unit tedts

R/antibiogram.R

@@ -1206,7 +1206,7 @@ retrieve_wisca_parameters <- function(wisca_model, ...) {
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::tbl_sum, antibiogram)
 tbl_sum.antibiogram <- function(x, ...) {
   dims <- paste(format(NROW(x), big.mark = ","), AMR_env$cross_icon, format(NCOL(x), big.mark = ","))
-  names(dims) <- "An Antibiogram"
+  names(dims) <- "An antibiogram"
   if (isTRUE(attributes(x)$wisca)) {
     dims <- c(dims, Type = paste0("WISCA with ", attributes(x)$conf_interval * 100, "% CI"))
   } else if (isTRUE(attributes(x)$formatting_type >= 13)) {
@@ -1226,8 +1226,7 @@ tbl_format_footer.antibiogram <- function(x, ...) {
   }
   c(footer, font_subtle(paste0(
     "# Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,\n",
-    "# or use it directly in R Markdown or ",
-    font_url("https://quarto.org", "Quarto"), ", see ", word_wrap("?antibiogram")
+    "# or use it directly in R Markdown or Quarto, see ", word_wrap("?antibiogram")
   )))
 }
 

R/bug_drug_combinations.R

@@ -129,16 +129,21 @@ bug_drug_combinations <- function(x,
       # turn and merge everything
       pivot <- lapply(x_mo_filter, function(x) {
         m <- as.matrix(table(as.sir(x), useNA = "always"))
+        na_idx <- which(is.na(rownames(m)))
+        get_row <- function(lbl) {
+          idx <- which(rownames(m) == lbl)
+          if (length(idx) == 1L) unname(m[idx, ]) else rep(0L, ncol(m))
+        }
         data.frame(
-          S = m["S", ],
-          SDD = m["SDD", ],
-          I = m["I", ],
-          R = m["R", ],
-          NI = m["NI", ],
-          WT = m["WT", ],
-          NWT = m["NWT", ],
-          NS = m["NS", ],
-          na = m[which(is.na(rownames(m))), ],
+          S = get_row("S"),
+          SDD = get_row("SDD"),
+          I = get_row("I"),
+          R = get_row("R"),
+          NI = get_row("NI"),
+          WT = get_row("WT"),
+          NWT = get_row("NWT"),
+          NS = get_row("NS"),
+          na = if (length(na_idx) == 1L) unname(m[na_idx, ]) else rep(0L, ncol(m)),
           stringsAsFactors = FALSE
         )
       })