(v1.7.1.9002) ab class selectors update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9001
+Version: 1.7.1.9002
-Date: 2021-06-05
+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

NEWS.md

@@ -1,8 +1,12 @@
-# `AMR` 1.7.1.9001
+# `AMR` 1.7.1.9002
-## <small>Last updated:  5 June 2021</small>
+## <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

R/ab_class_selectors.R

@@ -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)
   

R/count.R

@@ -83,6 +83,12 @@
 #'               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.
 #'   # Please mind that `susceptibility()` calculates percentages right away instead.
@@ -108,81 +114,97 @@
 #' }
 #' }
 count_resistant <- function(..., only_all_tested = FALSE) {
+  tryCatch(
     rsi_calc(...,
              ab_result = "R",
              only_all_tested = only_all_tested,
-           only_count = TRUE)
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_susceptible <- function(..., only_all_tested = FALSE) {
+  tryCatch(
     rsi_calc(...,
              ab_result = c("S", "I"),
              only_all_tested = only_all_tested,
-           only_count = TRUE)
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_R <- function(..., only_all_tested = FALSE) {
+  tryCatch(
     rsi_calc(...,
              ab_result = "R",
              only_all_tested = only_all_tested,
-           only_count = TRUE)
+             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")) {
+  if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
-    warning_("Using count_IR() is discouraged; use count_resistant() instead to not consider \"I\" being resistant.", call = FALSE)
+    message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" being resistant. This note will be shown once for this session.", as_note = FALSE)
     remember_thrown_message("count_IR")
   }
+  tryCatch(
     rsi_calc(...,
              ab_result = c("I", "R"),
              only_all_tested = only_all_tested,
-           only_count = TRUE)
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_I <- function(..., only_all_tested = FALSE) {
+  tryCatch(
     rsi_calc(...,
              ab_result = "I",
              only_all_tested = only_all_tested,
-           only_count = TRUE)
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_SI <- function(..., only_all_tested = FALSE) {
+  tryCatch(
     rsi_calc(...,
              ab_result = c("S", "I"),
              only_all_tested = only_all_tested,
-           only_count = TRUE)
+             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")) {
+  if (message_not_thrown_before("count_S", entire_session = TRUE)) {
-    warning_("Using count_S() is discouraged; use count_susceptible() instead to also consider \"I\" being susceptible.", call = FALSE)
+    message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
     remember_thrown_message("count_S")
   }
+  tryCatch(
     rsi_calc(...,
              ab_result = "S",
              only_all_tested = only_all_tested,
-           only_count = TRUE)
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_all <- function(..., only_all_tested = FALSE) {
+  tryCatch(
     rsi_calc(...,
              ab_result = c("S", "I", "R"),
              only_all_tested = only_all_tested,
-           only_count = TRUE)
+             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) {
+  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))
+                combine_SI_missing = missing(combine_SI)),
+    error = function(e) stop_(e$message, call = -5))
 }

R/deprecated.R

@@ -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)

R/first_isolate.R

@@ -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))

R/key_antimicrobials.R

@@ -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)

R/mdro.R

@@ -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)

R/mo.R

@@ -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$mo], 
                                                      collapse = NULL),
                                              collapse = NULL)
-    # throw a warning with the affected column name
+    # throw a warning with the affected column name(s)
-    mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
+    if (!is.null(mo_cols)) {
-                   error = function(e) NULL)
+      col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
-    if (!is.null(mo)) {
-      col <- paste0("Column '", mo, "'")
     } else {
       col <- "The data"
     }
@@ -2039,12 +2048,16 @@ parse_and_convert <- function(x) {
         x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
       }
     }
+    x_class <- class(x)
+    x <- as.character(x)
     x[is.null(x)] <- NA
     parsed <- iconv(x, to = "UTF-8")
     parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
     parsed <- gsub('"', "", parsed, fixed = TRUE)
     parsed <- gsub(" +", " ", parsed, perl = TRUE)
     parsed <- trimws(parsed)
+    class(parsed) <- x_class
+    parsed
   }, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
   parsed
 }

R/mo_property.R

@@ -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"))

R/plot.R

@@ -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)

R/proportion.R

@@ -167,12 +167,14 @@ resistance <- function(...,
                        minimum = 30,
                        as_percent = FALSE,
                        only_all_tested = FALSE) {
+  tryCatch(
     rsi_calc(...,
              ab_result = "R",
              minimum = minimum,
              as_percent = as_percent,
              only_all_tested = only_all_tested,
-           only_count = FALSE)
+             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) {
+  tryCatch(
     rsi_calc(...,
              ab_result = c("S", "I"),
              minimum = minimum,
              as_percent = as_percent,
              only_all_tested = only_all_tested,
-           only_count = FALSE)
+             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) {
+  tryCatch(
     rsi_calc(...,
              ab_result = "R",
              minimum = minimum,
              as_percent = as_percent,
              only_all_tested = only_all_tested,
-           only_count = FALSE)
+             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) {
+  tryCatch(
     rsi_calc(...,
              ab_result = c("I", "R"),
              minimum = minimum,
              as_percent = as_percent,
              only_all_tested = only_all_tested,
-           only_count = FALSE)
+             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) {
+  tryCatch(
     rsi_calc(...,
              ab_result = "I",
              minimum = minimum,
              as_percent = as_percent,
              only_all_tested = only_all_tested,
-           only_count = FALSE)
+             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) {
+  tryCatch(
     rsi_calc(...,
              ab_result = c("S", "I"),
              minimum = minimum,
              as_percent = as_percent,
              only_all_tested = only_all_tested,
-           only_count = FALSE)
+             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) {
+  tryCatch(
     rsi_calc(...,
              ab_result = "S",
              minimum = minimum,
              as_percent = as_percent,
              only_all_tested = only_all_tested,
-           only_count = FALSE)
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -268,6 +282,7 @@ proportion_df <- function(data,
                           as_percent = FALSE,
                           combine_SI = TRUE,
                           combine_IR = FALSE) {
+  tryCatch(
     rsi_calc_df(type = "proportion",
                 data = data,
                 translate_ab = translate_ab,
@@ -276,5 +291,6 @@ proportion_df <- function(data,
                 as_percent = as_percent,
                 combine_SI = combine_SI,
                 combine_IR = combine_IR,
-              combine_SI_missing = missing(combine_SI))
+                combine_SI_missing = missing(combine_SI)),
+    error = function(e) stop_(e$message, call = -5))
 }

R/resistance_predict.R

@@ -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

R/rsi.R

@@ -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"))

R/zzz.R

@@ -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({

data-raw/exploratory_data_analysis_test.R

@@ -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 = "|")))

docs/404.html

@@ -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>
 

docs/LICENSE-text.html

@@ -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>
 

docs/articles/datasets.html

@@ -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>

docs/articles/index.html

@@ -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>
 

docs/authors.html

@@ -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>
 

docs/index.html

@@ -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>

docs/news/index.html

@@ -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">
+    <div id="amr-1719002" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9001">
+<h1 class="page-header" data-toc-text="1.7.1.9002">
-<a href="#amr-1719001" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9001</h1>
+<a href="#amr-1719002" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9002</h1>
-<div id="last-updated-5-june-2021" class="section level2">
+<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> 

docs/pkgdown.yml

@@ -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

docs/reference/AMR.html

@@ -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>
 

docs/reference/count.html

@@ -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>
 
@@ -410,6 +410,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
               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>
   <span class='co'># Please mind that `susceptibility()` calculates percentages right away instead.</span>

docs/reference/index.html

@@ -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>

docs/reference/plot.html

@@ -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>,

docs/reference/resistance_predict.html

@@ -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>,

docs/survey.html

@@ -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>
 

inst/tinytest/test-zzz.R

@@ -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",
+  "ylab" = "ggplot2"
-  # resistance_predict
-  "aes" = "ggplot2",
-  "geom_errorbar" = "ggplot2",
-  "geom_point" = "ggplot2",
-  "geom_ribbon" = "ggplot2",
-  "ggplot" = "ggplot2",
-  "labs" = "ggplot2"
 )
 
 import_functions <- c(import_functions, call_functions)

man/count.Rd

@@ -168,6 +168,12 @@ if (require("dplyr")) {
               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.
   # Please mind that `susceptibility()` calculates percentages right away instead.

man/plot.Rd

@@ -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()}}}

man/resistance_predict.Rd

@@ -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,