(v2.1.1.9155) new mic_p50() and mic_p90() - updated AMR intro

R/aa_helper_functions.R

@@ -1390,6 +1390,9 @@ as_original_data_class <- function(df, old_class = NULL, extra_class = NULL) {
     fn <- function(x) base::as.data.frame(df, stringsAsFactors = FALSE)
   }
   out <- fn(df)
+  # don't keep row names
+  rownames(out) <- NULL
+  # add additional class if needed
   if (!is.null(extra_class)) {
     class(out) <- c(extra_class, class(out))
   }

R/antibiogram.R

@@ -923,19 +923,16 @@ antibiogram.default <- function(x,
     }
   }
   
-  out <- as_original_data_class(new_df, class(x), extra_class = "antibiogram")
+  out <- structure(as_original_data_class(new_df, class(x), extra_class = "antibiogram"),
+                   has_syndromic_group = has_syndromic_group,
+                   combine_SI = combine_SI,
+                   wisca = wisca,
+                   conf_interval = conf_interval,
+                   formatting_type = formatting_type,
+                   wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
+                   long_numeric = as_original_data_class(long_numeric, class(x)))
   rownames(out) <- NULL
-  rownames(wisca_parameters) <- NULL
-  rownames(long_numeric) <- NULL
-  structure(out,
-            has_syndromic_group = has_syndromic_group,
-            combine_SI = combine_SI,
-            wisca = wisca,
-            conf_interval = conf_interval,
-            formatting_type = formatting_type,
-            wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
-            long_numeric = as_original_data_class(long_numeric, class(x))
-  )
+  out
 }
 
 #' @method antibiogram grouped_df
@@ -1041,14 +1038,16 @@ antibiogram.grouped_df <- function(x,
   
   close(progress)
   
-  structure(as_original_data_class(out, class(x), extra_class = "antibiogram"),
-            has_syndromic_group = FALSE,
-            combine_SI = isTRUE(combine_SI),
-            wisca = isTRUE(wisca),
-            conf_interval = conf_interval,
-            formatting_type = formatting_type,
-            wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
-            long_numeric = as_original_data_class(long_numeric, class(x)))
+  out <- structure(as_original_data_class(out, class(x), extra_class = "antibiogram"),
+                   has_syndromic_group = FALSE,
+                   combine_SI = isTRUE(combine_SI),
+                   wisca = isTRUE(wisca),
+                   conf_interval = conf_interval,
+                   formatting_type = formatting_type,
+                   wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
+                   long_numeric = as_original_data_class(long_numeric, class(x)))
+  rownames(out) <- NULL
+  out
 }
 
 #' @export

R/bug_drug_combinations.R

@@ -185,8 +185,9 @@ bug_drug_combinations <- function(x,
   
   out <- as_original_data_class(out, class(x.bak)) # will remove tibble groups
   out <- out %pm>% pm_arrange(mo, ab)
+  class(out) <- c("bug_drug_combinations", if(data_has_groups) "grouped" else NULL, class(out))
   rownames(out) <- NULL
-  structure(out, class = c("bug_drug_combinations", if(data_has_groups) "grouped" else NULL, class(out)))
+  out
 }
 
 #' @method format bug_drug_combinations

R/mic.R

@@ -346,6 +346,21 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
   out
 }
 
+#' @rdname as.mic
+#' @details Use [mic_p50()] and [mic_p90()] to get the 50th and 90th percentile of MIC values. They return 'normal' [numeric] values.
+#' @export
+mic_p50 <- function(x, na.rm = FALSE, ...) {
+  x <- as.mic(x)
+  as.double(stats::quantile(x, probs = 0.5, na.rm = na.rm))
+}
+
+#' @rdname as.mic
+#' @export
+mic_p90 <- function(x, na.rm = FALSE, ...) {
+  x <- as.mic(x)
+  as.double(stats::quantile(x, probs = 0.9, na.rm = na.rm))
+}
+
 #' @method as.double mic
 #' @export
 #' @noRd

R/plotting.R

@@ -186,7 +186,7 @@
 #'     scale_colour_sir(language = "pt",
 #'                      name = "Support in 20 languages")
 #' }
-#' 
+#' }
 #' 
 #' # Plotting using base R's plot() ---------------------------------------
 #'

R/sir.R

@@ -1544,7 +1544,7 @@ sir_interpretation_history <- function(clean = FALSE) {
   if (pkg_is_available("tibble")) {
     out <- import_fn("as_tibble", "tibble")(out)
   }
-  structure(out, class = c("sir_log", class(out)))
+  as_original_data_class(out, class(out), extra_class = "sir_log")
 }
 
 #' @method print sir_log

R/sir_calc.R

@@ -383,8 +383,6 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
     # remove redundant columns
     out <- subset(out, select = -c(ci_min, ci_max, isolates))
   }
-
-  rownames(out) <- NULL
-  out <- as_original_data_class(out, class(data.bak)) # will remove tibble groups
-  structure(out, class = c("sir_df", class(out)))
+  
+  as_original_data_class(out, class(data.bak), extra_class = "sir_df") # will remove tibble groups
 }