(v0.8.0.9030) depend on tidyr >= 1.0.0

R/bug_drug_combinations.R

@@ -32,7 +32,7 @@
 #' @inheritParams rsi_df
 #' @inheritParams base::formatC
 #' @importFrom dplyr %>% rename group_by select mutate filter summarise ungroup
-#' @importFrom tidyr spread
+#' @importFrom tidyr pivot_longer
 #' @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}.
@@ -80,7 +80,7 @@ bug_drug_combinations <- function(x,
              FUN(...)) %>% 
     group_by(mo) %>% 
     select_if(is.rsi) %>% 
-    gather("ab", "value", -mo) %>% 
+    pivot_longer(-mo, names_to = "ab") %>% 
     group_by(mo, ab) %>% 
     summarise(S = sum(value == "S", na.rm = TRUE),
               I = sum(value == "I", na.rm = TRUE),
@@ -93,7 +93,7 @@ bug_drug_combinations <- function(x,
 }
 
 #' @importFrom dplyr everything rename %>% ungroup group_by summarise mutate_all arrange everything lag
-#' @importFrom tidyr spread
+#' @importFrom tidyr pivot_wider
 #' @importFrom cleaner percentage
 #' @exportMethod format.bug_drug_combinations
 #' @export
@@ -135,7 +135,7 @@ format.bug_drug_combinations <- function(x,
     }
     ab_txt
   }
-
+  
   y <- x %>%
     mutate(ab = as.ab(ab),
            ab_txt = give_ab_name(ab = ab, format = translate_ab, language = language)) %>% 
@@ -146,8 +146,9 @@ format.bug_drug_combinations <- function(x,
     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) %>% 
-    spread(mo, txt) %>%
+    select(ab, ab_txt, mo, txt) %>%
+    arrange(mo) %>% 
+    pivot_wider(names_from = mo, values_from = txt) %>% 
     mutate_all(~ifelse(is.na(.), "", .)) %>% 
     mutate(ab_group = ab_group(ab, language = language),
            ab_txt) %>%