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(v1.7.1.9002) ab class selectors update

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-06-14 22:04:04 +02:00
parent 683a0e748a
commit 99be4c7e7e
36 changed files with 416 additions and 198 deletions
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6
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9001
Date: 2021-06-05
Version: 1.7.1.9002
Date: 2021-06-14
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@ -59,7 +59,7 @@ Suggests:
tinytest,
xml2
VignetteBuilder: knitr,rmarkdown
URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
URL: https://github.com/msberends/AMR, https://msberends.github.io/AMR
BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8

10
NEWS.md
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@ -1,8 +1,12 @@
# `AMR` 1.7.1.9001
## <small>Last updated: 5 June 2021</small>
# `AMR` 1.7.1.9002
## <small>Last updated: 14 June 2021</small>
### Changed
* Added more antibiotic class selectors, such as `lincosamides()` and `lipoglycopeptides()`
* Added more antibiotic class selectors: `aminopenicillins()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()` and `ureidopenicillins()`
* Added `ggplot2::autoplot()` generic for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>`
* Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them
* Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail
* Fix for using antibiotic selectors multiple times in one call (e.g., using in `dplyr::filter()` and immediately after in `dplyr::select()`)
# `AMR` 1.7.1

2
R/ab_class_selectors.R
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@ -278,7 +278,7 @@ ab_selector <- function(function_name,
}
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
vars_df <- get_current_data(arg_name = NA, call = -3, reuse_equal_call = FALSE)
vars_df <- get_current_data(arg_name = NA, call = -3, reuse_from_1st_call = FALSE)
# to improve speed, get_column_abx() will only run once when e.g. in a select or group call
ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)

110
R/count.R
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@ -82,6 +82,12 @@
#' n1 = count_all(CIP), # the actual total; sum of all three
#' n2 = n_rsi(CIP), # same - analogous to n_distinct
#' total = n()) # NOT the number of tested isolates!
#'
#' # Number of available isolates for a whole antibiotic class
#' # (i.e., in this data set columns GEN, TOB, AMK, KAN)
#' example_isolates %>%
#' group_by(hospital_id) %>%
#' summarise(across(aminoglycosides(), n_rsi))
#'
#' # Count co-resistance between amoxicillin/clav acid and gentamicin,
#' # so we can see that combination therapy does a lot more than mono therapy.
@ -108,81 +114,97 @@
#' }
#' }
count_resistant <- function(..., only_all_tested = FALSE) {
rsi_calc(...,
ab_result = "R",
only_all_tested = only_all_tested,
only_count = TRUE)
tryCatch(
rsi_calc(...,
ab_result = "R",
only_all_tested = only_all_tested,
only_count = TRUE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname count
#' @export
count_susceptible <- function(..., only_all_tested = FALSE) {
rsi_calc(...,
ab_result = c("S", "I"),
only_all_tested = only_all_tested,
only_count = TRUE)
tryCatch(
rsi_calc(...,
ab_result = c("S", "I"),
only_all_tested = only_all_tested,
only_count = TRUE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname count
#' @export
count_R <- function(..., only_all_tested = FALSE) {
rsi_calc(...,
ab_result = "R",
only_all_tested = only_all_tested,
only_count = TRUE)
tryCatch(
rsi_calc(...,
ab_result = "R",
only_all_tested = only_all_tested,
only_count = TRUE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname count
#' @export
count_IR <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_IR")) {
warning_("Using count_IR() is discouraged; use count_resistant() instead to not consider \"I\" being resistant.", call = FALSE)
if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" being resistant. This note will be shown once for this session.", as_note = FALSE)
remember_thrown_message("count_IR")
}
rsi_calc(...,
ab_result = c("I", "R"),
only_all_tested = only_all_tested,
only_count = TRUE)
tryCatch(
rsi_calc(...,
ab_result = c("I", "R"),
only_all_tested = only_all_tested,
only_count = TRUE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname count
#' @export
count_I <- function(..., only_all_tested = FALSE) {
rsi_calc(...,
ab_result = "I",
only_all_tested = only_all_tested,
only_count = TRUE)
tryCatch(
rsi_calc(...,
ab_result = "I",
only_all_tested = only_all_tested,
only_count = TRUE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname count
#' @export
count_SI <- function(..., only_all_tested = FALSE) {
rsi_calc(...,
ab_result = c("S", "I"),
only_all_tested = only_all_tested,
only_count = TRUE)
tryCatch(
rsi_calc(...,
ab_result = c("S", "I"),
only_all_tested = only_all_tested,
only_count = TRUE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname count
#' @export
count_S <- function(..., only_all_tested = FALSE) {
if (message_not_thrown_before("count_S")) {
warning_("Using count_S() is discouraged; use count_susceptible() instead to also consider \"I\" being susceptible.", call = FALSE)
if (message_not_thrown_before("count_S", entire_session = TRUE)) {
message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
remember_thrown_message("count_S")
}
rsi_calc(...,
ab_result = "S",
only_all_tested = only_all_tested,
only_count = TRUE)
tryCatch(
rsi_calc(...,
ab_result = "S",
only_all_tested = only_all_tested,
only_count = TRUE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname count
#' @export
count_all <- function(..., only_all_tested = FALSE) {
rsi_calc(...,
ab_result = c("S", "I", "R"),
only_all_tested = only_all_tested,
only_count = TRUE)
tryCatch(
rsi_calc(...,
ab_result = c("S", "I", "R"),
only_all_tested = only_all_tested,
only_count = TRUE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname count
@ -196,11 +218,13 @@ count_df <- function(data,
language = get_locale(),
combine_SI = TRUE,
combine_IR = FALSE) {
rsi_calc_df(type = "count",
data = data,
translate_ab = translate_ab,
language = language,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI))
tryCatch(
rsi_calc_df(type = "count",
data = data,
translate_ab = translate_ab,
language = language,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI)),
error = function(e) stop_(e$message, call = -5))
}

6
R/deprecated.R
View File

@ -62,7 +62,7 @@ filter_first_weighted_isolate <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
}
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
@ -104,7 +104,7 @@ key_antibiotics <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
}
key_antimicrobials(x = x,
@ -170,7 +170,7 @@ filter_ab_class <- function(x,
if (missing(x) || is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- get_current_data(arg_name = "x", call = -2 - .call_depth)
x <- get_current_data(arg_name = "x", call = -2 - .call_depth, reuse_from_1st_call = FALSE)
.x_name <- "your_data"
}
meet_criteria(x, allow_class = "data.frame", .call_depth = .call_depth)

4
R/first_isolate.R
View File

@ -207,7 +207,7 @@ first_isolate <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
}
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
@ -618,7 +618,7 @@ filter_first_isolate <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
}
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))

4
R/key_antimicrobials.R
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@ -130,7 +130,7 @@ key_antimicrobials <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
}
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, allow_NA = TRUE, is_in = colnames(x))
@ -232,7 +232,7 @@ all_antimicrobials <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
}
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)

2
R/mdro.R
View File

@ -170,7 +170,7 @@ mdro <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
x <- tryCatch(get_current_data(arg_name = "x", call = -2, reuse_from_1st_call = FALSE), error = function(e) x)
}
meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
meet_criteria(guideline, allow_class = c("list", "character"), allow_NULL = TRUE)

27
R/mo.R
View File

@ -1664,16 +1664,25 @@ pillar_shaft.mo <- function(x, ...) {
out[is.na(x)] <- font_na(" NA")
out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
df <- tryCatch(get_current_data(arg_name = "x",
call = 0,
reuse_from_1st_call = FALSE),
error = function(e) NULL)
if (!is.null(df)) {
mo_cols <- vapply(FUN.VALUE = logical(1), df, is.mo)
} else {
mo_cols <- NULL
}
if (!all(x[!is.na(x)] %in% MO_lookup$mo) |
(!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% MO_lookup$mo))) {
# markup old mo codes
out[!x %in% MO_lookup$mo] <- font_italic(font_na(x[!x %in% MO_lookup$mo],
collapse = NULL),
collapse = NULL)
# throw a warning with the affected column name
mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
error = function(e) NULL)
if (!is.null(mo)) {
col <- paste0("Column '", mo, "'")
# throw a warning with the affected column name(s)
if (!is.null(mo_cols)) {
col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
} else {
col <- "The data"
}
@ -1681,7 +1690,7 @@ pillar_shaft.mo <- function(x, ...) {
"Please update your MO codes with `as.mo()`.",
call = FALSE)
}
# make it always fit exactly
max_char <- max(nchar(x))
if (is.na(max_char)) {
@ -2039,12 +2048,16 @@ parse_and_convert <- function(x) {
x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
}
}
x_class <- class(x)
x <- as.character(x)
x[is.null(x)] <- NA
parsed <- iconv(x, to = "UTF-8")
parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
parsed <- gsub('"', "", parsed, fixed = TRUE)
parsed <- gsub(" +", " ", parsed, perl = TRUE)
parsed <- trimws(parsed)
class(parsed) <- x_class
parsed
}, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
parsed
}

4
R/mo_property.R
View File

@ -747,7 +747,9 @@ mo_validate <- function(x, property, language, ...) {
find_mo_col <- function(fn) {
# this function tries to find an mo column in the data the function was called in,
# which is useful when functions are used within dplyr verbs
df <- get_current_data(arg_name = "x", call = -3) # will return an error if not found
df <- get_current_data(arg_name = "x",
call = -3,
reuse_from_1st_call = FALSE) # will return an error if not found
mo <- NULL
try({
mo <- suppressMessages(search_type_in_df(df, "mo"))

15
R/plot.R
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@ -287,6 +287,11 @@ ggplot.mic <- function(data,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method autoplot mic
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.mic <- ggplot.mic
#' @method plot disk
#' @export
#' @importFrom graphics barplot axis mtext legend
@ -506,6 +511,11 @@ ggplot.disk <- function(data,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method autoplot disk
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.disk <- ggplot.disk
#' @method plot rsi
#' @export
#' @importFrom graphics plot text axis
@ -657,6 +667,11 @@ ggplot.rsi <- function(data,
ggplot2::theme(legend.position = "none")
}
#' @method autoplot rsi
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.rsi <- ggplot.rsi
plot_prepare_table <- function(x, expand) {
x <- x[!is.na(x)]
stop_if(length(x) == 0, "no observations to plot", call = FALSE)

118
R/proportion.R
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@ -167,12 +167,14 @@ resistance <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
rsi_calc(...,
ab_result = "R",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE)
tryCatch(
rsi_calc(...,
ab_result = "R",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname proportion
@ -181,12 +183,14 @@ susceptibility <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
rsi_calc(...,
ab_result = c("S", "I"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE)
tryCatch(
rsi_calc(...,
ab_result = c("S", "I"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname proportion
@ -195,12 +199,14 @@ proportion_R <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
rsi_calc(...,
ab_result = "R",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE)
tryCatch(
rsi_calc(...,
ab_result = "R",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname proportion
@ -209,12 +215,14 @@ proportion_IR <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
rsi_calc(...,
ab_result = c("I", "R"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE)
tryCatch(
rsi_calc(...,
ab_result = c("I", "R"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname proportion
@ -223,12 +231,14 @@ proportion_I <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
rsi_calc(...,
ab_result = "I",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE)
tryCatch(
rsi_calc(...,
ab_result = "I",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname proportion
@ -237,12 +247,14 @@ proportion_SI <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
rsi_calc(...,
ab_result = c("S", "I"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE)
tryCatch(
rsi_calc(...,
ab_result = c("S", "I"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname proportion
@ -251,12 +263,14 @@ proportion_S <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE) {
rsi_calc(...,
ab_result = "S",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE)
tryCatch(
rsi_calc(...,
ab_result = "S",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
only_count = FALSE),
error = function(e) stop_(e$message, call = -5))
}
#' @rdname proportion
@ -268,13 +282,15 @@ proportion_df <- function(data,
as_percent = FALSE,
combine_SI = TRUE,
combine_IR = FALSE) {
rsi_calc_df(type = "proportion",
data = data,
translate_ab = translate_ab,
language = language,
minimum = minimum,
as_percent = as_percent,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI))
tryCatch(
rsi_calc_df(type = "proportion",
data = data,
translate_ab = translate_ab,
language = language,
minimum = minimum,
as_percent = as_percent,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI)),
error = function(e) stop_(e$message, call = -5))
}

36
R/resistance_predict.R
View File

@ -143,7 +143,7 @@ resistance_predict <- function(x,
meet_criteria(info, allow_class = "logical", has_length = 1)
stop_if(is.null(model), 'choose a regression model with the `model` argument, e.g. resistance_predict(..., model = "binomial")')
dots <- unlist(list(...))
if (length(dots) != 0) {
# backwards compatibility with old arguments
@ -321,7 +321,7 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
} else {
ylab <- "%IR"
}
plot(x = x$year,
y = x$value,
ylim = c(0, 1),
@ -351,20 +351,6 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
col = "grey40")
}
#' @method ggplot resistance_predict
#' @rdname resistance_predict
# will be exported using s3_register() in R/zzz.R
ggplot.resistance_predict <- function(x,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
...) {
x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")")
meet_criteria(main, allow_class = "character", has_length = 1)
meet_criteria(ribbon, allow_class = "logical", has_length = 1)
ggplot_rsi_predict(x = x, main = main, ribbon = ribbon, ...)
}
#' @rdname resistance_predict
#' @export
ggplot_rsi_predict <- function(x,
@ -407,3 +393,21 @@ ggplot_rsi_predict <- function(x,
colour = "grey40")
p
}
#' @method ggplot resistance_predict
#' @rdname resistance_predict
# will be exported using s3_register() in R/zzz.R
ggplot.resistance_predict <- function(x,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
...) {
x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")")
meet_criteria(main, allow_class = "character", has_length = 1)
meet_criteria(ribbon, allow_class = "logical", has_length = 1)
ggplot_rsi_predict(x = x, main = main, ribbon = ribbon, ...)
}
#' @method autoplot resistance_predict
#' @rdname resistance_predict
# will be exported using s3_register() in R/zzz.R
autoplot.resistance_predict <- ggplot.resistance_predict

6
R/rsi.R
View File

@ -349,7 +349,7 @@ as.rsi.mic <- function(x,
# for dplyr's across()
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0, reuse_from_1st_call = FALSE)), error = function(e) FALSE)) {
# try to get current column, which will only be available when in across()
ab <- tryCatch(cur_column_dplyr(),
error = function(e) ab)
@ -438,7 +438,7 @@ as.rsi.disk <- function(x,
# for dplyr's across()
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0, reuse_from_1st_call = FALSE)), error = function(e) FALSE)) {
# try to get current column, which will only be available when in across()
ab <- tryCatch(cur_column_dplyr(),
error = function(e) ab)
@ -448,7 +448,7 @@ as.rsi.disk <- function(x,
mo_var_found <- ""
if (is.null(mo)) {
tryCatch({
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
df <- get_current_data(arg_name = "mo", call = -3, reuse_from_1st_call = FALSE) # will return an error if not found
mo <- NULL
try({
mo <- suppressMessages(search_type_in_df(df, "mo"))

BIN
R/sysdata.rda
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4
R/zzz.R
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@ -65,6 +65,10 @@ if (utf8_supported && !is_latex) {
s3_register("ggplot2::ggplot", "mic")
s3_register("ggplot2::ggplot", "disk")
s3_register("ggplot2::ggplot", "resistance_predict")
s3_register("ggplot2::autoplot", "rsi")
s3_register("ggplot2::autoplot", "mic")
s3_register("ggplot2::autoplot", "disk")
s3_register("ggplot2::autoplot", "resistance_predict")
# if mo source exists, fire it up (see mo_source())
try({

BIN
data-raw/AMR_latest.tar.gz
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28
data-raw/exploratory_data_analysis_test.R Normal file
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@ -0,0 +1,28 @@
library(dplyr)
example_isolates %>%
select(mo, where(is.rsi)) %>%
tidyr::pivot_longer(cols = where(is.rsi)) %>%
# remove intrisic R
filter(!paste(mo, name) %in% AMR:::INTRINSIC_R) %>%
mutate(name = as.ab(name),
value = ifelse(value == "R", 1, 0),
class = ab_group(name)) %>%
group_by(mo, class) %>%
summarise(n = n(),
res = mean(value, na.rm = TRUE)) %>%
filter(n > 30, !is.na(res))
df <- example_isolates
search_mo <- "B_ESCHR_COLI"
intrinsic_res <- INTRINSIC_R[INTRINSIC_R %like% search_mo]
intrinsic_res <- gsub(".* (.*)", "\\1", intrinsic_res)
x <- df %>%
select(mo, where(is.rsi)) %>%
filter(mo == search_mo) %>%
# at least 30 results available
select(function(x) sum(!is.na(x)) >= 30) %>%
# remove intrisic R
select(!matches(paste(intrinsic_res, collapse = "|")))

2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

6
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -187,12 +187,12 @@
</header><script src="datasets_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
</header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">05 June 2021</h4>
<h4 class="date">14 June 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>
<div class="hidden name"><code>datasets.Rmd</code></div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

4
docs/index.html
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -213,7 +213,7 @@
<a href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="anchor"></a>With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!</h5>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>

29
docs/news/index.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -236,19 +236,24 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719001" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9001">
<a href="#amr-1719001" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9001</h1>
<div id="last-updated-5-june-2021" class="section level2">
<div id="amr-1719002" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9002">
<a href="#amr-1719002" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9002</h1>
<div id="last-updated-14-june-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-5-june-2021" class="anchor"></a><small>Last updated: 5 June 2021</small>
<a href="#last-updated-14-june-2021" class="anchor"></a><small>Last updated: 14 June 2021</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Added more antibiotic class selectors, such as <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>
<li>Added more antibiotic class selectors: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code>
</li>
<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">ggplot2::autoplot()</a></code> generic for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code>
</li>
<li>Fix to prevent introducing <code>NA</code>s for old MO codes when running <code><a href="../reference/as.mo.html">as.mo()</a></code> on them</li>
<li>Added more informative error messages when any of the <code>proportion_*()</code> and <code>count_*()</code> functions fail</li>
<li>Fix for using antibiotic selectors multiple times in one call (e.g., using in <code><a href="https://dplyr.tidyverse.org/reference/filter.html">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>)</li>
</ul>
</div>
</div>
@ -302,7 +307,7 @@
</ul>
</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>
</ul>
</div>
@ -403,7 +408,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</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>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></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>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@ -460,7 +465,7 @@
<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>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>
</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>
@ -498,7 +503,7 @@
<a href="#other-1" class="anchor"></a>Other</h3>
<ul>
<li>Big documentation updates</li>
<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
<li>Loading the package (i.e., <code><a href="https://github.com/msberends/AMR">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
</ul>
</div>
</div>
@ -629,7 +634,7 @@
<p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="va">intrinsic_resistant</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op">%&gt;%</span>

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-06-05T13:10Z
last_built: 2021-06-14T20:03Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/AMR.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

8
docs/reference/count.html
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@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -409,6 +409,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
n1 <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># the actual total; sum of all three</span>
n2 <span class='op'>=</span> <span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># same - analogous to n_distinct</span>
total <span class='op'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># NOT the number of tested isolates!</span>
<span class='co'># Number of available isolates for a whole antibiotic class</span>
<span class='co'># (i.e., in this data set columns GEN, TOB, AMK, KAN)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'><a href='antibiotic_class_selectors.html'>aminoglycosides</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>n_rsi</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>

6
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -508,7 +508,7 @@
</tr><tr>
<td>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
</td>
<td><p>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
</tr><tr>
@ -532,7 +532,7 @@
</tr><tr>
<td>
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">autoplot(<i>&lt;resistance_predict&gt;</i>)</a></code> </p>
</td>
<td><p>Predict antimicrobial resistance</p></td>
</tr><tr>

52
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View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -258,7 +258,23 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
@ -289,7 +305,23 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
@ -314,7 +346,19 @@
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,

12
docs/reference/resistance_predict.html
View File

@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -275,10 +275,18 @@
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

39
inst/tinytest/test-zzz.R
View File

@ -24,7 +24,7 @@
# ==================================================================== #
# Check if these function still exist in the package (all are in Suggests field)
# Since GitHub Action runs every night, we will get emailed when a dependency fails based on this unit test
# Since GitHub Actions runs every night, we will get emailed when a dependency fails based on this unit test
# functions used by import_fn()
import_functions <- c(
"anti_join" = "dplyr",
@ -53,14 +53,23 @@ call_functions <- c(
# skimr
"inline_hist" = "skimr",
"sfl" = "skimr",
# set_mo_source
# readxl
"read_excel" = "readxl",
# ggplot_rsi
# ggplot2
"aes" = "ggplot2",
"aes_string" = "ggplot2",
"arrow" = "ggplot2",
"autoplot" = "ggplot2",
"element_blank" = "ggplot2",
"element_line" = "ggplot2",
"element_text" = "ggplot2",
"expand_limits" = "ggplot2",
"facet_wrap" = "ggplot2",
"geom_errorbar" = "ggplot2",
"geom_path" = "ggplot2",
"geom_point" = "ggplot2",
"geom_ribbon" = "ggplot2",
"geom_segment" = "ggplot2",
"geom_text" = "ggplot2",
"ggplot" = "ggplot2",
"labs" = "ggplot2",
@ -70,31 +79,9 @@ call_functions <- c(
"scale_y_continuous" = "ggplot2",
"theme" = "ggplot2",
"theme_minimal" = "ggplot2",
# ggplot_pca
"aes" = "ggplot2",
"arrow" = "ggplot2",
"element_blank" = "ggplot2",
"element_line" = "ggplot2",
"element_text" = "ggplot2",
"expand_limits" = "ggplot2",
"geom_path" = "ggplot2",
"geom_point" = "ggplot2",
"geom_segment" = "ggplot2",
"geom_text" = "ggplot2",
"ggplot" = "ggplot2",
"labs" = "ggplot2",
"theme" = "ggplot2",
"theme_minimal" = "ggplot2",
"unit" = "ggplot2",
"xlab" = "ggplot2",
"ylab" = "ggplot2",
# resistance_predict
"aes" = "ggplot2",
"geom_errorbar" = "ggplot2",
"geom_point" = "ggplot2",
"geom_ribbon" = "ggplot2",
"ggplot" = "ggplot2",
"labs" = "ggplot2"
"ylab" = "ggplot2"
)
import_functions <- c(import_functions, call_functions)

6
man/count.Rd
View File

@ -167,6 +167,12 @@ if (require("dplyr")) {
n1 = count_all(CIP), # the actual total; sum of all three
n2 = n_rsi(CIP), # same - analogous to n_distinct
total = n()) # NOT the number of tested isolates!
# Number of available isolates for a whole antibiotic class
# (i.e., in this data set columns GEN, TOB, AMK, KAN)
example_isolates \%>\%
group_by(hospital_id) \%>\%
summarise(across(aminoglycosides(), n_rsi))
# Count co-resistance between amoxicillin/clav acid and gentamicin,
# so we can see that combination therapy does a lot more than mono therapy.

44
man/plot.Rd
View File

@ -4,10 +4,13 @@
\alias{plot}
\alias{plot.mic}
\alias{ggplot.mic}
\alias{autoplot.mic}
\alias{plot.disk}
\alias{ggplot.disk}
\alias{autoplot.disk}
\alias{plot.rsi}
\alias{ggplot.rsi}
\alias{autoplot.rsi}
\title{Plotting for Classes \code{rsi}, \code{mic} and \code{disk}}
\usage{
\method{plot}{mic}(
@ -39,6 +42,21 @@
...
)
\method{autoplot}{mic}(
data,
mapping = NULL,
title = paste("MIC values of", deparse(substitute(data))),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...
)
\method{plot}{disk}(
x,
main = paste("Disk zones of", deparse(substitute(x))),
@ -68,6 +86,21 @@
...
)
\method{autoplot}{disk}(
data,
mapping = NULL,
title = paste("Disk zones of", deparse(substitute(data))),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
expand = TRUE,
...
)
\method{plot}{rsi}(
x,
ylab = "Percentage",
@ -86,6 +119,17 @@
language = get_locale(),
...
)
\method{autoplot}{rsi}(
data,
mapping = NULL,
title = paste("Resistance Overview of", deparse(substitute(data))),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
language = get_locale(),
...
)
}
\arguments{
\item{x, data}{MIC values created with \code{\link[=as.mic]{as.mic()}} or disk diffusion values created with \code{\link[=as.disk]{as.disk()}}}

12
man/resistance_predict.Rd
View File

@ -4,8 +4,9 @@
\alias{resistance_predict}
\alias{rsi_predict}
\alias{plot.resistance_predict}
\alias{ggplot.resistance_predict}
\alias{ggplot_rsi_predict}
\alias{ggplot.resistance_predict}
\alias{autoplot.resistance_predict}
\title{Predict antimicrobial resistance}
\usage{
resistance_predict(
@ -40,9 +41,16 @@ rsi_predict(
\method{plot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ...)
ggplot_rsi_predict(
x,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,
...
)
\method{ggplot}{resistance_predict}(x, main = paste("Resistance Prediction of", x_name), ribbon = TRUE, ...)
ggplot_rsi_predict(
\method{autoplot}{resistance_predict}(
x,
main = paste("Resistance Prediction of", x_name),
ribbon = TRUE,