use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

inst/tinytest/test-zzz.R

@@ -32,11 +32,21 @@
 
 # functions used by import_fn()
 import_functions <- c(
+  "%>%" = "dplyr",
   "%chin%" = "data.table",
+  "across" = "dplyr",
   "anti_join" = "dplyr",
+  "arrange" = "dplyr",
+  "bind_rows" = "dplyr",
   "chmatch" = "data.table",
+  "count" = "dplyr",
   "cur_column" = "dplyr",
+  "desc" = "dplyr",
+  "distinct" = "dplyr",
+  "everything" = "dplyr",
   "full_join" = "dplyr",
+  "group_by" = "dplyr",
+  "group_vars" = "dplyr",
   "has_internet" = "curl",
   "html_attr" = "rvest",
   "html_children" = "rvest",
@@ -46,13 +56,24 @@ import_functions <- c(
   "html_text" = "rvest",
   "inner_join" = "dplyr",
   "insertText" = "rstudioapi",
+  "kable" = "knitr",
+  "lag" = "dplyr",
   "left_join" = "dplyr",
+  "mutate" = "dplyr",
+  "n_distinct" = "dplyr",
   "new_pillar_shaft_simple" = "pillar",
+  "pivot_longer" = "tidyr",
   "progress_bar" = "progress",
+  "pull" = "dplyr",
   "read_html" = "xml2",
+  "rename" = "dplyr",
   "right_join" = "dplyr",
+  "row_number" = "dplyr",
+  "select" = "dplyr",
   "semi_join" = "dplyr",
-  "showQuestion" = "rstudioapi"
+  "showQuestion" = "rstudioapi",
+  "summarise" = "dplyr",
+  "ungroup" = "dplyr"
 )
 
 # functions that are called directly with ::
@@ -71,6 +92,7 @@ call_functions <- c(
   "element_text" = "ggplot2",
   "expand_limits" = "ggplot2",
   "facet_wrap" = "ggplot2",
+  "geom_col" = "ggplot2",
   "geom_errorbar" = "ggplot2",
   "geom_path" = "ggplot2",
   "geom_point" = "ggplot2",
@@ -115,7 +137,7 @@ for (i in seq_len(length(import_functions))) {
   # function should exist in foreign pkg namespace
   if (AMR:::pkg_is_available(pkg,
     also_load = FALSE,
-    min_version = if (pkg == "dplyr") "1.0.0" else NULL
+    min_version = if (pkg %in% c("dplyr", "tidyr")) "1.0.0" else NULL
   )) {
     tst <- !is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE))
     expect_true(tst,