0 210.0 200.0 220.0 250 25</span>
<span class="co"># as.mo("MRSA") 12.0 14.0 21.0 15.0 17.0 56 25</span>
<span class="co"># as.mo("VISA") 20.0 23.0 33.0 25.0 51.0 59 25</span></code></pre></div>
<span class="co"># as.mo("sau") 12.0 13.0 19.0 14 16.0 49 25</span>
<span class="co"># as.mo("stau") 55.0 58.0 80.0 91 96.0 110 25</span>
<span class="co"># as.mo("STAU") 57.0 63.0 79.0 66 96.0 110 25</span>
<span class="co"># as.mo("staaur") 13.0 13.0 19.0 14 16.0 48 25</span>
<span class="co"># as.mo("STAAUR") 13.0 13.0 22.0 15 17.0 48 25</span>
<span class="co"># as.mo("S. aureus") 27.0 30.0 42.0 33 62.0 67 25</span>
<span class="co"># as.mo("S aureus") 28.0 30.0 37.0 32 34.0 64 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.5 3.9 5.5 4 4.4 38 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 260.0 270.0 280.0 270 290.0 370 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 170.0 200.0 210.0 210 230.0 250 25</span>
<span class="co"># as.mo("MRSA") 13.0 14.0 20.0 15 15.0 51 25</span>
<span class="co"># as.mo("VISA") 22.0 23.0 33.0 25 27.0 64 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 200 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 id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
<a href="#repetitive-results" class="anchor" aria-hidden="true"></a>Repetitive results</h3>
<p>Repetitive results are values that are present more than once in a vector. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. So running <code><a href="../reference/as.mo.html">as.mo(c("E. coli", "E. coli"))</a></code> will check the value <code>"E. coli"</code> only once.</p>
<p>To prove this, we will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for testing - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># start with the example_isolates data set</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="co"># take all MO codes from the 'mo' column</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="co"># and copy them a thousand times</span>
<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="co"># then scramble them</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span><span class="op">(</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</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 &lt;mo&gt;</span>
<span class="co"># [1] B_STPHY_CONS B_ESCHR_COLI B_STPHY_AURS B_STRPT_PYGN B_ESCHR_COLI</span>
<span class="co"># [6] B_HMPHL_INFL</span>
<span class="co"># [1] B_SERRT_MRCS B_STRPT_ORLS B_STPHY_CPTS B_STPHY_HMNS B_ESCHR_COLI</span>
<span class="co"># [6] B_ESCHR_COLI</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">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</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>
<span class="co"># [1] 2000000</span>
<span class="co"># and how many unique values do we have?</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co"># [1] 90</span>
<span class="co"># now let's see:</span>
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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>,
<span class="va">run_it</span> <span class="op">&lt;-</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">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://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="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 165 238 258 246 253 369 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.246 seconds. That is 123 nanoseconds on average. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 190 210 273 248 347 419 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.248 seconds. That is 124 nanoseconds on average. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
<a href="#precalculated-results" class="anchor" aria-hidden="true"></a>Precalculated results</h3>
<p>What about precalculated results? If the input is an already precalculated result of a helper function such as <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all. In other words, if you run <code><a href="../reference/mo_property.html">mo_name()</a></code> on a valid taxonomic name, it will return the results immediately (see ‘C’ below):</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</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_name</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
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">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://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="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 8.20 8.33 13.30 8.53 9.71 53.2 10</span>
<span class="co"># B 22.80 23.50 29.20 24.60 26.80 69.3 10</span>
<span class="co"># C 1.82 2.04 2.25 2.16 2.38 2.9 10</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 8.72 9.35 9.96 10.20 10.40 11.10 10</span>
<span class="co"># B 24.20 25.00 31.40 27.10 27.50 77.90 10</span>
<span class="co"># C 1.80 1.84 2.20 2.18 2.59 2.67 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0022 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">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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>,
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</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>,
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>,
D <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"Staphylococcaceae"</span><span class="op">)</span>,
@@ -306,22 +308,22 @@
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">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://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="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.66 1.70 1.86 1.77 1.90 2.41 10</span>
<span class="co"># B 1.61 1.71 1.99 1.84 2.37 2.56 10</span>
<span class="co"># C 1.64 1.72 1.79 1.74 1.77 2.14 10</span>
<span class="co"># D 1.68 1.71 2.06 2.06 2.23 2.77 10</span>
<span class="co"># E 1.63 1.71 1.85 1.75 1.92 2.43 10</span>
<span class="co"># F 1.61 1.67 1.80 1.75 1.86 2.22 10</span>
<span class="co"># G 1.63 1.67 4.37 1.96 2.58 25.70 10</span>
<span class="co"># H 1.67 1.73 1.88 1.83 2.01 2.28 10</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.73 1.79 1.89 1.84 1.95 2.31 10</span>
<span class="co"># B 1.73 1.75 1.91 1.89 1.99 2.26 10</span>
<span class="co"># C 1.76 1.81 1.90 1.83 1.98 2.17 10</span>
<span class="co"># D 1.71 1.78 1.97 1.83 2.12 2.77 10</span>
<span class="co"># E 1.70 1.74 1.80 1.80 1.85 1.89 10</span>
<span class="co"># F 1.73 1.74 1.82 1.77 1.84 2.20 10</span>
<span class="co"># G 1.69 1.75 1.91 1.79 1.85 2.70 10</span>
<span class="co"># H 1.66 1.74 1.84 1.81 1.82 2.27 10</span></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></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 id="results-in-other-languages" class="section level3">
<h3 class="hasAnchor">
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
<a href="#results-in-other-languages" class="anchor" aria-hidden="true"></a>Results in other languages</h3>
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on an English system</span>
@@ -333,7 +335,7 @@
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
<span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span>
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>en <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span>,
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>en <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span>,
de <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span>,
nl <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>,
es <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>,
@@ -341,16 +343,16 @@
fr <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"fr"</span><span class="op">)</span>,
pt <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"pt"</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">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://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="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 19.99 20.43 25.64 21.15 22.38 82.52 100</span>
<span class="co"># de 31.03 31.96 38.34 32.88 35.27 82.31 100</span>
<span class="co"># nl 35.25 36.19 43.25 37.63 39.66 85.19 100</span>
<span class="co"># es 35.01 35.85 40.89 36.91 38.58 83.68 100</span>
<span class="co"># it 24.35 24.90 30.43 25.81 28.03 78.90 100</span>
<span class="co"># fr 23.87 25.02 31.72 26.03 27.46 83.88 100</span>
<span class="co"># pt 24.00 24.99 31.16 26.05 28.06 80.74 100</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 20.17 20.83 23.58 21.44 22.59 69.64 100</span>
<span class="co"># de 31.48 32.42 42.10 34.02 36.34 204.60 100</span>
<span class="co"># nl 35.21 36.63 45.71 37.75 40.25 97.01 100</span>
<span class="co"># es 35.09 36.14 43.52 37.44 39.09 90.89 100</span>
<span class="co"># it 24.46 25.36 31.24 26.06 28.11 77.93 100</span>
<span class="co"># fr 24.11 25.02 29.21 25.70 27.61 74.69 100</span>
<span class="co"># pt 24.44 25.27 29.79 26.05 28.12 70.28 100</span></code></pre></div>
<p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>
@@ -364,11 +366,13 @@
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<p></p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
</div>
</footer>
@@ -377,5 +381,7 @@
</body>
</html>

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Side by Side Swipe Overlay

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@@ -0,0 +1,12 @@
// 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);
}
});

170
docs/articles/datasets.html
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@@ -27,6 +27,8 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
@@ -39,7 +41,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -164,7 +166,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<a href="https://github.com/msberends/AMR" class="external-link">
<span class="fab fa-github"></span>
Source Code
@@ -192,9 +194,9 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">12 July 2021</h4>
<h4 data-toc-skip class="date">23 July 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
</div>
@@ -208,40 +210,40 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</p>
<div id="microorganisms-currently-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<a href="#microorganisms-currently-accepted-names" class="anchor" aria-hidden="true"></a>Microorganisms (currently accepted names)</h2>
<p>A data set with 70,026 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 11 March 2021 20:59:32 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/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (2.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">Excel file</a> (6.4 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/microorganisms.txt">plain text file</a> (14.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (14.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas">SAS file</a> (27.4 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (27.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (27.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (27.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">Stata file</a> (25.1 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (25.1 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>
<div id="source" class="section level3">
<h3 class="hasAnchor">
<a href="#source" class="anchor"></a>Source</h3>
<a href="#source" class="anchor" aria-hidden="true"></a>Source</h3>
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
<ul>
<li>
<a href="http://www.catalogueoflife.org">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">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: March 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">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: March 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 id="example-content" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content" class="anchor"></a>Example content</h3>
<a href="#example-content" class="anchor" aria-hidden="true"></a>Example content</h3>
<p>Included (sub)species per taxonomic kingdom:</p>
<table class="table">
<thead><tr class="header">
@@ -428,39 +430,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="microorganisms-previously-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms-previously-accepted-names" class="anchor"></a>Microorganisms (previously accepted names)</h2>
<a href="#microorganisms-previously-accepted-names" class="anchor" aria-hidden="true"></a>Microorganisms (previously accepted names)</h2>
<p>A data set with 14,100 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 5 March 2021 09:46:55 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/master/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.2 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/microorganisms.old.xlsx">Excel file</a> (0.5 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/microorganisms.old.txt">plain text file</a> (0.9 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (0.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas">SAS file</a> (2.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/microorganisms.old.sav">SPSS file</a> (2.2 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta">Stata file</a> (2 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
</ul>
<div id="source-1" class="section level3">
<h3 class="hasAnchor">
<a href="#source-1" class="anchor"></a>Source</h3>
<a href="#source-1" class="anchor" aria-hidden="true"></a>Source</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>
<ul>
<li>
<a href="http://www.catalogueoflife.org">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">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: March 2021)</li>
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: March 2021)</li>
</ul>
</div>
<div id="example-content-1" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-1" class="anchor"></a>Example content</h3>
<a href="#example-content-1" class="anchor" aria-hidden="true"></a>Example content</h3>
<p>Example rows when filtering on <em>Escherichia</em>:</p>
<table class="table">
<thead><tr class="header">
@@ -494,39 +496,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="antibiotic-agents" class="section level2">
<h2 class="hasAnchor">
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
<a href="#antibiotic-agents" class="anchor" aria-hidden="true"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</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 23 June 2021 13:07:57 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/master/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (32 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">Excel file</a> (65 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antibiotics.txt">plain text file</a> (0.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antibiotics.sas">SAS file</a> (1.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antibiotics.sav">SPSS file</a> (0.3 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antibiotics.dta">Stata file</a> (0.3 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
</ul>
<div id="source-2" class="section level3">
<h3 class="hasAnchor">
<a href="#source-2" class="anchor"></a>Source</h3>
<a href="#source-2" class="anchor" aria-hidden="true"></a>Source</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>
<ul>
<li>
<a href="https://www.whocc.no/atc_ddd_index/">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">PubChem by the US National Library of Medicine</a></li>
<li><a href="https://whonet.org">WHONET software 2019</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>
<div id="example-content-2" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-2" class="anchor"></a>Example content</h3>
<table class="table">
<a href="#example-content-2" class="anchor" aria-hidden="true"></a>Example content</h3>
<table style="width:100%;" class="table">
<colgroup>
<col width="1%">
<col width="2%">
@@ -662,37 +664,37 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="antiviral-agents" class="section level2">
<h2 class="hasAnchor">
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
<a href="#antiviral-agents" class="anchor" aria-hidden="true"></a>Antiviral agents</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><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file</a> (5 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antivirals.xlsx">Excel file</a> (14 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antivirals.txt">plain text file</a> (16 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antivirals.sas">SAS file</a> (80 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antivirals.sav">SPSS file</a> (68 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/antivirals.dta">Stata file</a> (67 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
</ul>
<div id="source-3" class="section level3">
<h3 class="hasAnchor">
<a href="#source-3" class="anchor"></a>Source</h3>
<a href="#source-3" class="anchor" aria-hidden="true"></a>Source</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>
<ul>
<li>
<a href="https://www.whocc.no/atc_ddd_index/">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">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 id="example-content-3" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-3" class="anchor"></a>Example content</h3>
<a href="#example-content-3" class="anchor" aria-hidden="true"></a>Example content</h3>
<table class="table">
<colgroup>
<col width="4%">
@@ -789,32 +791,32 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="intrinsic-bacterial-resistance" class="section level2">
<h2 class="hasAnchor">
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
<a href="#intrinsic-bacterial-resistance" class="anchor" aria-hidden="true"></a>Intrinsic bacterial resistance</h2>
<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</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 5 March 2021 09:46:55 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/master/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (69 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (69 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel file</a> (0.9 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/intrinsic_resistant.txt">plain text file</a> (3.5 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (3.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas">SAS file</a> (7.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (7.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file</a> (7.9 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (7.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">Stata file</a> (7 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (7 MB)</li>
</ul>
<div id="source-4" class="section level3">
<h3 class="hasAnchor">
<a href="#source-4" class="anchor"></a>Source</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/">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.2</a> (2020).</p>
<a href="#source-4" class="anchor" aria-hidden="true"></a>Source</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’ v3.2</a> (2020).</p>
</div>
<div id="example-content-4" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-4" class="anchor"></a>Example content</h3>
<a href="#example-content-4" class="anchor" aria-hidden="true"></a>Example content</h3>
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
<table class="table">
<thead><tr class="header">
@@ -1004,32 +1006,32 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
<h2 class="hasAnchor">
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor" aria-hidden="true"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 22,000 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</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 12 July 2021 10:54:20 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/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (37 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel file</a> (0.7 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (2.4 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3.5 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.5 MB)</li>
</ul>
<div id="source-5" class="section level3">
<h3 class="hasAnchor">
<a href="#source-5" class="anchor"></a>Source</h3>
<a href="#source-5" class="anchor" aria-hidden="true"></a>Source</h3>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2020) and EUCAST (2011-2021).</p>
</div>
<div id="example-content-5" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-5" class="anchor"></a>Example content</h3>
<a href="#example-content-5" class="anchor" aria-hidden="true"></a>Example content</h3>
<table class="table">
<colgroup>
<col width="8%">
@@ -1134,33 +1136,33 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="dosage-guidelines-from-eucast" class="section level2">
<h2 class="hasAnchor">
<a href="#dosage-guidelines-from-eucast" class="anchor"></a>Dosage guidelines from EUCAST</h2>
<a href="#dosage-guidelines-from-eucast" class="anchor" aria-hidden="true"></a>Dosage guidelines from EUCAST</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><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.rds">R file</a> (3 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/dosage.xlsx">Excel file</a> (14 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/dosage.txt">plain text file</a> (15 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/dosage.sas">SAS file</a> (52 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/dosage.sav">SPSS file</a> (45 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/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/master/data-raw/../data-raw/dosage.dta">Stata file</a> (44 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
</ul>
<div id="source-6" class="section level3">
<h3 class="hasAnchor">
<a href="#source-6" class="anchor"></a>Source</h3>
<a href="#source-6" class="anchor" aria-hidden="true"></a>Source</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/">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</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 id="example-content-6" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-6" class="anchor"></a>Example content</h3>
<a href="#example-content-6" class="anchor" aria-hidden="true"></a>Example content</h3>
<table class="table">
<thead><tr class="header">
<th align="center">ab</th>
@@ -1257,11 +1259,13 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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@@ -1270,5 +1274,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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@@ -54,6 +54,8 @@
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@@ -65,9 +67,15 @@
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<body data-spy="scroll" data-target="#toc">
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@@ -81,7 +89,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9021</span>
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@@ -268,11 +276,11 @@
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</header><script src="resistance_predict_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
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<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/resistance_predict.Rmd"><code>vignettes/resistance_predict.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
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@@ -202,20 +204,20 @@
<div id="needed-r-packages" class="section level2">
<h2 class="hasAnchor">
<a href="#needed-r-packages" class="anchor"></a>Needed R packages</h2>
<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
<a href="#needed-r-packages" class="anchor" aria-hidden="true"></a>Needed R packages</h2>
<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</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">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org">ggplot2</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://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://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://github.com/msberends/AMR" class="external-link">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>
</div>
<div id="prediction-analysis" class="section level2">
<h2 class="hasAnchor">
<a href="#prediction-analysis" class="anchor"></a>Prediction analysis</h2>
<a href="#prediction-analysis" class="anchor" aria-hidden="true"></a>Prediction analysis</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>
@@ -283,11 +285,11 @@
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
<div id="choosing-the-right-model" class="section level3">
<h3 class="hasAnchor">
<a href="#choosing-the-right-model" class="anchor"></a>Choosing the right model</h3>
<a href="#choosing-the-right-model" class="anchor" aria-hidden="true"></a>Choosing the right model</h3>
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
@@ -311,21 +313,21 @@
<td>
<code>"binomial"</code> or <code>"binom"</code> or <code>"logit"</code>
</td>
<td><code><a href="https://rdrr.io/r/stats/glm.html">glm(..., family = binomial)</a></code></td>
<td><code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">glm(..., family = binomial)</a></code></td>
<td>Generalised linear model with binomial distribution</td>
</tr>
<tr class="even">
<td>
<code>"loglin"</code> or <code>"poisson"</code>
</td>
<td><code><a href="https://rdrr.io/r/stats/glm.html">glm(..., family = poisson)</a></code></td>
<td><code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">glm(..., family = poisson)</a></code></td>
<td>Generalised linear model with poisson distribution</td>
</tr>
<tr class="odd">
<td>
<code>"lin"</code> or <code>"linear"</code>
</td>
<td><code><a href="https://rdrr.io/r/stats/lm.html">lm()</a></code></td>
<td><code><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm()</a></code></td>
<td>Linear model</td>
</tr>
</tbody>
@@ -333,7 +335,7 @@
<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
@@ -341,14 +343,14 @@
<p>This seems more likely, doesn’t it?</p>
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span>
<code class="sourceCode R"><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">family</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">family</span>
<span class="co"># </span>
<span class="co"># Family: binomial </span>
<span class="co"># Link function: logit</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span>
<span class="co"># Estimate Std. Error z value Pr(&gt;|z|)</span>
<span class="co"># (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05</span>
<span class="co"># year 0.09883005 0.02295317 4.305725 1.664395e-05</span></code></pre></div>
@@ -367,11 +369,13 @@
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@@ -47,14 +49,14 @@
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@@ -63,77 +65,77 @@
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Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -142,14 +144,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -164,7 +166,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<a href="https://github.com/msberends/AMR" class="external-link">
<span class="fab fa-github"></span>
Source Code
@@ -172,7 +174,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -187,13 +189,13 @@
</header><script src="welcome_to_AMR_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
</header><script src="welcome_to_AMR_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Welcome to the AMR package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
<div class="hidden name"><code>welcome_to_AMR.Rmd</code></div>
</div>
@@ -203,14 +205,14 @@
<p><strong>READ ALL VIGNETTES <a href="https://msberends.github.io/AMR/articles/">ON OUR WEBSITE</a>.</strong></p>
<div id="welcome-to-the-amr-package" class="section level1">
<h1 class="hasAnchor">
<a href="#welcome-to-the-amr-package" class="anchor"></a>Welcome to the AMR package</h1>
<a href="#welcome-to-the-amr-package" class="anchor" aria-hidden="true"></a>Welcome to the AMR package</h1>
<p><code>AMR</code> is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows <strong>~70,000 distinct microbial species</strong> and all <strong>~550 antibiotic, antimycotic and antiviral drugs</strong> by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This R package is actively maintained (see Changelog) and is free software (see Copyright).</p>
<p>Since its first public release in early 2018, this package has been downloaded from more than 100 countries.</p>
<div id="usage-examples" class="section level2">
<h2 class="hasAnchor">
<a href="#usage-examples" class="anchor"></a>Usage examples</h2>
<a href="#usage-examples" class="anchor" aria-hidden="true"></a>Usage examples</h2>
<p>This package can be used for:</p>
<ul>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</li>
@@ -245,11 +247,13 @@
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<p></p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -258,5 +262,7 @@
</body>
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@@ -0,0 +1,12 @@
// 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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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -65,9 +67,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-citation-authors">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -81,7 +89,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -252,6 +260,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
<h1>Authors</h1>
</div>
<ul class="list-unstyled">
<li>
<p><strong><a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a></strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7620-1800' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
@@ -318,7 +327,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
</p>
</li>
</ul>
</div>
</div>
@@ -327,11 +336,11 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -340,6 +349,8 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
</body>
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@@ -76,6 +76,10 @@ li a[href="#read-more-on-our-website-"] {
display: none !important;
}
code {
color: black;
background-color: #f4f4f4;
}
/* make colour darker and better readable for links */
code a, code a:hover, code a:focus,
pre a, pre a:hover, pre a:focus,
@@ -92,6 +96,7 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
/* adjusted colour for all real links; having href attribute */
color: #128f76;
}
.ot, .dv, .fl, .cn {
/* numbers and TRUE/FALSE */
color: slategray;

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@@ -47,16 +47,19 @@ $(document).ready(function() {
$(".template-reference-topic h2#value").text("Returned value");
// replace \donttest and \dontrun texts in Examples
if ($("pre.examples").length > 0) {
$("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", ""));
$("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", ""));
$("pre.examples").html($("pre.examples").html().replaceAll("# }", ""));
if ($(".ref-examples pre").length > 0) {
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\donttest{", ""));
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\dontrun{", ""));
$(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# }", ""));
}
// remove leading newline in code examples on changelog
if ($("body .template-news").length > 0) {
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
}
// change H1 header on dev version on changelog, since pkgdown uses the version number from the installed version
// (rather then using the DESCRIPTION file)
$("h1[id^=unreleased]").text("Current development version");
// PR for 'R for Data Science' on How To pages
if ($(".template-article").length > 0) {

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@@ -30,6 +30,8 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-home">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
@@ -42,7 +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="Latest development version">1.7.1.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -194,15 +196,15 @@
<div class="contents col-md-9">
<div id="amr-for-r-" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
<a href="#amr-for-r-" class="anchor" aria-hidden="true"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
</h1></div>
<div id="what-is-amr-for-r" class="section level3">
<h3 class="hasAnchor">
<a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
<a href="#what-is-amr-for-r" class="anchor" aria-hidden="true"></a>What is <code>AMR</code> (for R)?</h3>
<p><em>(To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.)</em></p>
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~70,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~550 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
<div class="main-content" style="display: inline-block;">
<p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 162 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 162 countries. Click the map to enlarge and to see the country names.
@@ -210,17 +212,17 @@
</div>
<div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5">
<h5 class="hasAnchor">
<a href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="anchor"></a>With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!</h5>
<a href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="anchor" aria-hidden="true"></a>With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!</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">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="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/AMR" class="external-link">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">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,
<span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,
<span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
<span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
@@ -330,25 +332,25 @@
<p>A base R equivalent would be, giving the exact same results:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span>
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span>
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span>
<span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,
<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
<span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></code></pre></div>
</div>
<div id="partners" class="section level4">
<h4 class="hasAnchor">
<a href="#partners" class="anchor"></a>Partners</h4>
<a href="#partners" class="anchor" aria-hidden="true"></a>Partners</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"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG"><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="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>
</div>
</div>
</div>
<div id="what-can-you-do-with-this-package" class="section level3">
<h3 class="hasAnchor">
<a href="#what-can-you-do-with-this-package" class="anchor"></a>What can you do with this package?</h3>
<a href="#what-can-you-do-with-this-package" class="anchor" aria-hidden="true"></a>What can you do with this package?</h3>
<p>This package can be used for:</p>
<ul>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
<li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
@@ -368,72 +370,72 @@
</div>
<div id="get-this-package" class="section level3">
<h3 class="hasAnchor">
<a href="#get-this-package" class="anchor"></a>Get this package</h3>
<a href="#get-this-package" class="anchor" aria-hidden="true"></a>Get this package</h3>
<div id="latest-released-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
<p><a href="https://cran.r-project.org/package=AMR"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
<a href="#latest-released-version" class="anchor" aria-hidden="true"></a>Latest released version</h4>
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
</div>
<div id="latest-development-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
<p><a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
<a href="#latest-development-version" class="anchor" aria-hidden="true"></a>Latest development version</h4>
<p><a href="https://codecov.io/gh/msberends/AMR?branch=master" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
<ol>
<ol style="list-style-type: decimal">
<li>
<p>Manually, using:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
</li>
<li>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’):</p>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code><a href="https://rdrr.io/r/utils/install.packages.html">install.packages("AMR")</a></code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages("AMR")</a></code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
</li>
</ol>
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
</div>
</div>
<div id="get-started" class="section level3">
<h3 class="hasAnchor">
<a href="#get-started" class="anchor"></a>Get started</h3>
<a href="#get-started" class="anchor" aria-hidden="true"></a>Get started</h3>
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
</div>
<div id="short-introduction" class="section level3">
<h3 class="hasAnchor">
<a href="#short-introduction" class="anchor"></a>Short introduction</h3>
<a href="#short-introduction" class="anchor" aria-hidden="true"></a>Short introduction</h3>
<div id="microbial-taxonomic-reference-data" class="section level4">
<h4 class="hasAnchor">
<a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</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">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus">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>
<a href="#microbial-taxonomic-reference-data" class="anchor" aria-hidden="true"></a>Microbial (taxonomic) reference data</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>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
</div>
<div id="antimicrobial-reference-data" class="section level4">
<h4 class="hasAnchor">
<a href="#antimicrobial-reference-data" class="anchor"></a>Antimicrobial reference data</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="uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm">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="uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
<a href="#antimicrobial-reference-data" class="anchor" aria-hidden="true"></a>Antimicrobial reference data</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><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>
<div id="whonet--ears-net" class="section level4">
<h4 class="hasAnchor">
<a href="#whonet--ears-net" class="anchor"></a>WHONET / EARS-Net</h4>
<a href="#whonet--ears-net" class="anchor" aria-hidden="true"></a>WHONET / EARS-Net</h4>
<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
</div>
<div id="overview-of-functions" class="section level4">
<h4 class="hasAnchor">
<a href="#overview-of-functions" class="anchor"></a>Overview of functions</h4>
<a href="#overview-of-functions" class="anchor" aria-hidden="true"></a>Overview of functions</h4>
<p>The <code>AMR</code> package basically does four important things:</p>
<ol>
<ol style="list-style-type: decimal">
<li>
<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
<ul>
@@ -446,13 +448,13 @@
<li>
<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
<ul>
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
<ul>
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
</ul>
</li>
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code><a href="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
</ul>
@@ -460,7 +462,7 @@
<li>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>)</li>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
</ul>
@@ -482,7 +484,7 @@
</div>
<div id="copyright" class="section level3">
<h3 class="hasAnchor">
<a href="#copyright" class="anchor"></a>Copyright</h3>
<a href="#copyright" class="anchor" aria-hidden="true"></a>Copyright</h3>
<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
<ul>
<li><p>May be used for commercial purposes</p></li>
@@ -511,7 +513,7 @@
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<div class="links">
<h2>Links</h2>
<h2 data-toc-skip>Links</h2>
<ul class="list-unstyled">
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=AMR">https://​cloud.r-project.org/​package=AMR</a>
</li>
@@ -521,22 +523,26 @@
</li>
</ul>
</div>
<div class="license">
<h2>License</h2>
<h2 data-toc-skip>License</h2>
<ul class="list-unstyled">
<li>
<a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a> | file <a href="LICENSE-text.html">LICENSE</a>
</li>
</ul>
</div>
<div class="citation">
<h2>Citation</h2>
<h2 data-toc-skip>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html">Citing AMR</a></li>
</ul>
</div>
<div class="developers">
<h2>Developers</h2>
<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
<li>
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
@@ -550,20 +556,24 @@
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li><a href="authors.html">All authors...</a></li>
<li><a href="authors.html">More on authors...</a></li>
</ul>
</div>
</div>
</div>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<p></p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p>
</div>
</footer>
@@ -572,5 +582,7 @@
</body>
</html>

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@@ -264,21 +264,16 @@ table {
/* Syntax highlighting ---------------------------------------------------- */
pre {
word-wrap: normal;
word-break: normal;
border: 1px solid #eee;
}
pre, code {
pre, pre code {
background-color: #f8f8f8;
color: #333;
white-space: pre-wrap;
word-break: break-all;
overflow-wrap: break-word;
}
pre code {
overflow: auto;
word-wrap: normal;
white-space: pre;
pre {
border: 1px solid #eee;
}
pre .img {
@@ -305,9 +300,8 @@ a.sourceLine:hover {
.kw {color: #264D66;} /* keyword */
.co {color: #888888;} /* comment */
.message { color: black; font-weight: bolder;}
.error { color: orange; font-weight: bolder;}
.warning { color: #6A0366; font-weight: bolder;}
.error {font-weight: bolder;}
.warning {font-weight: bolder;}
/* Clipboard --------------------------*/

2
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@@ -80,7 +80,7 @@
$(document).ready(function() {
var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>";
$(".examples, div.sourceCode").addClass("hasCopyButton");
$("div.sourceCode").addClass("hasCopyButton");
// Insert copy buttons:
$(copyButton).prependTo(".hasCopyButton");

10
docs/pkgdown.yml
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@@ -1,6 +1,6 @@
pandoc: 2.11.4
pkgdown: 1.6.1
pkgdown_sha: ~
pkgdown: 1.6.1.9001
pkgdown_sha: ce9781a15c7ea07df9fb17a11295ba4abec0b54b
articles:
AMR: AMR.html
EUCAST: EUCAST.html
@@ -12,8 +12,8 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-07-12T20:09Z
last_built: 2021-07-23T19:23Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

52
docs/reference/AMR-deprecated.html
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. <strong>They will be removed in a future release.</strong> Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
</div>
<pre class="usage"><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span>
<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -415,7 +423,7 @@
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@@ -444,11 +452,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
</div>
</footer>
@@ -457,6 +465,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
</body>
</html>

48
docs/reference/AMR.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -306,11 +314,11 @@ The Netherlands
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
</div>
</footer>
@@ -319,6 +327,8 @@ The Netherlands
</body>
</html>

52
docs/reference/WHOCC.html
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
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<li>
<a href="../articles/benchmarks.html">
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<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -260,11 +268,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='as.ab.html'>as.ab</a></span><span class='op'>(</span><span class='st'>"meropenem"</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'><a href='as.ab.html'>as.ab</a></span><span class='op'>(</span><span class='st'>"meropenem"</span><span class='op'>)</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"J01DH02"</span><span class='op'>)</span>
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span><span class='op'>(</span><span class='st'>"flucloxacillin"</span><span class='op'>)</span>
</pre>
</code></pre></div>
</div>
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@@ -276,11 +284,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -289,6 +297,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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50
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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<a href="../articles/AMR.html">
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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<a href="../articles/WHONET.html">
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Work with WHONET data
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<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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<a href="../reference/mo_property.html">
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Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
</div>
<pre class="usage"><span class='va'>WHONET</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>WHONET</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -298,11 +306,11 @@
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -311,6 +319,8 @@
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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<a href="../articles/AMR.html">
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</a>
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Predict antimicrobial resistance
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Data sets for download / own use
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Conduct principal component analysis for AMR
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<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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Work with WHONET data
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<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
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<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
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Apply EUCAST rules
</a>
</li>
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<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>Use this function on e.g. clinical texts from health care records. It returns a <a href='https://rdrr.io/r/base/list.html'>list</a> with all antimicrobial drugs, doses and forms of administration found in the texts.</p>
</div>
<pre class="usage"><span class='fu'>ab_from_text</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ab_from_text</span><span class='op'>(</span>
<span class='va'>text</span>,
type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span><span class='op'>)</span>,
collapse <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -250,7 +258,7 @@
thorough_search <span class='op'>=</span> <span class='cn'>NULL</span>,
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -290,14 +298,26 @@
<p>A <a href='https://rdrr.io/r/base/list.html'>list</a>, or a <a href='https://rdrr.io/r/base/character.html'>character</a> if <code>collapse</code> is not <code>NULL</code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the <code><a href='as.ab.html'>as.ab()</a></code> function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Argument <code>type</code></h3>
<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the <code><a href='as.ab.html'>as.ab()</a></code> function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.</p><h3 class='hasAnchor' id='argument-'><a class='anchor' aria-hidden='true' href='#argument-'></a>Argument <code>type</code></h3>
<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> values that are higher than 100 and do not resemble years. The output will be <a href='https://rdrr.io/r/base/numeric.html'>numeric</a>. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p><h3 class='hasAnchor' id='list-type-'><a class='anchor' aria-hidden='true' href='#list-type-'></a>Argument <code>type</code></h3>
<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href='as.ab.html'>as.ab()</a></code> internally, it will correct for misspelling.</p>
<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> values that are higher than 100 and do not resemble years. The output will be <a href='https://rdrr.io/r/base/numeric.html'>numeric</a>. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Argument <code>collapse</code></h3>
<h3 class='hasAnchor' id='argument-'><a class='anchor' aria-hidden='true' href='#argument-'></a>Argument <code>collapse</code></h3>
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
<code>df %&gt;% mutate(abx = ab_from_text(clinical_text))</code></p>
<p>The returned AB codes can be transformed to official names, groups, etc. with all <code><a href='ab_property.html'>ab_*</a></code> functions such as <code><a href='ab_property.html'>ab_name()</a></code> and <code><a href='ab_property.html'>ab_group()</a></code>, or by using the <code>translate_ab</code> argument.</p>
<p>With using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/character.html'>character</a>:<br />
<code>df %&gt;% mutate(abx = ab_from_text(clinical_text, collapse = "|"))</code></p><h3 class='hasAnchor' id='list-collapse-'><a class='anchor' aria-hidden='true' href='#list-collapse-'></a>Argument <code>collapse</code></h3>
<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
@@ -320,7 +340,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># mind the bad spelling of amoxicillin in this line, </span>
<span class='co'># straight from a true health care record:</span>
<span class='fu'>ab_from_text</span><span class='op'>(</span><span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span><span class='op'>)</span>
@@ -353,7 +373,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -365,11 +385,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -378,6 +398,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

24
docs/reference/ab_property.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Use these functions to return a specific property of an antibiotic from the <a href='antibiotics.html'>antibiotics</a> data set. All input values will be evaluated internally with <code><a href='as.ab.html'>as.ab()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>ab_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, tolower <span class='op'>=</span> <span class='cn'>FALSE</span>, snake_case <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ab_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, tolower <span class='op'>=</span> <span class='cn'>FALSE</span>, snake_case <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -266,7 +274,7 @@
<span class='fu'>ab_url</span><span class='op'>(</span><span class='va'>x</span>, open <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"name"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>ab_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"name"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -352,7 +360,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># all properties:</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># all properties:</span>
<span class='fu'>ab_name</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># "Amoxicillin"</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># J01CA04 (ATC code from the WHO)</span>
<span class='fu'>ab_cid</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># 33613 (Compound ID from PubChem)</span>
@@ -389,7 +397,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"cephtriaxone"</span><span class='op'>)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"cephthriaxone"</span><span class='op'>)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"seephthriaaksone"</span><span class='op'>)</span>
</pre>
</code></pre></div>
</div>
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@@ -401,11 +409,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -414,6 +422,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

54
docs/reference/age.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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Predict antimicrobial resistance
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<span class="fas fa-compress"></span>
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Conduct principal component analysis for AMR
</a>
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<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
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<a href="../articles/WHONET.html">
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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Survey
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@@ -242,7 +250,7 @@
<p>Calculates age in years based on a reference date, which is the sytem date at default.</p>
</div>
<pre class="usage"><span class='fu'>age</span><span class='op'>(</span><span class='va'>x</span>, reference <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span>, exact <span class='op'>=</span> <span class='cn'>FALSE</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>age</span><span class='op'>(</span><span class='va'>x</span>, reference <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span>, exact <span class='op'>=</span> <span class='cn'>FALSE</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -293,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p>To split ages into groups, use the <code><a href='age_groups.html'>age_groups()</a></code> function.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># 10 random birth dates</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># 10 random birth dates</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>birth_date <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Uniform.html'>runif</a></span><span class='op'>(</span><span class='fl'>10</span><span class='op'>)</span> <span class='op'>*</span> <span class='fl'>25000</span><span class='op'>)</span>
<span class='co'># add ages</span>
<span class='va'>df</span><span class='op'>$</span><span class='va'>age</span> <span class='op'>&lt;-</span> <span class='fu'>age</span><span class='op'>(</span><span class='va'>df</span><span class='op'>$</span><span class='va'>birth_date</span><span class='op'>)</span>
@@ -301,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='va'>df</span><span class='op'>$</span><span class='va'>age_exact</span> <span class='op'>&lt;-</span> <span class='fu'>age</span><span class='op'>(</span><span class='va'>df</span><span class='op'>$</span><span class='va'>birth_date</span>, exact <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>df</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -313,11 +321,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -326,6 +334,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

54
docs/reference/age_groups.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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Determine multi-drug resistance (MDR)
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Get properties of a microorganism
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>Split ages into age groups defined by the <code>split</code> argument. This allows for easier demographic (antimicrobial resistance) analysis.</p>
</div>
<pre class="usage"><span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>x</span>, split_at <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span><span class='op'>)</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>x</span>, split_at <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>12</span>, <span class='fl'>25</span>, <span class='fl'>55</span>, <span class='fl'>75</span><span class='op'>)</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -294,7 +302,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p>To determine ages, based on one or more reference dates, use the <code><a href='age.html'>age()</a></code> function.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>ages</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>ages</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>8</span>, <span class='fl'>16</span>, <span class='fl'>54</span>, <span class='fl'>31</span>, <span class='fl'>76</span>, <span class='fl'>101</span>, <span class='fl'>43</span>, <span class='fl'>21</span><span class='op'>)</span>
<span class='co'># split into 0-49 and 50+</span>
<span class='fu'>age_groups</span><span class='op'>(</span><span class='va'>ages</span>, <span class='fl'>50</span><span class='op'>)</span>
@@ -325,7 +333,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='st'>"age_group"</span>, minimum <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -337,11 +345,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -350,6 +358,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

26
docs/reference/antibiotic_class_selectors.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
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@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
</div>
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@@ -286,7 +294,7 @@
<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>ureidopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<span class='fu'>ureidopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -308,7 +316,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selection helpers</a> such as <code><a href='https://tidyselect.r-lib.org/reference/everything.html'>everything()</a></code>, but also work in base <span style="R">R</span> and not only in <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, see <em>Examples</em>.</p>
<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the <code>ab_class()</code> function to filter/select on a manually defined antibiotic class.</p>
<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the <code>ab_class()</code> function to filter/select on a manually defined antibiotic class.</p>
<h2 class="hasAnchor" id="full-list-of-supported-agents"><a class="anchor" href="#full-list-of-supported-agents"></a>Full list of supported agents</h2>
@@ -357,7 +365,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># base R ------------------------------------------------------------------</span>
@@ -436,7 +444,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.x</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -448,11 +456,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -461,6 +469,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
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182
docs/reference/antibiotics.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
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@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
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<a href="../index.html">
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Home
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
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Predict antimicrobial resistance
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,15 +250,87 @@
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href='as.ab.html'>as.ab()</a></code> or one of the <code><a href='ab_property.html'>ab_*</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes.</p>
</div>
<pre class="usage"><span class='va'>antibiotics</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>antibiotics</span>
<span class='va'>antivirals</span></pre>
<span class='va'>antivirals</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<h3 class='hasAnchor' id='for-the-'><a class='anchor' aria-hidden='true' href='#for-the-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='list-antibiotics-'><a class='anchor' aria-hidden='true' href='#list-antibiotics-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='-data-set-a-'><a class='anchor' aria-hidden='true' href='#-data-set-a-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='list-data-frame-'><a class='anchor' aria-hidden='true' href='#list-data-frame-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='-with-observations-and-variables-'><a class='anchor' aria-hidden='true' href='#-with-observations-and-variables-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
@@ -270,7 +350,59 @@
</ul>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<h3 class='hasAnchor' id='for-the-'><a class='anchor' aria-hidden='true' href='#for-the-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='list-antivirals-'><a class='anchor' aria-hidden='true' href='#list-antivirals-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='-data-set-a-'><a class='anchor' aria-hidden='true' href='#-data-set-a-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='list-data-frame-'><a class='anchor' aria-hidden='true' href='#list-data-frame-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='-with-observations-and-variables-'><a class='anchor' aria-hidden='true' href='#-with-observations-and-variables-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
@@ -294,7 +426,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='direct-download'><a class='anchor' aria-hidden='true' href='#direct-download'></a>Direct download</h3>
<p>These data sets are available as 'flat files' for use even without <span style="R">R</span> - you can find the files here:</p><ul>
@@ -342,11 +474,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -355,6 +487,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
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<body data-spy="scroll" data-target="#toc">
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@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -242,9 +250,9 @@
<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href='antibiotics.html'>antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
</div>
<pre class="usage"><span class='fu'>as.ab</span><span class='op'>(</span><span class='va'>x</span>, flag_multiple_results <span class='op'>=</span> <span class='cn'>TRUE</span>, info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.ab</span><span class='op'>(</span><span class='va'>x</span>, flag_multiple_results <span class='op'>=</span> <span class='cn'>TRUE</span>, info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is.ab</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
<span class='fu'>is.ab</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -325,7 +333,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"J01FA01"</span><span class='op'>)</span>
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"J 01 FA 01"</span><span class='op'>)</span>
<span class='fu'>as.ab</span><span class='op'>(</span><span class='st'>"Erythromycin"</span><span class='op'>)</span>
@@ -356,7 +364,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -368,11 +376,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -381,6 +389,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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@@ -66,9 +68,15 @@
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@@ -90,14 +98,14 @@
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Conduct principal component analysis for AMR
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,9 +250,9 @@
<p>This transforms a vector to a new class <code>disk</code>, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.</p>
</div>
<pre class="usage"><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.disk</span><span class='op'>(</span><span class='va'>x</span>, na.rm <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre>
<span class='fu'>is.disk</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -282,7 +290,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='co'># transform existing disk zones to the `disk` class</span>
<span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
AMP <span class='op'>=</span> <span class='fl'>20</span>,
@@ -301,7 +309,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
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@@ -313,11 +321,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -326,6 +334,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -242,7 +250,7 @@
<p>Use this function to determine a valid microorganism code (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
</div>
<pre class="usage"><span class='fu'>as.mo</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.mo</span><span class='op'>(</span>
<span class='va'>x</span>,
Becker <span class='op'>=</span> <span class='cn'>FALSE</span>,
Lancefield <span class='op'>=</span> <span class='cn'>FALSE</span>,
@@ -260,7 +268,7 @@
<span class='fu'>mo_uncertainties</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>mo_renamed</span><span class='op'>(</span><span class='op'>)</span></pre>
<span class='fu'>mo_renamed</span><span class='op'>(</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -311,10 +319,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>General Info</h3>
<h3 class='hasAnchor' id='general-info'><a class='anchor' aria-hidden='true' href='#general-info'></a>General Info</h3>
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre> Code Full name
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre><code> Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNMN Klebsiella pneumoniae
@@ -326,7 +334,7 @@
| \----&gt; genus, a 5-7 letter acronym
\----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</pre>
</code></pre>
<p>Values that cannot be coerced will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<p>Use the <code><a href='mo_property.html'>mo_*</a></code> functions to get properties based on the returned code, see <em>Examples</em>.</p>
@@ -339,7 +347,7 @@
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Coping with Uncertain Results</h3>
<h3 class='hasAnchor' id='coping-with-uncertain-results'><a class='anchor' aria-hidden='true' href='#coping-with-uncertain-results'></a>Coping with Uncertain Results</h3>
<p>In addition, the <code>as.mo()</code> function can differentiate four levels of uncertainty to guess valid results:</p><ul>
@@ -363,7 +371,7 @@
</ul>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Microbial Prevalence of Pathogens in Humans</h3>
<h3 class='hasAnchor' id='microbial-prevalence-of-pathogens-in-humans'><a class='anchor' aria-hidden='true' href='#microbial-prevalence-of-pathogens-in-humans'></a>Microbial Prevalence of Pathogens in Humans</h3>
<p>The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href='microorganisms.html'>microorganisms</a> and <a href='microorganisms.old.html'>microorganisms.old</a> data sets. The grouping into human pathogenic prevalence is explained in the section <em>Matching Score for Microorganisms</em> below.</p>
@@ -429,7 +437,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<p>The <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_genus()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>) to get properties based on the returned code.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='co'># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"sau"</span><span class='op'>)</span> <span class='co'># WHONET code</span>
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"stau"</span><span class='op'>)</span>
@@ -466,7 +474,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># returns "Gram negative"</span>
<span class='fu'><a href='mo_property.html'>mo_is_intrinsic_resistant</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"vanco"</span><span class='op'>)</span> <span class='co'># returns TRUE</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -478,11 +486,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -491,6 +499,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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42
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@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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<body data-spy="scroll" data-target="#toc">
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@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9020</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <code>S &lt; I &lt; R</code>.</p>
</div>
<pre class="usage"><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is.rsi</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
@@ -283,7 +291,7 @@
conserve_capped_values <span class='op'>=</span> <span class='cn'>FALSE</span>,
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>,
reference_data <span class='op'>=</span> <span class='fu'>AMR</span><span class='fu'>::</span><span class='va'><a href='rsi_translation.html'>rsi_translation</a></span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -340,43 +348,43 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>How it Works</h3>
<h3 class='hasAnchor' id='how-it-works'><a class='anchor' aria-hidden='true' href='#how-it-works'></a>How it Works</h3>
<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre class='sourceCode r'><code><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</pre></li>
</code></pre></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre class='sourceCode r'><code><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.disk</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</pre></li>
</code></pre></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
</ol>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported Guidelines</h3>
<h3 class='hasAnchor' id='supported-guidelines'><a class='anchor' aria-hidden='true' href='#supported-guidelines'></a>Supported Guidelines</h3>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2020"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After Interpretation</h3>
<h3 class='hasAnchor' id='after-interpretation'><a class='anchor' aria-hidden='true' href='#after-interpretation'></a>After Interpretation</h3>
<p>After using <code>as.rsi()</code>, you can use the <code><a href='eucast_rules.html'>eucast_rules()</a></code> defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine-Readable Interpretation Guidelines</h3>
<h3 class='hasAnchor' id='machine-readable-interpretation-guidelines'><a class='anchor' aria-hidden='true' href='#machine-readable-interpretation-guidelines'></a>Machine-Readable Interpretation Guidelines</h3>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 22,000 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>
<h3 class='hasAnchor' id='other'><a class='anchor' aria-hidden='true' href='#other'></a>Other</h3>
<p>The function <code>is.rsi()</code> detects if the input contains class <code>&lt;rsi&gt;</code>. If the input is a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, it iterates over all columns and returns a <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector.</p>
@@ -418,7 +426,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code>, <code><a href='as.mo.html'>as.mo()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://docs.ropensci.org/skimr/'>"skimr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># class &lt;rsi&gt; supported in skim() too:</span>
@@ -501,7 +509,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># mutate(across(where(is.rsi.eligible), as.rsi))</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
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@@ -513,11 +521,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -526,6 +534,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p>
</div>
<pre class="usage"><span class='fu'>atc_online_property</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>atc_online_property</span><span class='op'>(</span>
<span class='va'>atc_code</span>,
<span class='va'>property</span>,
administration <span class='op'>=</span> <span class='st'>"O"</span>,
@@ -252,7 +260,7 @@
<span class='fu'>atc_online_groups</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>atc_online_ddd</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>atc_online_ddd</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -327,7 +335,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"curl"</span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"rvest"</span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"xml2"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span><span class='op'>)</span>
@@ -338,7 +346,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, property <span class='op'>=</span> <span class='st'>"groups"</span><span class='op'>)</span> <span class='co'># search hierarchical groups of amoxicillin</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@@ -363,6 +371,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -55,6 +55,8 @@
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<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. <code><a href='proportion.html'>susceptibility()</a></code> and <code><a href='proportion.html'>resistance()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>availability</span><span class='op'>(</span><span class='va'>tbl</span>, width <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>availability</span><span class='op'>(</span><span class='va'>tbl</span>, width <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -277,7 +285,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>availability</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>availability</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
@@ -286,7 +294,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>availability</span><span class='op'>(</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -298,11 +306,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
</div>
</footer>
@@ -311,6 +319,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

24
docs/reference/bug_drug_combinations.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -242,7 +250,7 @@
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publishable/printable format, see <em>Examples</em>.</p>
</div>
<pre class="usage"><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for bug_drug_combinations</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span>
@@ -257,7 +265,7 @@
decimal.mark <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"OutDec"</span><span class='op'>)</span>,
big.mark <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>decimal.mark</span> <span class='op'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -342,7 +350,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<span class='va'>x</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span><span class='op'>(</span><span class='va'>x</span>, translate_ab <span class='op'>=</span> <span class='st'>"name (atc)"</span><span class='op'>)</span>
@@ -356,7 +364,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='st'>"E. coli"</span>,
<span class='st'>"Others"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -368,11 +376,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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</footer>
@@ -381,6 +389,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

52
docs/reference/catalogue_of_life.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
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<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
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@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -277,7 +285,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># Get version info of included data set</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># Get version info of included data set</span>
<span class='fu'><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></span><span class='op'>(</span><span class='op'>)</span>
@@ -305,7 +313,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<span class='co'>#&gt; [1] "Fungi" # Fungi?!</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
<span class='co'>#&gt; [1] "Cladosporium elegans" # Because a microorganism was found</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -317,11 +325,11 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -330,6 +338,8 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
</body>
</html>

50
docs/reference/catalogue_of_life_version.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
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<a href="../index.html">
<span class="fas fa-home"></span>
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Home
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>This function returns information about the included data from the Catalogue of Life.</p>
</div>
<pre class="usage"><span class='fu'>catalogue_of_life_version</span><span class='op'>(</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>catalogue_of_life_version</span><span class='op'>(</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -278,11 +286,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -291,6 +299,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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@@ -56,6 +56,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -67,9 +69,15 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -83,7 +91,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -91,14 +99,14 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -107,77 +115,77 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -186,14 +194,14 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -216,7 +224,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -244,7 +252,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.</p>
</div>
<pre class="usage"><span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>count_susceptible</span><span class='op'>(</span><span class='va'>...</span>, only_all_tested <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
@@ -268,7 +276,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -337,7 +345,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href='proportion.html'>susceptibility()</a></code> works to calculate the %SI:</p><pre>--------------------------------------------------------------------
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href='proportion.html'>susceptibility()</a></code> works to calculate the %SI:</p><pre><code>--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as
@@ -353,15 +361,15 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
R &lt;NA&gt; - - - -
&lt;NA&gt; &lt;NA&gt; - - - -
--------------------------------------------------------------------
</pre>
</code></pre>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre class='sourceCode r'><code> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'><a href='proportion.html'>proportion_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>=</span> <span class='fl'>1</span>
</pre>
</code></pre>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre class='sourceCode r'><code> <span class='fu'>count_S</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_I</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'>count_R</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'><a href='proportion.html'>proportion_S</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_I</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>+</span> <span class='fu'><a href='proportion.html'>proportion_R</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&gt;=</span> <span class='fl'>1</span>
</pre>
</code></pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
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@@ -374,7 +382,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<div class='dont-index'><p><code><a href='proportion.html'>proportion_*</a></code> to calculate microbial resistance and susceptibility.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># example_isolates is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># example_isolates is a data set available in the AMR package.</span>
<span class='op'>?</span><span class='va'>example_isolates</span>
<span class='fu'>count_resistant</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMX</span><span class='op'>)</span> <span class='co'># counts "R"</span>
@@ -440,7 +448,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'>count_df</span><span class='op'>(</span>translate <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
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@@ -452,11 +460,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -465,6 +473,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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44
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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</div>
@@ -242,7 +250,7 @@
<p>Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in <code><a href='eucast_rules.html'>eucast_rules()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -263,14 +271,14 @@
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Basics</h3>
<h3 class='hasAnchor' id='basics'><a class='anchor' aria-hidden='true' href='#basics'></a>Basics</h3>
<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<p>If you are familiar with the <code><a href='https://dplyr.tidyverse.org/reference/case_when.html'>case_when()</a></code> function of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what <span style="R">R</span> considers to be the 'formula notation'. The rule itself is written <em>before</em> the tilde (<code><a href='https://rdrr.io/r/base/tilde.html'>~</a></code>) and the consequence of the rule is written <em>after</em> the tilde:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
</pre>
</code></pre>
<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p><pre><span class='va'>x</span>
<p>These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:</p><pre class='sourceCode r'><code><span class='va'>x</span>
<span class='co'>#&gt; A set of custom EUCAST rules:</span>
<span class='co'>#&gt; </span>
<span class='co'>#&gt; 1. If TZP is S then set to S:</span>
@@ -278,9 +286,9 @@
<span class='co'>#&gt; </span>
<span class='co'>#&gt; 2. If TZP is R then set to R:</span>
<span class='co'>#&gt; amoxicillin (AMX), ampicillin (AMP)</span>
</pre>
</code></pre>
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p><pre><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"K. pneumoniae"</span><span class='op'>)</span>,
<p>The rules (the part <em>before</em> the tilde, in above example <code>TZP == "S"</code> and <code>TZP == "R"</code>) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column <code>TZP</code> must exist. We will create a sample data set and test the rules set:</p><pre class='sourceCode r'><code><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"K. pneumoniae"</span><span class='op'>)</span>,
TZP <span class='op'>=</span> <span class='st'>"R"</span>,
amox <span class='op'>=</span> <span class='st'>""</span>,
AMP <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span>
@@ -293,23 +301,23 @@
<span class='co'>#&gt; mo TZP amox AMP</span>
<span class='co'>#&gt; 1 E. coli R R R </span>
<span class='co'>#&gt; 2 K. pneumoniae R R R </span>
</pre>
</code></pre>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Using taxonomic properties in rules</h3>
<h3 class='hasAnchor' id='using-taxonomic-properties-in-rules'><a class='anchor' aria-hidden='true' href='#using-taxonomic-properties-in-rules'></a>Using taxonomic properties in rules</h3>
<p>There is one exception in variables used for the rules: all column names of the <a href='microorganisms.html'>microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>mo</code>, <code>fullname</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code>, <code>rank</code>, <code>ref</code>, <code>species_id</code>, <code>source</code>, <code>prevalence</code> and <code>snomed</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p><pre><span class='va'>y</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<p>There is one exception in variables used for the rules: all column names of the <a href='microorganisms.html'>microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: <code>mo</code>, <code>fullname</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code>, <code>rank</code>, <code>ref</code>, <code>species_id</code>, <code>source</code>, <code>prevalence</code> and <code>snomed</code>. Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p><pre class='sourceCode r'><code><span class='va'>y</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"S"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"S"</span>,
<span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>df</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>y</span><span class='op'>)</span>
<span class='co'>#&gt; mo TZP amox AMP</span>
<span class='co'>#&gt; 1 E. coli R </span>
<span class='co'>#&gt; 2 K. pneumoniae R R R</span>
</pre>
</code></pre>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage of antibiotic group names</h3>
<h3 class='hasAnchor' id='usage-of-antibiotic-group-names'><a class='anchor' aria-hidden='true' href='#usage-of-antibiotic-group-names'></a>Usage of antibiotic group names</h3>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the antibiotic agents that will be matched when running the rule.</p><ul>
@@ -354,7 +362,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>example_isolates</span>,
rules <span class='op'>=</span> <span class='st'>"custom"</span>,
@@ -365,7 +373,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='va'>x2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>x</span>,
<span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>carbapenems</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>x2</span>
</pre>
</code></pre></div>
</div>
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@@ -377,11 +385,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -390,6 +398,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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50
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@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -66,9 +68,15 @@
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<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
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@@ -82,7 +90,7 @@
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
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Import data from SPSS/SAS/Stata
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with <code><a href='eucast_rules.html'>eucast_dosage()</a></code>.</p>
</div>
<pre class="usage"><span class='va'>dosage</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>dosage</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -284,11 +292,11 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -297,6 +305,8 @@
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@@ -56,6 +56,8 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -67,9 +69,15 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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@@ -83,7 +91,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
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</span>
</div>
@@ -244,7 +252,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see <em>Details</em>.</p>
</div>
<pre class="usage"><span class='fu'>eucast_rules</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>eucast_rules</span><span class='op'>(</span>
<span class='va'>x</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
@@ -258,7 +266,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='va'>ab</span>, administration <span class='op'>=</span> <span class='st'>"iv"</span>, version_breakpoints <span class='op'>=</span> <span class='fl'>11</span><span class='op'>)</span></pre>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='va'>ab</span>, administration <span class='op'>=</span> <span class='st'>"iv"</span>, version_breakpoints <span class='op'>=</span> <span class='fl'>11</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -337,17 +345,17 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br /></p>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>March 2021</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Custom Rules</h3>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>March 2021</a>.</p><h3 class='hasAnchor' id='custom-rules'><a class='anchor' aria-hidden='true' href='#custom-rules'></a>Custom Rules</h3>
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>example_isolates</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>x</span><span class='op'>)</span>
</pre>
</code></pre>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' Rules</h3>
<h3 class='hasAnchor' id='-other-rules'><a class='anchor' aria-hidden='true' href='#-other-rules'></a>'Other' Rules</h3>
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
@@ -384,7 +392,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='va'>a</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>,
@@ -426,7 +434,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># }</span>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"tobra"</span>, <span class='st'>"genta"</span>, <span class='st'>"cipro"</span><span class='op'>)</span>, <span class='st'>"iv"</span><span class='op'>)</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -438,11 +446,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -451,6 +459,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

50
docs/reference/example_isolates.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span>
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How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
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Predict antimicrobial resistance
</a>
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Data sets for download / own use
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<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
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<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
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<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
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<li>
<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
</a>
@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read <a href='https://msberends.github.io/AMR/articles/AMR.html'>the tutorial on our website</a>.</p>
</div>
<pre class="usage"><span class='va'>example_isolates</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>example_isolates</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -282,11 +290,11 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -295,6 +303,8 @@
</body>
</html>

50
docs/reference/example_isolates_unclean.html
View File

@@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -90,14 +98,14 @@
<ul class="nav navbar-nav">
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<a href="../index.html">
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<span class="fa fa-home"></span>
Home
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</li>
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<span class="fas fa-question-circle"></span>
<span class="fa fa-question-circle"></span>
How to
@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
<span class="fas fa-directions"></span>
<span class="fa fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
<span class="fa fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
@@ -185,14 +193,14 @@
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
<span class="fa fa-book-open"></span>
Manual
</a>
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<a href="../authors.html">
<span class="fas fa-users"></span>
<span class="fa fa-users"></span>
Authors
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@@ -215,7 +223,7 @@
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,7 +250,7 @@
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.</p>
</div>
<pre class="usage"><span class='va'>example_isolates_unclean</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>example_isolates_unclean</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -277,11 +285,11 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -290,6 +298,8 @@
</body>
</html>

34
docs/reference/first_isolate.html
View File

@@ -56,6 +56,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -67,9 +69,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -83,7 +91,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
@@ -244,7 +252,7 @@
). To determine patient episodes not necessarily based on microorganisms, use <code><a href='get_episode.html'>is_new_episode()</a></code> that also supports grouping with the <code>dplyr</code> package.</p>
</div>
<pre class="usage"><span class='fu'>first_isolate</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>first_isolate</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
@@ -275,7 +283,7 @@
episode_days <span class='op'>=</span> <span class='fl'>365</span>,
method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"phenotype-based"</span>, <span class='st'>"episode-based"</span>, <span class='st'>"patient-based"</span>, <span class='st'>"isolate-based"</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -377,7 +385,7 @@
<p>To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.</p>
<p>These functions are context-aware. This means that the <code>x</code> argument can be left blank if used inside a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> call, see <em>Examples</em>.</p>
<p>The <code>first_isolate()</code> function is a wrapper around the <code><a href='get_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Different methods</h3>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='different-methods'><a class='anchor' aria-hidden='true' href='#different-methods'></a>Different methods</h3>
<p>According to Hindler <em>et al.</em> (2007, doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a>
@@ -405,23 +413,23 @@
</table>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Isolate-based</h4>
<h4 class='hasAnchor' id='isolate-based'><a class='anchor' aria-hidden='true' href='#isolate-based'></a>Isolate-based</h4>
<p>This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the <code>first_isolate()</code> function. For example, the default setting for <code>include_unknown</code> (<code>FALSE</code>) will omit selection of rows without a microbial ID.</p>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Patient-based</h4>
<h4 class='hasAnchor' id='patient-based'><a class='anchor' aria-hidden='true' href='#patient-based'></a>Patient-based</h4>
<p>To include every genus-species combination per patient once, set the <code>episode_days</code> to <code>Inf</code>. Although often inappropriate, this method makes sure that no duplicate isolates are selected from the same patient. In a large longitudinal data set, this could mean that isolates are <em>excluded</em> that were found years after the initial isolate.</p>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Episode-based</h4>
<h4 class='hasAnchor' id='episode-based'><a class='anchor' aria-hidden='true' href='#episode-based'></a>Episode-based</h4>
<p>To include every genus-species combination per patient episode once, set the <code>episode_days</code> to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data, long episodes are common for analysing regional and national data.</p>
<p>This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) isolate cannot be differentiated from a wildtype <em>Staphylococcus aureus</em> isolate.</p>
<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Phenotype-based</h4>
<h4 class='hasAnchor' id='phenotype-based'><a class='anchor' aria-hidden='true' href='#phenotype-based'></a>Phenotype-based</h4>
<p>This is a more reliable method, since it also <em>weighs</em> the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:</p><ol>
@@ -454,7 +462,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='key_antimicrobials.html'>key_antimicrobials()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>]</span>
@@ -494,7 +502,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># when you (erroneously) would have used all isolates for analysis.</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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@@ -506,11 +514,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p><code>g.test()</code> performs chi-squared contingency table tests and goodness-of-fit tests, just like <code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code> but is more reliable (1). A <em>G</em>-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a <strong><em>G</em>-test of goodness-of-fit</strong>), or to see whether the proportions of one variable are different for different values of the other variable (called a <strong><em>G</em>-test of independence</strong>).</p>
</div>
<pre class="usage"><span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span>, y <span class='op'>=</span> <span class='cn'>NULL</span>, p <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>/</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, rescale.p <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span>, y <span class='op'>=</span> <span class='cn'>NULL</span>, p <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>/</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, rescale.p <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -305,14 +313,25 @@
<p>If <code>x</code> is a <a href='https://rdrr.io/r/base/matrix.html'>matrix</a> with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of <code>x</code> must be non-negative integers. Otherwise, <code>x</code> and <code>y</code> must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.</p>
<p>The p-value is computed from the asymptotic chi-squared distribution of the test statistic.</p>
<p>In the contingency table case simulation is done by random sampling from the set of all contingency tables with given marginals, and works only if the marginals are strictly positive. Note that this is not the usual sampling situation assumed for a chi-squared test (such as the <em>G</em>-test) but rather that for Fisher's exact test.</p>
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)</h3>
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p><h3 class='hasAnchor' id='list-g-'><a class='anchor' aria-hidden='true' href='#list-g-'></a><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)</h3>
<p>Use the <em>G</em>-test of goodness-of-fit when you have one nominal variable with two or more values (such as male and female, or red, pink and white flowers). You compare the observed counts of numbers of observations in each category with the expected counts, which you calculate using some kind of theoretical expectation (such as a 1:1 sex ratio or a 1:2:1 ratio in a genetic cross).</p>
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>).</p>
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p><h3 class='hasAnchor' id='-test-of-goodness-of-fit-likelihood-ratio-test-'><a class='anchor' aria-hidden='true' href='#-test-of-goodness-of-fit-likelihood-ratio-test-'></a><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)</h3>
<p>Use the <em>G</em>-test of goodness-of-fit when you have one nominal variable with two or more values (such as male and female, or red, pink and white flowers). You compare the observed counts of numbers of observations in each category with the expected counts, which you calculate using some kind of theoretical expectation (such as a 1:1 sex ratio or a 1:2:1 ratio in a genetic cross).</p>
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>).</p>
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a><em>G</em>-test of Independence</h3>
<h3 class='hasAnchor' id='list-g-'><a class='anchor' aria-hidden='true' href='#list-g-'></a><em>G</em>-test of Independence</h3>
<p>Use the <em>G</em>-test of independence when you have two nominal variables, each with two or more possible values. You want to know whether the proportions for one variable are different among values of the other variable.</p>
<p>It is also possible to do a <em>G</em>-test of independence with more than two nominal variables. For example, Jackson et al. (2013) also had data for children under 3, so you could do an analysis of old vs. young, thigh vs. arm, and reaction vs. no reaction, all analyzed together.</p>
<p>Fisher's exact test (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>) is an <strong>exact</strong> test, where the <em>G</em>-test is still only an <strong>approximation</strong>. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.</p>
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>), and they will give approximately the same results.</p><h3 class='hasAnchor' id='-test-of-independence'><a class='anchor' aria-hidden='true' href='#-test-of-independence'></a><em>G</em>-test of Independence</h3>
<p>Use the <em>G</em>-test of independence when you have two nominal variables, each with two or more possible values. You want to know whether the proportions for one variable are different among values of the other variable.</p>
@@ -320,14 +339,14 @@
<p>Fisher's exact test (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>) is an <strong>exact</strong> test, where the <em>G</em>-test is still only an <strong>approximation</strong>. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.</p>
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>), and they will give approximately the same results.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>How the Test Works</h3>
<h3 class='hasAnchor' id='how-the-test-works'><a class='anchor' aria-hidden='true' href='#how-the-test-works'></a>How the Test Works</h3>
<p>Unlike the exact test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
<p>The <em>G</em>-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a <em>G</em>-statistic is:</p>
<p>\(G = 2 * sum(x * log(x / E))\)</p>
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre><span class='va'>p</span> <span class='op'>&lt;-</span> <span class='fu'>stats</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span><span class='op'>(</span><span class='va'>G</span>, <span class='va'>df</span>, lower.tail <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
</pre>
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre class='sourceCode r'><code><span class='va'>p</span> <span class='op'>&lt;-</span> <span class='fu'>stats</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span><span class='op'>(</span><span class='va'>G</span>, <span class='va'>df</span>, lower.tail <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
</code></pre>
<p>where <code>df</code> are the degrees of freedom.</p>
<p>If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use <em>G</em>-tests for each category, of course.</p>
@@ -355,7 +374,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<div class='dont-index'><p><code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># = EXAMPLE 1 =</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># = EXAMPLE 1 =</span>
<span class='co'># Shivrain et al. (2006) crossed clearfield rice (which are resistant</span>
<span class='co'># to the herbicide imazethapyr) with red rice (which are susceptible to</span>
<span class='co'># imazethapyr). They then crossed the hybrid offspring and examined the</span>
@@ -387,7 +406,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
<span class='co'># There is a significant difference from a 1:1 ratio.</span>
<span class='co'># Meaning: there are significantly more left-billed birds.</span>
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<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
<span class="fa fa-clipboard-list"></span>
Survey
</a>
@@ -242,9 +250,9 @@
<p>These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis. The <code>get_episode()</code> function returns the index number of the episode per group, while the <code>is_new_episode()</code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode.</p>
</div>
<pre class="usage"><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -293,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span> <span class='co'># indices</span>
@@ -353,7 +361,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>flag_episode <span class='op'>=</span> <span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, <span class='fl'>365</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -365,11 +373,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -378,6 +386,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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56
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View File

@@ -55,6 +55,8 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
@@ -66,9 +68,15 @@
</head>
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<div class="container template-reference-topic">
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@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/AMR.html">
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>Produces a <code>ggplot2</code> variant of a so-called <a href='https://en.wikipedia.org/wiki/Biplot'>biplot</a> for PCA (principal component analysis), but is more flexible and more appealing than the base <span style="R">R</span> <code><a href='https://rdrr.io/r/stats/biplot.html'>biplot()</a></code> function.</p>
</div>
<pre class="usage"><span class='fu'>ggplot_pca</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ggplot_pca</span><span class='op'>(</span>
<span class='va'>x</span>,
choices <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>,
scale <span class='op'>=</span> <span class='fl'>1</span>,
@@ -265,7 +273,7 @@
arrows_alpha <span class='op'>=</span> <span class='fl'>0.75</span>,
base_textsize <span class='op'>=</span> <span class='fl'>10</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -393,7 +401,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a 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.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
@@ -418,7 +426,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='op'>}</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -430,11 +438,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -443,6 +451,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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View File

@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
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@@ -82,7 +90,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
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Conduct principal component analysis for AMR
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Get properties of a microorganism
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<span class="fas fa-capsules"></span>
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Get properties of an antibiotic
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<a href="../articles/benchmarks.html">
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Other: benchmarks
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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<span class="fas fa-clipboard-list"></span>
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@@ -242,7 +250,7 @@
<p>Use these functions to create bar plots for AMR data analysis. All functions rely on <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> functions.</p>
</div>
<pre class="usage"><span class='fu'>ggplot_rsi</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>ggplot_rsi</span><span class='op'>(</span>
<span class='va'>data</span>,
position <span class='op'>=</span> <span class='cn'>NULL</span>,
x <span class='op'>=</span> <span class='st'>"antibiotic"</span>,
@@ -299,7 +307,7 @@
combine_IR <span class='op'>=</span> <span class='cn'>FALSE</span>,
datalabels.size <span class='op'>=</span> <span class='fl'>3</span>,
datalabels.colour <span class='op'>=</span> <span class='st'>"grey15"</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -404,7 +412,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href='count.html'>count_df()</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>The Functions</h3>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href='count.html'>count_df()</a></code>.</p><h3 class='hasAnchor' id='the-functions'><a class='anchor' aria-hidden='true' href='#the-functions'></a>The Functions</h3>
<p><code>geom_rsi()</code> will take any variable from the data that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
@@ -429,7 +437,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&amp;</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
@@ -507,7 +515,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
datalabels <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -519,11 +527,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -532,6 +540,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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@@ -242,12 +250,12 @@
<p>This tries to find a column name in a data set based on information from the <a href='antibiotics.html'>antibiotics</a> data set. Also supports WHONET abbreviations.</p>
</div>
<pre class="usage"><span class='fu'>guess_ab_col</span><span class='op'>(</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>guess_ab_col</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
search_string <span class='op'>=</span> <span class='cn'>NULL</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span></pre>
<span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -290,7 +298,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>amox <span class='op'>=</span> <span class='st'>"S"</span>,
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>amox <span class='op'>=</span> <span class='st'>"S"</span>,
tetr <span class='op'>=</span> <span class='st'>"R"</span><span class='op'>)</span>
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"amoxicillin"</span><span class='op'>)</span>
@@ -317,7 +325,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
AMP_ED20 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span>
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"ampicillin"</span><span class='op'>)</span>
<span class='co'># [1] "AMP_ED20"</span>
</pre>
</code></pre></div>
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -342,6 +350,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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@@ -54,6 +54,8 @@
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@@ -81,7 +89,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9021</span>
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</span>
</div>
@@ -418,7 +426,7 @@
<tr>
<th colspan="2">
<h2 id="section-preparing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-preparing-data-antimicrobial-resistance" class="anchor"></a>Preparing data: antimicrobial resistance</h2>
<p class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></p>
<p class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></p>
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@@ -685,11 +693,11 @@
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -698,6 +706,8 @@
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
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@@ -82,7 +90,7 @@
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
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Get properties of an antibiotic
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,7 +250,7 @@
<p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
</div>
<pre class="usage"><span class='va'>intrinsic_resistant</span></pre>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>intrinsic_resistant</span></code></pre></div>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@@ -268,7 +276,7 @@
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>intrinsic_resistant</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>antibiotic</span> <span class='op'>==</span> <span class='st'>"Vancomycin"</span>, <span class='va'>microorganism</span> <span class='op'>%like%</span> <span class='st'>"Enterococcus"</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
@@ -276,7 +284,7 @@
<span class='co'># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -288,11 +296,11 @@
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -301,6 +309,8 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@@ -90,14 +98,14 @@
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@@ -106,77 +114,77 @@
<ul class="dropdown-menu" role="menu">
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Determine multi-drug resistance (MDR)
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@@ -185,14 +193,14 @@
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@@ -215,7 +223,7 @@
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@@ -242,9 +250,9 @@
<p>According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.</p>
</div>
<pre class="usage"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>italicize_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span></pre>
<span class='fu'>italicize_taxonomy</span><span class='op'>(</span><span class='va'>string</span>, type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"markdown"</span>, <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -277,21 +285,21 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of Staphylococcus aureus isolates"</span><span class='op'>)</span>
<span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/cat.html'>cat</a></span><span class='op'>(</span><span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"An overview of S. aureus isolates"</span>, type <span class='op'>=</span> <span class='st'>"ansi"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># since ggplot2 supports no markdown (yet), use</span>
<span class='co'># italicise_taxonomy() and the `ggtext` pkg for titles:</span>
<span class='co'># italicise_taxonomy() and the `ggtext` package for titles:</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://wilkelab.org/ggtext/'>"ggtext"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMC</span>,
title <span class='op'>=</span> <span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"Amoxi/clav in E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>AMC</span>,
title <span class='op'>=</span> <span class='fu'>italicise_taxonomy</span><span class='op'>(</span><span class='st'>"Amoxi/clav in E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>+</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></span><span class='op'>(</span>plot.title <span class='op'>=</span> <span class='fu'>ggtext</span><span class='fu'>::</span><span class='fu'><a href='https://wilkelab.org/ggtext/reference/element_markdown.html'>element_markdown</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@@ -303,11 +311,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@@ -316,6 +324,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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@@ -55,6 +55,8 @@
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@@ -66,9 +68,15 @@
</head>
<body data-spy="scroll" data-target="#toc">
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@@ -82,7 +90,7 @@
</button>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
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@@ -242,7 +250,7 @@
<p>Join the data set <a href='microorganisms.html'>microorganisms</a> easily to an existing data set or to a <a href='https://rdrr.io/r/base/character.html'>character</a> vector.</p>
</div>
<pre class="usage"><span class='fu'>inner_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>inner_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, suffix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"2"</span>, <span class='st'>""</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -252,7 +260,7 @@
<span class='fu'>semi_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>anti_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>anti_join_microorganisms</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -296,7 +304,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"K. pneumoniae"</span><span class='op'>)</span><span class='op'>)</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"K. pneumoniae"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>left_join_microorganisms</span><span class='op'>(</span><span class='st'>"B_KLBSL_PNMN"</span><span class='op'>)</span>
<span class='co'># \donttest{</span>
@@ -316,7 +324,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>colnames</a></span><span class='op'>(</span><span class='va'>df_joined</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@@ -328,11 +336,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -341,6 +349,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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