diff --git a/DESCRIPTION b/DESCRIPTION
index 564520f7..0dc6a5bd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
-Version: 0.7.1.9090
-Date: 2019-09-26
+Version: 0.7.1.9091
+Date: 2019-09-30
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@@ -34,7 +34,7 @@ Depends:
R (>= 3.1.0)
Imports:
backports,
- clean (>= 1.1.0),
+ clean (>= 1.1.0.9000),
crayon (>= 1.3.0),
data.table (>= 1.9.0),
dplyr (>= 0.7.0),
diff --git a/NAMESPACE b/NAMESPACE
index 65f89121..a0f3b09f 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -233,6 +233,7 @@ exportMethods(summary.mo)
exportMethods(summary.rsi)
importFrom(clean,freq)
importFrom(clean,freq.default)
+importFrom(clean,percentage)
importFrom(clean,top_freq)
importFrom(crayon,bgGreen)
importFrom(crayon,bgRed)
@@ -305,7 +306,6 @@ importFrom(pillar,pillar_shaft)
importFrom(pillar,type_sum)
importFrom(rlang,as_label)
importFrom(rlang,enquos)
-importFrom(scales,percent)
importFrom(stats,complete.cases)
importFrom(stats,glm)
importFrom(stats,lm)
@@ -314,7 +314,6 @@ importFrom(stats,predict)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(utils,browseURL)
-importFrom(utils,installed.packages)
importFrom(utils,menu)
importFrom(utils,read.csv)
importFrom(utils,write.csv)
diff --git a/NEWS.md b/NEWS.md
index 3ed9abaf..f6da67e1 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
-# AMR 0.7.1.9090
-Last updated: 26-Sep-2019
+# AMR 0.7.1.9091
+Last updated: 30-Sep-2019
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
diff --git a/R/amr.R b/R/amr.R
index cbff6fb2..5351cf9d 100644
--- a/R/amr.R
+++ b/R/amr.R
@@ -67,5 +67,4 @@
#' @rdname AMR
# # prevent NOTE on R >= 3.6
#' @importFrom microbenchmark microbenchmark
-#' @importFrom scales percent
NULL
diff --git a/R/availability.R b/R/availability.R
index 2163b5e1..7a830d55 100644
--- a/R/availability.R
+++ b/R/availability.R
@@ -27,6 +27,7 @@
#' @details The function returns a \code{data.frame} with columns \code{"resistant"} and \code{"visual_resistance"}. The values in that columns are calculated with \code{\link{portion_R}}.
#' @return \code{data.frame} with column names of \code{tbl} as row names
#' @inheritSection AMR Read more on our website!
+#' @importFrom clean percentage
#' @export
#' @examples
#' availability(example_isolates)
@@ -47,7 +48,7 @@ availability <- function(tbl, width = NULL) {
n <- base::sapply(tbl, function(x) base::length(x[!base::is.na(x)]))
R <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), portion_R(x, minimum = 0), NA))
R_print <- character(length(R))
- R_print[!is.na(R)] <- percent(R[!is.na(R)], round = 1, force_zero = TRUE)
+ R_print[!is.na(R)] <- percentage(R[!is.na(R)])
R_print[is.na(R)] <- ""
if (is.null(width)) {
@@ -77,7 +78,7 @@ availability <- function(tbl, width = NULL) {
x_chars_empty <- strrep("-", width - nchar(x_chars))
df <- data.frame(count = n,
- available = percent(x, round = 1, force_zero = TRUE),
+ available = percentage(x),
visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"),
resistant = R_print,
visual_resistance = vis_resistance)
diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R
index 326380d9..088d58b3 100644
--- a/R/bug_drug_combinations.R
+++ b/R/bug_drug_combinations.R
@@ -33,7 +33,7 @@
#' @inheritParams base::formatC
#' @importFrom dplyr %>% rename group_by select mutate filter pull
#' @importFrom tidyr spread
-#' @importFrom clean freq
+#' @importFrom clean freq percentage
#' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
#'
#' The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.
@@ -140,7 +140,7 @@ format.bug_drug_combinations <- function(x,
summarise(isolates = sum(isolates, na.rm = TRUE),
total = sum(total, na.rm = TRUE)) %>%
ungroup() %>%
- mutate(txt = paste0(percent(isolates / total, force_zero = TRUE, decimal.mark = decimal.mark, big.mark = big.mark),
+ mutate(txt = paste0(percentage(isolates / total, decimal.mark = decimal.mark, big.mark = big.mark),
" (", trimws(format(isolates, big.mark = big.mark)), "/",
trimws(format(total, big.mark = big.mark)), ")")) %>%
select(ab, ab_txt, mo, txt) %>%
diff --git a/R/first_isolate.R b/R/first_isolate.R
index 0d9af640..9b4becd3 100755
--- a/R/first_isolate.R
+++ b/R/first_isolate.R
@@ -75,6 +75,7 @@
#' @export
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange pull ungroup
#' @importFrom crayon blue bold silver
+#' @importFrom clean percentage
#' @return Logical vector
#' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website!
@@ -525,8 +526,8 @@ first_isolate <- function(x,
if (info == TRUE) {
n_found <- base::sum(all_first, na.rm = TRUE)
- p_found_total <- percent(n_found / nrow(x), force_zero = TRUE)
- p_found_scope <- percent(n_found / scope.size, force_zero = TRUE)
+ p_found_total <- percentage(n_found / nrow(x))
+ p_found_scope <- percentage(n_found / scope.size)
# mark up number of found
n_found <- base::format(n_found, big.mark = big.mark, decimal.mark = decimal.mark)
if (p_found_total != p_found_scope) {
diff --git a/R/freq.R b/R/freq.R
index a0b36256..62aa56f7 100755
--- a/R/freq.R
+++ b/R/freq.R
@@ -25,22 +25,26 @@ clean::freq
#' @exportMethod freq.mo
#' @importFrom dplyr n_distinct
-#' @importFrom clean freq.default
+#' @importFrom clean freq.default percentage
#' @export
#' @noRd
freq.mo <- function(x, ...) {
x_noNA <- as.mo(x[!is.na(x)]) # as.mo() to get the newest mo codes
grams <- mo_gramstain(x_noNA, language = NULL)
+ digits <- list(...)$digits
+ if (is.null(digits)) {
+ digits <- 2
+ }
freq.default(x = x, ...,
.add_header = list(`Gram-negative` = paste0(format(sum(grams == "Gram-negative", na.rm = TRUE),
big.mark = ",",
decimal.mark = "."),
- " (", percent(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams), force_zero = TRUE, round = 2),
+ " (", percentage(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams), digits = digits),
")"),
`Gram-positive` = paste0(format(sum(grams == "Gram-positive", na.rm = TRUE),
big.mark = ",",
decimal.mark = "."),
- " (", percent(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), force_zero = TRUE, round = 2),
+ " (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), digits = digits),
")"),
`Nr of genera` = n_distinct(mo_genus(x_noNA, language = NULL)),
`Nr of species` = n_distinct(paste(mo_genus(x_noNA, language = NULL),
diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R
index 4a4df5fd..cfb1ec5d 100755
--- a/R/ggplot_rsi.R
+++ b/R/ggplot_rsi.R
@@ -58,7 +58,6 @@
#'
#' \code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
#' @rdname ggplot_rsi
-#' @importFrom utils installed.packages
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
@@ -338,6 +337,7 @@ facet_rsi <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
}
#' @rdname ggplot_rsi
+#' @importFrom clean percentage
#' @export
scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
stopifnot_installed_package("ggplot2")
@@ -346,7 +346,7 @@ scale_y_percent <- function(breaks = seq(0, 1, 0.1), limits = NULL) {
breaks <- breaks / 100
}
ggplot2::scale_y_continuous(breaks = breaks,
- labels = percent(breaks),
+ labels = percentage(breaks),
limits = limits)
}
@@ -387,6 +387,7 @@ theme_rsi <- function() {
#' @rdname ggplot_rsi
#' @importFrom dplyr mutate %>% group_by_at
+#' @importFrom clean percentage
#' @export
labels_rsi_count <- function(position = NULL,
x = "antibiotic",
@@ -417,7 +418,7 @@ labels_rsi_count <- function(position = NULL,
combine_SI = combine_SI,
combine_IR = combine_IR) %>%
group_by_at(x_name) %>%
- mutate(lbl = paste0(percent(value / sum(value, na.rm = TRUE), force_zero = TRUE),
+ mutate(lbl = paste0(percentage(value / sum(value, na.rm = TRUE)),
"\n(n=", isolates, ")"))
})
}
diff --git a/R/misc.R b/R/misc.R
index 214521ec..70753c68 100755
--- a/R/misc.R
+++ b/R/misc.R
@@ -29,22 +29,6 @@ addin_insert_like <- function() {
rstudioapi::insertText(" %like% ")
}
-percent_clean <- clean:::percent
-# No export, no Rd
-percent <- function(x, round = 1, force_zero = FALSE, decimal.mark = getOption("OutDec"), big.mark = ",", ...) {
- if (decimal.mark == big.mark) {
- if (decimal.mark == ",") {
- big.mark <- "."
- } else if (decimal.mark == ".") {
- big.mark <- ","
- } else {
- big.mark <- " "
- }
- }
- percent_clean(x = x, round = round, force_zero = force_zero,
- decimal.mark = decimal.mark, big.mark = big.mark, ...)
-}
-
#' @importFrom crayon blue bold red
#' @importFrom dplyr %>% pull
search_type_in_df <- function(x, type) {
diff --git a/R/mo.R b/R/mo.R
index 9ca635b3..a712f6bd 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -268,6 +268,7 @@ is.mo <- function(x) {
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
#' @importFrom data.table data.table as.data.table setkey
#' @importFrom crayon magenta red blue silver italic
+#' @importFrom clean percentage
# param property a column name of AMR::microorganisms
# param initial_search logical - is FALSE when coming from uncertain tries, which uses exec_as.mo internally too
# param dyslexia_mode logical - also check for characters that resemble others
@@ -1575,7 +1576,7 @@ exec_as.mo <- function(x,
total_failures <- length(x_input[as.character(x_input) %in% as.character(failures) & !x_input %in% c(NA, NULL, NaN)])
total_n <- length(x_input[!x_input %in% c(NA, NULL, NaN)])
msg <- paste0(nr2char(n_distinct(failures)), " unique ", plural[1],
- " (covering ", percent(total_failures / total_n, round = 1, force_zero = TRUE),
+ " (covering ", percentage(total_failures / total_n),
") could not be coerced and ", plural[3], " considered 'unknown'")
if (n_distinct(failures) <= 10) {
msg <- paste0(msg, ": ", paste('"', unique(failures), '"', sep = "", collapse = ', '))
diff --git a/R/portion.R b/R/portion.R
index 7357eb32..bffd5ed0 100755
--- a/R/portion.R
+++ b/R/portion.R
@@ -26,7 +26,7 @@
#' \code{portion_R} and \code{portion_IR} can be used to calculate resistance, \code{portion_S} and \code{portion_SI} can be used to calculate susceptibility.\cr
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.
#' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.
-#' @param as_percent a logical to indicate whether the output must be returned as a hundred fold with \% sign (a character). A value of \code{0.123456} will then be returned as \code{"12.3\%"}.
+#' @param as_percent a logical to indicate whether the output must be returned as a hundred fold with \% sign (a character) using\code{\link[clean]{percentage}}. A value of \code{0.123456} will then be returned as \code{"12.3\%"}.
#' @param only_all_tested (for combination therapies, i.e. using more than one variable for \code{...}) a logical to indicate that isolates must be tested for all antibiotics, see section \emph{Combination therapy} below
#' @param data a \code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})
#' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{ab_property}}
diff --git a/R/rsi_calc.R b/R/rsi_calc.R
index e80fb2c1..0947eef4 100755
--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@@ -39,6 +39,7 @@ dots2vars <- function(...) {
}
#' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all
+#' @importFrom clean percentage
rsi_calc <- function(...,
ab_result,
minimum = 0,
@@ -162,7 +163,7 @@ rsi_calc <- function(...,
}
if (as_percent == TRUE) {
- percent(fraction, force_zero = TRUE)
+ percentage(fraction, digits = 1)
} else {
fraction
}
diff --git a/docs/404.html b/docs/404.html
index 67f11399..74fd8376 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -84,7 +84,7 @@
AMR (for R)
- 0.7.1.9090
+ 0.7.1.9091
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index c429c417..8d0f7a2c 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -84,7 +84,7 @@
AMR (for R)
- 0.7.1.9090
+ 0.7.1.9091
diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html
index 46756e10..d502016e 100644
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@@ -13,8 +13,9 @@
-
-
+
+
+
@@ -40,7 +41,7 @@
AMR (for R)
- 0.7.1.9079
+ 0.7.1.9091
@@ -165,7 +166,7 @@
-