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(v1.7.1.9009) fix for ab class selectors
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@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 1.7.1.9008
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Version: 1.7.1.9009
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Date: 2021-06-23
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Date: 2021-07-03
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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Authors@R: c(
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person(role = c("aut", "cre"),
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person(role = c("aut", "cre"),
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6
NEWS.md
6
NEWS.md
@ -1,5 +1,5 @@
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# `AMR` 1.7.1.9008
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# `AMR` 1.7.1.9009
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## <small>Last updated: 23 June 2021</small>
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## <small>Last updated: 3 July 2021</small>
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### Changed
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### Changed
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* Antibiotic class selectors (see `ab_class()`)
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* Antibiotic class selectors (see `ab_class()`)
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@ -13,6 +13,8 @@
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* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
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* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
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* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
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* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
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* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
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* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
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* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish
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* More informative warnings for all `count_*()`, `proportion_*()` functions (and `resistant()` and `susceptible()`) when they return NA because of too few test results. The warnings now include the official drug name and if used, the `dplyr` group name.
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# `AMR` 1.7.1
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# `AMR` 1.7.1
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@ -736,22 +736,22 @@ get_current_data <- function(arg_name, call) {
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}
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}
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# try a manual (base R) method, by going over all underlying environments with sys.frames()
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# try a manual (base R) method, by going over all underlying environments with sys.frames()
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for (el in sys.frames()) {
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for (env in sys.frames()) {
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if (!is.null(el$`.Generic`)) {
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if (!is.null(env$`.Generic`)) {
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# don't check `".Generic" %in% names(el)`, because in R < 3.2, `names(el)` is always NULL
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# don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL
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if (!is.null(el$`.data`) && is.data.frame(el$`.data`)) {
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if (!is.null(env$`.data`) && is.data.frame(env$`.data`)) {
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# an element `.data` will be in the environment when using `dplyr::select()`
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# an element `.data` will be in the environment when using `dplyr::select()`
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# (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
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# (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
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return(structure(el$`.data`, type = "dplyr_selector"))
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return(structure(env$`.data`, type = "dplyr_selector"))
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} else if (!is.null(el$xx) && is.data.frame(el$xx)) {
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} else if (!is.null(env$xx) && is.data.frame(env$xx)) {
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# an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
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# an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
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return(structure(el$xx, type = "base_R"))
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return(structure(env$xx, type = "base_R"))
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} else if (!is.null(el$x) && is.data.frame(el$x)) {
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} else if (!is.null(env$x) && is.data.frame(env$x)) {
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# an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
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# an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
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return(structure(el$x, type = "base_R"))
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return(structure(env$x, type = "base_R"))
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}
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}
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}
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}
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}
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}
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@ -786,19 +786,19 @@ get_current_column <- function() {
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}
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}
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}
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}
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# cur_column() doesn't always work (only allowed for conditions set by dplyr), but it's probably still possible:
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# cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
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frms <- lapply(sys.frames(), function(el) {
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frms <- lapply(sys.frames(), function(env) {
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if ("i" %in% names(el)) {
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if (!is.null(env$i)) {
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if ("tibble_vars" %in% names(el)) {
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if (!is.null(env$tibble_vars)) {
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# for mutate_if()
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# for mutate_if()
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el$tibble_vars[el$i]
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env$tibble_vars[env$i]
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} else {
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} else {
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# for mutate(across())
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# for mutate(across())
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df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
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df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
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if (is.data.frame(df)) {
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if (is.data.frame(df)) {
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colnames(df)[el$i]
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colnames(df)[env$i]
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} else {
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} else {
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el$i
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env$i
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}
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}
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}
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}
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} else {
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} else {
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@ -816,7 +816,7 @@ get_current_column <- function() {
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}
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}
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is_null_or_grouped_tbl <- function(x) {
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is_null_or_grouped_tbl <- function(x) {
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# attribute "grouped_df" might change at one point, so only set in one place; here.
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# class "grouped_df" might change at one point, so only set in one place; here.
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is.null(x) || inherits(x, "grouped_df")
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is.null(x) || inherits(x, "grouped_df")
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}
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}
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@ -825,7 +825,7 @@ unique_call_id <- function(entire_session = FALSE) {
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c(envir = "session",
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c(envir = "session",
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call = "session")
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call = "session")
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} else {
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} else {
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# combination of environment ID (like "0x7fed4ee8c848")
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# combination of environment ID (such as "0x7fed4ee8c848")
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# and highest system call
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# and highest system call
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call <- paste0(deparse(sys.calls()[[1]]), collapse = "")
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call <- paste0(deparse(sys.calls()[[1]]), collapse = "")
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if (!interactive() || call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
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if (!interactive() || call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
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@ -299,7 +299,7 @@ ab_selector <- function(function_name,
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# get the columns with a group names in the chosen ab class
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# get the columns with a group names in the chosen ab class
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agents <- ab_in_data[names(ab_in_data) %in% abx]
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agents <- ab_in_data[names(ab_in_data) %in% abx]
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if (message_not_thrown_before(function_name)) {
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if (message_not_thrown_before(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))) {
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if (length(agents) == 0) {
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if (length(agents) == 0) {
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message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
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message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
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} else {
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} else {
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@ -315,7 +315,7 @@ ab_selector <- function(function_name,
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ifelse(length(agents) == 1, "column: ", "columns: "),
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ifelse(length(agents) == 1, "column: ", "columns: "),
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vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
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vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
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}
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}
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remember_thrown_message(function_name)
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remember_thrown_message(paste0(function_name, ".", paste(pkg_env$get_column_abx.out, collapse = "|")))
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}
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}
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if (!is.null(attributes(vars_df)$type) &&
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if (!is.null(attributes(vars_df)$type) &&
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@ -97,16 +97,39 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
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}
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}
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get_column_abx <- function(x,
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get_column_abx <- function(x,
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...,
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soft_dependencies = NULL,
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soft_dependencies = NULL,
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hard_dependencies = NULL,
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hard_dependencies = NULL,
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verbose = FALSE,
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verbose = FALSE,
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info = TRUE,
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info = TRUE,
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only_rsi_columns = FALSE,
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only_rsi_columns = FALSE,
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sort = TRUE,
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sort = TRUE,
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...) {
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reuse_previous_result = TRUE) {
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# check if retrieved before, then get it from package environment
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# check if retrieved before, then get it from package environment
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if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
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if (isTRUE(reuse_previous_result) && identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
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# so within the same call, within the same environment, we got here again.
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# but we could've come from another function within the same call, so now only check the columns that changed
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# first remove the columns that are not existing anymore
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previous <- pkg_env$get_column_abx.out
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current <- previous[previous %in% colnames(x)]
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# then compare columns in current call with columns in original call
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new_cols <- colnames(x)[!colnames(x) %in% pkg_env$get_column_abx.checked_cols]
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if (length(new_cols) > 0) {
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# these columns did not exist in the last call, so add them
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new_cols_rsi <- get_column_abx(x[, new_cols, drop = FALSE], reuse_previous_result = FALSE, info = FALSE, sort = FALSE)
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current <- c(current, new_cols_rsi)
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# order according to data in current call
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current <- current[match(colnames(x)[colnames(x) %in% current], current)]
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}
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# update pkg environment to improve speed on next run
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pkg_env$get_column_abx.out <- current
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pkg_env$get_column_abx.checked_cols <- colnames(x)
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# and return right values
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return(pkg_env$get_column_abx.out)
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return(pkg_env$get_column_abx.out)
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}
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}
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@ -123,6 +146,7 @@ get_column_abx <- function(x,
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}
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}
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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x.bak <- x
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if (only_rsi_columns == TRUE) {
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if (only_rsi_columns == TRUE) {
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x <- x[, which(is.rsi(x)), drop = FALSE]
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x <- x[, which(is.rsi(x)), drop = FALSE]
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}
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}
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@ -163,8 +187,8 @@ get_column_abx <- function(x,
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abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)),
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abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)),
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stringsAsFactors = FALSE)
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stringsAsFactors = FALSE)
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df_trans <- df_trans[!is.na(df_trans$abcode), , drop = FALSE]
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df_trans <- df_trans[!is.na(df_trans$abcode), , drop = FALSE]
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x <- as.character(df_trans$colnames)
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out <- as.character(df_trans$colnames)
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names(x) <- df_trans$abcode
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names(out) <- df_trans$abcode
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# add from self-defined dots (...):
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# add from self-defined dots (...):
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# such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
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# such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
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@ -177,33 +201,34 @@ get_column_abx <- function(x,
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immediate = TRUE)
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immediate = TRUE)
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}
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}
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# turn all NULLs to NAs
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# turn all NULLs to NAs
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dots <- unlist(lapply(dots, function(x) if (is.null(x)) NA else x))
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dots <- unlist(lapply(dots, function(dot) if (is.null(dot)) NA else dot))
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names(dots) <- newnames
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names(dots) <- newnames
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dots <- dots[!is.na(names(dots))]
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dots <- dots[!is.na(names(dots))]
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# merge, but overwrite automatically determined ones by 'dots'
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# merge, but overwrite automatically determined ones by 'dots'
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x <- c(x[!x %in% dots & !names(x) %in% names(dots)], dots)
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out <- c(out[!out %in% dots & !names(out) %in% names(dots)], dots)
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# delete NAs, this will make e.g. eucast_rules(... TMP = NULL) work to prevent TMP from being used
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# delete NAs, this will make e.g. eucast_rules(... TMP = NULL) work to prevent TMP from being used
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x <- x[!is.na(x)]
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out <- out[!is.na(out)]
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}
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}
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if (length(x) == 0) {
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if (length(out) == 0) {
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if (info == TRUE) {
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if (info == TRUE) {
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message_("No columns found.")
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message_("No columns found.")
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}
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}
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pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
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pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
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pkg_env$get_column_abx.out <- x
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pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
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return(x)
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pkg_env$get_column_abx.out <- out
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return(out)
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}
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}
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# sort on name
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# sort on name
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if (sort == TRUE) {
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if (sort == TRUE) {
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x <- x[order(names(x), x)]
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out <- out[order(names(out), out)]
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}
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}
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duplicates <- c(x[duplicated(x)], x[duplicated(names(x))])
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duplicates <- c(out[duplicated(out)], out[duplicated(names(out))])
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duplicates <- duplicates[unique(names(duplicates))]
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duplicates <- duplicates[unique(names(duplicates))]
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x <- c(x[!names(x) %in% names(duplicates)], duplicates)
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out <- c(out[!names(out) %in% names(duplicates)], duplicates)
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if (sort == TRUE) {
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if (sort == TRUE) {
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x <- x[order(names(x), x)]
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out <- out[order(names(out), out)]
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}
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}
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# succeeded with auto-guessing
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# succeeded with auto-guessing
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@ -211,14 +236,14 @@ get_column_abx <- function(x,
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message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
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message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
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}
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}
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for (i in seq_len(length(x))) {
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for (i in seq_len(length(out))) {
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if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
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if (info == TRUE & verbose == TRUE & !names(out[i]) %in% names(duplicates)) {
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message_("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
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message_("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
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" (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
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" (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ").")
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}
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}
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if (info == TRUE & names(x[i]) %in% names(duplicates)) {
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if (info == TRUE & names(out[i]) %in% names(duplicates)) {
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warning_(paste0("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
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warning_(paste0("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
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" (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
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" (", ab_name(names(out)[i], tolower = TRUE, language = NULL),
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"), although it was matched for multiple antibiotics or columns."),
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"), although it was matched for multiple antibiotics or columns."),
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add_fn = font_red,
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add_fn = font_red,
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call = FALSE,
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call = FALSE,
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@ -228,18 +253,18 @@ get_column_abx <- function(x,
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if (!is.null(hard_dependencies)) {
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if (!is.null(hard_dependencies)) {
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hard_dependencies <- unique(hard_dependencies)
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hard_dependencies <- unique(hard_dependencies)
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if (!all(hard_dependencies %in% names(x))) {
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if (!all(hard_dependencies %in% names(out))) {
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# missing a hard dependency will return NA and consequently the data will not be analysed
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# missing a hard dependency will return NA and consequently the data will not be analysed
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missing <- hard_dependencies[!hard_dependencies %in% names(x)]
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missing <- hard_dependencies[!hard_dependencies %in% names(out)]
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generate_warning_abs_missing(missing, any = FALSE)
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generate_warning_abs_missing(missing, any = FALSE)
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return(NA)
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return(NA)
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}
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}
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}
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}
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if (!is.null(soft_dependencies)) {
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if (!is.null(soft_dependencies)) {
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soft_dependencies <- unique(soft_dependencies)
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soft_dependencies <- unique(soft_dependencies)
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if (info == TRUE & !all(soft_dependencies %in% names(x))) {
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if (info == TRUE & !all(soft_dependencies %in% names(out))) {
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# missing a soft dependency may lower the reliability
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# missing a soft dependency may lower the reliability
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missing <- soft_dependencies[!soft_dependencies %in% names(x)]
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missing <- soft_dependencies[!soft_dependencies %in% names(out)]
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missing_msg <- vector_and(paste0(ab_name(missing, tolower = TRUE, language = NULL),
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missing_msg <- vector_and(paste0(ab_name(missing, tolower = TRUE, language = NULL),
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" (", font_bold(missing, collapse = NULL), ")"),
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" (", font_bold(missing, collapse = NULL), ")"),
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quotes = FALSE)
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quotes = FALSE)
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@ -249,8 +274,9 @@ get_column_abx <- function(x,
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}
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}
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pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
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pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
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pkg_env$get_column_abx.out <- x
|
pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
|
||||||
x
|
pkg_env$get_column_abx.out <- out
|
||||||
|
out
|
||||||
}
|
}
|
||||||
|
|
||||||
generate_warning_abs_missing <- function(missing, any = FALSE) {
|
generate_warning_abs_missing <- function(missing, any = FALSE) {
|
||||||
|
|||||||
20
R/rsi.R
20
R/rsi.R
@ -284,10 +284,26 @@ as.rsi.default <- function(x, ...) {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
x <- as.character(unlist(x))
|
# trim leading and trailing spaces, new lines, etc.
|
||||||
|
x <- trimws2(as.character(unlist(x)))
|
||||||
x.bak <- x
|
x.bak <- x
|
||||||
|
|
||||||
na_before <- length(x[is.na(x) | x == ""])
|
na_before <- length(x[is.na(x) | x == ""])
|
||||||
|
|
||||||
|
# correct for translations
|
||||||
|
trans_R <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
|
||||||
|
LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
|
||||||
|
trans_S <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
|
||||||
|
LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
|
||||||
|
trans_I <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern %in% c("Incr. exposure", "Intermediate")),
|
||||||
|
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)
|
||||||
# remove all spaces
|
# remove all spaces
|
||||||
x <- gsub(" +", "", x)
|
x <- gsub(" +", "", x)
|
||||||
# remove all MIC-like values: numbers, operators and periods
|
# remove all MIC-like values: numbers, operators and periods
|
||||||
|
|||||||
31
R/rsi_calc.R
31
R/rsi_calc.R
@ -27,7 +27,12 @@ dots2vars <- function(...) {
|
|||||||
# this function is to give more informative output about
|
# this function is to give more informative output about
|
||||||
# variable names in count_* and proportion_* functions
|
# variable names in count_* and proportion_* functions
|
||||||
dots <- substitute(list(...))
|
dots <- substitute(list(...))
|
||||||
vector_and(as.character(dots)[2:length(dots)], quotes = FALSE)
|
agents <- as.character(dots)[2:length(dots)]
|
||||||
|
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
|
||||||
|
agents_names <- ab_name(agents, tolower = TRUE, language = NULL)
|
||||||
|
need_name <- generalise_antibiotic_name(agents) != agents_names
|
||||||
|
agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
|
||||||
|
vector_and(agents_formatted, quotes = FALSE)
|
||||||
}
|
}
|
||||||
|
|
||||||
rsi_calc <- function(...,
|
rsi_calc <- function(...,
|
||||||
@ -163,8 +168,30 @@ rsi_calc <- function(...,
|
|||||||
if (denominator < minimum) {
|
if (denominator < minimum) {
|
||||||
if (data_vars != "") {
|
if (data_vars != "") {
|
||||||
data_vars <- paste(" for", data_vars)
|
data_vars <- paste(" for", data_vars)
|
||||||
|
# also add group name if used in dplyr::group_by()
|
||||||
|
cur_group <- import_fn("cur_group", "dplyr", error_on_fail = FALSE)
|
||||||
|
if (!is.null(cur_group)) {
|
||||||
|
group_df <- tryCatch(cur_group(), error = function(e) data.frame())
|
||||||
|
if (NCOL(group_df) > 0) {
|
||||||
|
# transform factors to characters
|
||||||
|
group <- vapply(FUN.VALUE = character(1), group_df, function(x) {
|
||||||
|
if (is.numeric(x)) {
|
||||||
|
format(x)
|
||||||
|
} else if (is.logical(x)) {
|
||||||
|
as.character(x)
|
||||||
|
} else {
|
||||||
|
paste0('"', x, '"')
|
||||||
}
|
}
|
||||||
warning_("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` = ", minimum, ").", call = FALSE)
|
})
|
||||||
|
data_vars <- paste0(data_vars, " in group: ", paste0(names(group), " = ", group, collapse = ", "))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
warning_("Introducing NA: ",
|
||||||
|
ifelse(denominator == 0, "no", paste("only", denominator)),
|
||||||
|
" results available",
|
||||||
|
data_vars,
|
||||||
|
" (`minimum` = ", minimum, ").", call = FALSE)
|
||||||
fraction <- NA_real_
|
fraction <- NA_real_
|
||||||
} else {
|
} else {
|
||||||
fraction <- numerator / denominator
|
fraction <- numerator / denominator
|
||||||
|
|||||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
Binary file not shown.
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -89,14 +89,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="index.html">
|
<a href="index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -105,77 +105,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/AMR.html">
|
<a href="articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/resistance_predict.html">
|
<a href="articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/datasets.html">
|
<a href="articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/PCA.html">
|
<a href="articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/MDR.html">
|
<a href="articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/WHONET.html">
|
<a href="articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/EUCAST.html">
|
<a href="articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/mo_property.html">
|
<a href="reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/ab_property.html">
|
<a href="reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/benchmarks.html">
|
<a href="articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -184,14 +184,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/index.html">
|
<a href="reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="authors.html">
|
<a href="authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -214,7 +214,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="survey.html">
|
<a href="survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<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">1.7.1.9008</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -89,14 +89,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="index.html">
|
<a href="index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -105,77 +105,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/AMR.html">
|
<a href="articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/resistance_predict.html">
|
<a href="articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/datasets.html">
|
<a href="articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/PCA.html">
|
<a href="articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/MDR.html">
|
<a href="articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/WHONET.html">
|
<a href="articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/EUCAST.html">
|
<a href="articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/mo_property.html">
|
<a href="reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/ab_property.html">
|
<a href="reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
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|
||||||
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|
||||||
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||||||
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||||||
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|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
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|
|||||||
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||||||
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|
||||||
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|
||||||
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||||||
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||||||
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|
||||||
Authors
|
Authors
|
||||||
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|
||||||
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|
|||||||
</li>
|
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|
||||||
<li>
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|
||||||
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|
||||||
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|
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|
||||||
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|
||||||
Survey
|
Survey
|
||||||
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|||||||
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|
||||||
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|
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|
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Determine multi-drug resistance (MDR)
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||||||
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||||||
Import data from SPSS/SAS/Stata
|
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|
||||||
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|
||||||
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||||||
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|
||||||
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|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
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|
||||||
</li>
|
</li>
|
||||||
<li>
|
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|
||||||
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|
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|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
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|
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|
||||||
<span class="fas fa-capsules"></span>
|
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|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
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|
||||||
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|
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|
||||||
<span class="fas fa-shipping-fast"></span>
|
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|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -142,14 +142,14 @@
|
|||||||
</li>
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|
||||||
<li>
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<a href="../reference/index.html">
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Authors
|
Authors
|
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|
||||||
@ -172,7 +172,7 @@
|
|||||||
</li>
|
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|
||||||
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|
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|
||||||
<a href="../survey.html">
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<a href="../survey.html">
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||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
@ -187,12 +187,12 @@
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
</header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
|
</header><script src="datasets_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||||
<div class="col-md-9 contents">
|
<div class="col-md-9 contents">
|
||||||
<div class="page-header toc-ignore">
|
<div class="page-header toc-ignore">
|
||||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||||
|
|
||||||
<h4 class="date">23 June 2021</h4>
|
<h4 class="date">03 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"><code>vignettes/datasets.Rmd</code></a></small>
|
||||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||||
@ -497,7 +497,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
|||||||
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
|
<a href="#antibiotic-agents" class="anchor"></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>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>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 07:50:24 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>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>
|
<p><strong>Direct download links:</strong></p>
|
||||||
<ul>
|
<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">R file</a> (32 kB)<br>
|
||||||
|
|||||||
@ -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);
|
||||||
|
}
|
||||||
|
});
|
||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9008</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
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</div>
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|
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|
||||||
@ -89,14 +89,14 @@
|
|||||||
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|
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|
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|
|
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How to
|
How to
|
||||||
|
|
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@ -105,77 +105,77 @@
|
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|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
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|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
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|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
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|
||||||
<a href="../articles/datasets.html">
|
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|
||||||
<span class="fas fa-database"></span>
|
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|
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|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
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</a>
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</a>
|
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|
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<li>
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|
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<a href="../articles/PCA.html">
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<span class="fas fa-compress"></span>
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|
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Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
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</a>
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<span class="fas fa-skull-crossbones"></span>
|
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|
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Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
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|
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</li>
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<span class="fas fa-globe-americas"></span>
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|
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|
|
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Work with WHONET data
|
Work with WHONET data
|
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</a>
|
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|
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|
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|
||||||
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|
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|
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<span class="fas fa-file-upload"></span>
|
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|
||||||
|
|
||||||
Import data from SPSS/SAS/Stata
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
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|
||||||
<li>
|
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|
||||||
<a href="../articles/EUCAST.html">
|
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|
||||||
<span class="fas fa-exchange-alt"></span>
|
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|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
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|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
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|
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</li>
|
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|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -184,14 +184,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -214,7 +214,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<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">1.7.1.9008</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -89,14 +89,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="index.html">
|
<a href="index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -105,77 +105,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/AMR.html">
|
<a href="articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/resistance_predict.html">
|
<a href="articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/datasets.html">
|
<a href="articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/PCA.html">
|
<a href="articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/MDR.html">
|
<a href="articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/WHONET.html">
|
<a href="articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/EUCAST.html">
|
<a href="articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/mo_property.html">
|
<a href="reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/ab_property.html">
|
<a href="reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/benchmarks.html">
|
<a href="articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -184,14 +184,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/index.html">
|
<a href="reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="authors.html">
|
<a href="authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -214,7 +214,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="survey.html">
|
<a href="survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -42,7 +42,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<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">1.7.1.9008</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -50,14 +50,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="index.html">
|
<a href="index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -66,77 +66,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/AMR.html">
|
<a href="articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/resistance_predict.html">
|
<a href="articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/datasets.html">
|
<a href="articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/PCA.html">
|
<a href="articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/MDR.html">
|
<a href="articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/WHONET.html">
|
<a href="articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/EUCAST.html">
|
<a href="articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/mo_property.html">
|
<a href="reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/ab_property.html">
|
<a href="reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/benchmarks.html">
|
<a href="articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -145,14 +145,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/index.html">
|
<a href="reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="authors.html">
|
<a href="authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -175,7 +175,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="survey.html">
|
<a href="survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9008</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -89,14 +89,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -105,77 +105,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -184,14 +184,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -214,7 +214,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
@ -236,12 +236,12 @@
|
|||||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div id="amr-1719008" class="section level1">
|
<div id="amr-1719009" class="section level1">
|
||||||
<h1 class="page-header" data-toc-text="1.7.1.9008">
|
<h1 class="page-header" data-toc-text="1.7.1.9009">
|
||||||
<a href="#amr-1719008" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9008</h1>
|
<a href="#amr-1719009" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9009</h1>
|
||||||
<div id="last-updated-23-june-2021" class="section level2">
|
<div id="last-updated-3-july-2021" class="section level2">
|
||||||
<h2 class="hasAnchor">
|
<h2 class="hasAnchor">
|
||||||
<a href="#last-updated-23-june-2021" class="anchor"></a><small>Last updated: 23 June 2021</small>
|
<a href="#last-updated-3-july-2021" class="anchor"></a><small>Last updated: 3 July 2021</small>
|
||||||
</h2>
|
</h2>
|
||||||
<div id="changed" class="section level3">
|
<div id="changed" class="section level3">
|
||||||
<h3 class="hasAnchor">
|
<h3 class="hasAnchor">
|
||||||
@ -265,6 +265,9 @@
|
|||||||
<li>Improved automatic column selector when <code>col_*</code> arguments are left blank, e.g. in <code><a href="../reference/first_isolate.html">first_isolate()</a></code>
|
<li>Improved automatic column selector when <code>col_*</code> arguments are left blank, e.g. in <code><a href="../reference/first_isolate.html">first_isolate()</a></code>
|
||||||
</li>
|
</li>
|
||||||
<li>The right input types for <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> are now enforced</li>
|
<li>The right input types for <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code> and <code><a href="../reference/random.html">random_rsi()</a></code> are now enforced</li>
|
||||||
|
<li>
|
||||||
|
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> can now correct for textual input (such as “Susceptible”, “Resistant”) in Dutch, English, French, German, Italian, Portuguese and Spanish</li>
|
||||||
|
<li>More informative warnings for all <code>count_*()</code>, <code>proportion_*()</code> functions (and <code>resistant()</code> and <code>susceptible()</code>) when they return NA because of too few test results. The warnings now include the official drug name and if used, the <code>dplyr</code> group name.</li>
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
@ -318,7 +321,7 @@
|
|||||||
</ul>
|
</ul>
|
||||||
</li>
|
</li>
|
||||||
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
|
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
|
||||||
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
|
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
@ -419,7 +422,7 @@
|
|||||||
<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
|
<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
|
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
|
||||||
<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
|
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code><mic></code> and <code><disk></code></p></li>
|
||||||
<li>
|
<li>
|
||||||
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
|
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
|
||||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||||
@ -476,7 +479,7 @@
|
|||||||
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
|
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
|
||||||
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
|
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
|
||||||
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
|
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
|
||||||
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
|
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
|
||||||
</ul>
|
</ul>
|
||||||
</li>
|
</li>
|
||||||
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
|
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
|
||||||
|
|||||||
@ -12,7 +12,7 @@ articles:
|
|||||||
datasets: datasets.html
|
datasets: datasets.html
|
||||||
resistance_predict: resistance_predict.html
|
resistance_predict: resistance_predict.html
|
||||||
welcome_to_AMR: welcome_to_AMR.html
|
welcome_to_AMR: welcome_to_AMR.html
|
||||||
last_built: 2021-06-23T08:16Z
|
last_built: 2021-07-03T19:56Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://msberends.github.io/AMR//reference
|
reference: https://msberends.github.io/AMR//reference
|
||||||
article: https://msberends.github.io/AMR//articles
|
article: https://msberends.github.io/AMR//articles
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9007</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -90,14 +90,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
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</li>
|
</li>
|
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<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
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<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -106,77 +106,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
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<li>
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<li>
|
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<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
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|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
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<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -185,14 +185,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -215,7 +215,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9007</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -90,14 +90,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -106,77 +106,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -185,14 +185,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -215,7 +215,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9007</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -91,14 +91,14 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -107,77 +107,77 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -186,14 +186,14 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -216,7 +216,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -83,7 +83,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9005</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -91,14 +91,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -107,77 +107,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -186,14 +186,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -216,7 +216,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9008</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -89,14 +89,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -105,77 +105,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -184,14 +184,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -214,7 +214,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9005</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -90,14 +90,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -106,77 +106,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -185,14 +185,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -215,7 +215,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9007</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -90,14 +90,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -106,77 +106,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -185,14 +185,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -215,7 +215,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9005</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -90,14 +90,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -106,77 +106,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -185,14 +185,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -215,7 +215,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<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">1.7.1.9005</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -90,14 +90,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -106,77 +106,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -185,14 +185,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -215,7 +215,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<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">1.7.1.9008</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9009</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -89,14 +89,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="index.html">
|
<a href="index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -105,77 +105,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/AMR.html">
|
<a href="articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/resistance_predict.html">
|
<a href="articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/datasets.html">
|
<a href="articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/PCA.html">
|
<a href="articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/MDR.html">
|
<a href="articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/WHONET.html">
|
<a href="articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/SPSS.html">
|
<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
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/EUCAST.html">
|
<a href="articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/mo_property.html">
|
<a href="reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/ab_property.html">
|
<a href="reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="articles/benchmarks.html">
|
<a href="articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -184,14 +184,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="reference/index.html">
|
<a href="reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="authors.html">
|
<a href="authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -214,7 +214,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="survey.html">
|
<a href="survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user