(v1.1.0.9004) lose dependencies

R/bug_drug_combinations.R

@@ -32,7 +32,6 @@
 #' @param ... arguments passed on to `FUN`
 #' @inheritParams rsi_df
 #' @inheritParams base::formatC
-#' @importFrom dplyr %>% rename group_by select mutate filter summarise ungroup
 #' @importFrom tidyr pivot_longer
 #' @details The function [format()] calculates the resistance per bug-drug combination. Use `combine_IR = FALSE` (default) to test R vs. S+I and `combine_IR = TRUE` to test R+I vs. S. 
 #' 
@@ -74,13 +73,15 @@ bug_drug_combinations <- function(x,
     stop("`col_mo` must be set.", call. = FALSE)
   }
   
-  x <- x %>%
-    as.data.frame(stringsAsFactors = FALSE) %>% 
-    mutate(mo = x %>% 
-             pull(col_mo) %>% 
-             FUN(...)) %>% 
-    group_by(mo) %>% 
-    select_if(is.rsi) %>% 
+  select_rsi <- function(.data) {
+    .data[, c(col_mo, names(which(sapply(.data, is.rsi))))]
+  }
+  
+  x <- x %>% as.data.frame(stringsAsFactors = FALSE)
+  x$mo <- FUN(x[, col_mo, drop = TRUE])
+
+  x <- x %>% 
+    select_rsi() %>% 
     pivot_longer(-mo, names_to = "ab") %>% 
     group_by(mo, ab) %>% 
     summarise(S = sum(value == "S", na.rm = TRUE),
@@ -93,9 +94,7 @@ bug_drug_combinations <- function(x,
   structure(.Data = x, class = c("bug_drug_combinations", class(x)))
 }
 
-#' @importFrom dplyr everything rename %>% ungroup group_by summarise mutate_all arrange everything lag
 #' @importFrom tidyr pivot_wider
-#' @importFrom cleaner percentage
 #' @exportMethod format.bug_drug_combinations
 #' @export
 #' @rdname bug_drug_combinations
@@ -110,10 +109,10 @@ format.bug_drug_combinations <- function(x,
                                          decimal.mark = getOption("OutDec"),
                                          big.mark = ifelse(decimal.mark == ",", ".", ","),
                                          ...) {
-  x <- x %>% filter(total >= minimum)
+  x <- x %>% subset(total >= minimum)
   
   if (remove_intrinsic_resistant == TRUE) {
-    x <- x %>% filter(R != total)
+    x <- x %>% subset(R != total)
   }
   if (combine_SI == TRUE | combine_IR == FALSE) {
     x$isolates <- x$R
@@ -137,26 +136,46 @@ format.bug_drug_combinations <- function(x,
     ab_txt
   }
   
+  remove_NAs <- function(.data) {
+    as.data.frame(sapply(.data, function(x) ifelse(is.na(x), "", x), simplify = FALSE))
+  }
+  
+  create_var <- function(.data, ...) {
+    dots <- list(...)
+    for (i in seq_len(length(dots))) {
+      .data[, names(dots)[i]] <- dots[[i]]
+    }
+    .data
+  }
+  
   y <- x %>%
-    mutate(ab = as.ab(ab),
-           ab_txt = give_ab_name(ab = ab, format = translate_ab, language = language)) %>% 
+    create_var(ab = as.ab(x$ab),
+               ab_txt = give_ab_name(ab = x$ab, format = translate_ab, language = language)) %>%
     group_by(ab, ab_txt, mo) %>% 
     summarise(isolates = sum(isolates, na.rm = TRUE),
               total = sum(total, na.rm = TRUE)) %>% 
-    ungroup() %>% 
-    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)), ")")) %>% 
+    ungroup()
+  
+  y <- y %>% 
+    create_var(txt = paste0(percentage(y$isolates / y$total, decimal.mark = decimal.mark, big.mark = big.mark), 
+                                          " (", trimws(format(y$isolates, big.mark = big.mark)), "/",
+                                          trimws(format(y$total, big.mark = big.mark)), ")")) %>% 
     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) %>% 
-    select(ab_group, ab_txt, everything(), -ab) %>% 
-    arrange(ab_group, ab_txt) %>% 
-    mutate(ab_group = ifelse(ab_group != lag(ab_group) | is.na(lag(ab_group)), ab_group, ""))
+    remove_NAs()
   
+  select_ab_vars <- function(.data) {
+    .data[, c("ab_group", "ab_txt", colnames(.data)[!colnames(.data) %in% c("ab_group", "ab_txt", "ab")])]
+  }
+  
+  y <- y %>% 
+    create_var(ab_group = ab_group(y$ab, language = language)) %>% 
+    select_ab_vars() %>% 
+    arrange(ab_group, ab_txt)
+  y <- y %>% 
+    create_var(ab_group = ifelse(y$ab_group != lag(y$ab_group) | is.na(lag(y$ab_group)), y$ab_group, ""))
+
   if (add_ab_group == FALSE) {
     y <- y %>% select(-ab_group) %>% rename("Drug" = ab_txt)
     colnames(y)[1] <- translate_AMR(colnames(y)[1], language = get_locale(), only_unknown = FALSE)
@@ -170,8 +189,7 @@ format.bug_drug_combinations <- function(x,
 
 #' @exportMethod print.bug_drug_combinations
 #' @export
-#' @importFrom crayon blue
 print.bug_drug_combinations <- function(x, ...) {
   print(as.data.frame(x, stringsAsFactors = FALSE))
-  message(blue("NOTE: Use 'format()' on this result to get a publicable/printable format."))
+  message(font_blue("NOTE: Use 'format()' on this result to get a publicable/printable format."))
 }