(v1.3.0.9010) S3 extensions without dependencies

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.3.0.9009
-Date: 2020-08-26
+Version: 1.3.0.9010
+Date: 2020-08-28
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NAMESPACE

@@ -40,11 +40,6 @@ S3method(format,bug_drug_combinations)
 S3method(kurtosis,data.frame)
 S3method(kurtosis,default)
 S3method(kurtosis,matrix)
-S3method(pillar_shaft,ab)
-S3method(pillar_shaft,disk)
-S3method(pillar_shaft,mic)
-S3method(pillar_shaft,mo)
-S3method(pillar_shaft,rsi)
 S3method(plot,mic)
 S3method(plot,resistance_predict)
 S3method(plot,rsi)
@@ -63,11 +58,6 @@ S3method(skewness,matrix)
 S3method(summary,mic)
 S3method(summary,mo)
 S3method(summary,rsi)
-S3method(type_sum,ab)
-S3method(type_sum,disk)
-S3method(type_sum,mic)
-S3method(type_sum,mo)
-S3method(type_sum,rsi)
 export("%like%")
 export("%like_case%")
 export(ab_atc)

NEWS.md

@@ -1,7 +1,8 @@
-# AMR 1.3.0.9009
-## <small>Last updated: 26 August 2020</small>
+# AMR 1.3.0.9010
+## <small>Last updated: 28 August 2020</small>
 
 ### New
+* A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html
 * Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`.
 
   Curious about which enterococci are actually intrinsic resistant to vancomycin?
@@ -38,7 +39,7 @@
 * Overall speed improvement by tweaking joining functions
 * Function `mo_shortname()` now returns the genus for input where the species is unknown
 * BORSA is now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus"
-* Support for coloured `tibble` printing of classes `ab`, `mo`, `rsi`, `mic` and `disk`
+* Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: `tibble` printing support for classes `<rsi>`, `<mic>`, `<disk>`, `<ab>` and `<mo>`. When using `tibble`s containing antimicrobial columns (class `<rsi>`), "S" will print in green, "I" will print in yellow and "R" will print in red. Microbial IDs (class `<mo>`) will emphasise on the genus and species, not on the kingdom.
 
 # AMR 1.3.0
 
@@ -102,8 +103,8 @@
   
   Negative effects of this change are:
   * Function `freq()` that was borrowed from the `cleaner` package was removed. Use `cleaner::freq()`, or run `library("cleaner")` before you use `freq()`.
-  * Printing values of class `mo` or `rsi` in a tibble will no longer be in colour and printing `rsi` in a tibble will show the class `<ord>`, not `<rsi>` anymore. This is purely a visual effect.
-  * All functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) are noticeably slower when running on hundreds of thousands of rows.
+  * ~~Printing values of class `mo` or `rsi` in a tibble will no longer be in colour and printing `rsi` in a tibble will show the class `<ord>`, not `<rsi>` anymore. This is purely a visual effect.~~
+  * ~~All functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) are noticeably slower when running on hundreds of thousands of rows.~~
   * For developers: classes `mo` and `ab` now both also inherit class `character`, to support any data transformation. This change invalidates code that checks for class length == 1.
 
 ### Changed

R/aa_helper_functions.R

@@ -444,6 +444,9 @@ font_red_bg <- function(..., collapse = " ") {
 font_yellow_bg <- function(..., collapse = " ") {
   try_colour(..., before = "\033[43m", after = "\033[49m", collapse = collapse)
 }
+font_na <- function(..., collapse = " ") {
+  font_red(..., collapse = collapse)
+}
 font_bold <- function(..., collapse = " ") {
   try_colour(..., before = "\033[1m", after = "\033[22m", collapse = collapse)
 }
@@ -477,6 +480,61 @@ progress_estimated <- function(n = 1, n_min = 0, ...) {
   }
 }
 
+create_pillar_column <- function(x, ...) {
+  new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
+  if (!is.null(new_pillar_shaft_simple)) {
+    new_pillar_shaft_simple(x, ...)  
+  } else {
+    # does not exist in package 'pillar' anymore
+    structure(list(x),
+              class = "pillar_shaft_simple",
+              ...)
+  }
+}
+
+# copied from vctrs::s3_register by their permission
+s3_register <- function(generic, class, method = NULL) {
+  stopifnot(is.character(generic), length(generic) == 1)
+  stopifnot(is.character(class), length(class) == 1)
+  pieces <- strsplit(generic, "::")[[1]]
+  stopifnot(length(pieces) == 2)
+  package <- pieces[[1]]
+  generic <- pieces[[2]]
+  caller <- parent.frame()
+  get_method_env <- function() {
+    top <- topenv(caller)
+    if (isNamespace(top)) {
+      asNamespace(environmentName(top))
+    }
+    else {
+      caller
+    }
+  }
+  get_method <- function(method, env) {
+    if (is.null(method)) {
+      get(paste0(generic, ".", class), envir = get_method_env())
+    }
+    else {
+      method
+    }
+  }
+  method_fn <- get_method(method)
+  stopifnot(is.function(method_fn))
+  setHook(packageEvent(package, "onLoad"), function(...) {
+    ns <- asNamespace(package)
+    method_fn <- get_method(method)
+    registerS3method(generic, class, method_fn, envir = ns)
+  })
+  if (!isNamespaceLoaded(package)) {
+    return(invisible())
+  }
+  envir <- asNamespace(package)
+  if (exists(generic, envir)) {
+    registerS3method(generic, class, method_fn, envir = envir)
+  }
+  invisible()
+}
+
 # works exactly like round(), but rounds `round2(44.55, 1)` to 44.6 instead of 44.5
 # and adds decimal zeroes until `digits` is reached when force_zero = TRUE
 round2 <- function(x, digits = 0, force_zero = TRUE) {

R/ab.R

@@ -467,22 +467,14 @@ is.ab <- function(x) {
   inherits(x, "ab")
 }
 
-
-#' @method pillar_shaft ab
-#' @export
+# will be exported using s3_register() in R/zzz.R
 pillar_shaft.ab <- function(x, ...) {
-  # import from the pillar package, without being dependent on it!
-  style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
-  new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
-  out <- format(x)
-  out[is.na(x)] <- style_na(NA)
-  new_pillar_shaft_simple(out,
-                          align = "left", 
-                          min_width = 4)
+  out <- trimws(format(x))
+  out[is.na(x)] <- font_na(NA)
+  create_pillar_column(out, align = "left", min_width = 4)
 }
 
-#' @method type_sum ab
-#' @export
+# will be exported using s3_register() in R/zzz.R
 type_sum.ab <- function(x, ...) {
   "ab"
 }

R/disk.R

@@ -114,18 +114,14 @@ is.disk <- function(x) {
   inherits(x, "disk")
 }
 
-#' @method pillar_shaft disk
-#' @export
+# will be exported using s3_register() in R/zzz.R
 pillar_shaft.disk <- function(x, ...) {
-  style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
-  new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
   out <- trimws(format(x))
-  out[is.na(x)] <- style_na(NA)
-  new_pillar_shaft_simple(out, align = "right", min_width = 3)
+  out[is.na(x)] <- font_na(NA)
+  create_pillar_column(out, align = "right", width = 2)
 }
 
-#' @method type_sum disk
-#' @export
+# will be exported using s3_register() in R/zzz.R
 type_sum.disk <- function(x, ...) {
   "disk"
 }

R/mic.R

@@ -171,18 +171,14 @@ droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...)
   x
 }
 
-#' @method pillar_shaft mic
-#' @export
+# will be exported using s3_register() in R/zzz.R
 pillar_shaft.mic <- function(x, ...) {
-  style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
-  new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
   out <- trimws(format(x))
-  out[is.na(x)] <- style_na(NA)
-  new_pillar_shaft_simple(out, align = "right", min_width = 4)
+  out[is.na(x)] <- font_na(NA)
+  create_pillar_column(out, align = "right", min_width = 4)
 }
 
-#' @method type_sum mic
-#' @export
+# will be exported using s3_register() in R/zzz.R
 type_sum.mic <- function(x, ...) {
   "mic"
 }

R/mo.R

@@ -181,7 +181,7 @@ as.mo <- function(x,
   x <- parse_and_convert(x)
   # replace mo codes used in older package versions
   x <- replace_old_mo_codes(x, property = "mo")
-
+  
   # WHONET: xxx = no growth
   x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
   # Laboratory systems: remove entries like "no growth" etc
@@ -384,7 +384,7 @@ exec_as.mo <- function(x,
     x <- data.frame(fullname = x, stringsAsFactors = FALSE) %>% 
       left_join_MO_lookup(by = "fullname") %>% 
       pull(property)
-
+    
   } else if (all(toupper(x) %in% microorganisms.codes$code)) {
     # commonly used MO codes
     x <- data.frame(code = toupper(x), stringsAsFactors = FALSE) %>%
@@ -1526,41 +1526,54 @@ format_uncertainty_as_df <- function(uncertainty_level,
   df
 }
 
-#' @method pillar_shaft mo
-#' @export
+# will be exported using s3_register() in R/zzz.R
 pillar_shaft.mo <- function(x, ...) {
-  # import from the pillar package, without being dependent on it!
-  style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
-  style_subtle <- import_fn("style_subtle", "pillar", error_on_fail = FALSE)
-  new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
-  if (is.null(style_na) | is.null(style_subtle) | is.null(new_pillar_shaft_simple)) {
-    return(x)
-  }
-  
   out <- format(x)
   # grey out the kingdom (part until first "_")
-  out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(style_subtle("\\1"), "\\2"), out[!is.na(x)])
+  out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)])
   # and grey out every _
-  out[!is.na(x)] <- gsub("_", style_subtle("_"), out[!is.na(x)])
+  out[!is.na(x)] <- gsub("_", font_subtle("_"), out[!is.na(x)])
   
   # markup NA and UNKNOWN
-  out[is.na(x)] <- style_na("  NA")
-  out[x == "UNKNOWN"] <- style_na("  UNKNOWN")
+  out[is.na(x)] <- font_na("  NA")
+  out[x == "UNKNOWN"] <- font_na("  UNKNOWN")
   
   # make it always fit exactly
-  new_pillar_shaft_simple(out,
-                          align = "left", 
-                          width = max(nchar(x)) + ifelse(length(x[x %in% c(NA, "UNKNOWN")]) > 0, 
-                                                         2,
-                                                         0))
+  create_pillar_column(out,
+                       align = "left", 
+                       width = max(nchar(x)) + ifelse(any(x %in% c(NA, "UNKNOWN")), 2, 0))
 }
 
-#' @method type_sum mo
-#' @export
+# will be exported using s3_register() in R/zzz.R
 type_sum.mo <- function(x, ...) {
   "mo"
 }
 
+# will be exported using s3_register() in R/zzz.R
+freq.mo <- function(x, ...) {
+  x_noNA <- as.mo(x[!is.na(x)]) # as.mo() to get the newest mo codes
+  grams <- mo_gramstain(x_noNA, language = NULL)
+  digits <- list(...)$digits
+  if (is.null(digits)) {
+    digits <- 2
+  }
+  freq.default <- import_fn("freq.default", "cleaner", error_on_fail = FALSE)
+  freq.default(x = x, ...,
+               .add_header = list(`Gram-negative` = paste0(format(sum(grams == "Gram-negative", na.rm = TRUE),
+                                                                  big.mark = ",",
+                                                                  decimal.mark = "."),
+                                                           " (", percentage(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams), digits = digits),
+                                                           ")"),
+                                  `Gram-positive` = paste0(format(sum(grams == "Gram-positive", na.rm = TRUE),
+                                                                  big.mark = ",",
+                                                                  decimal.mark = "."),
+                                                           " (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), digits = digits),
+                                                           ")"),
+                                  `No. of genera` = n_distinct(mo_genus(x_noNA, language = NULL)),
+                                  `No. of species` = n_distinct(paste(mo_genus(x_noNA, language = NULL),
+                                                                      mo_species(x_noNA, language = NULL)))))
+}
+
 #' @method print mo
 #' @export
 #' @noRd
@@ -1584,11 +1597,11 @@ summary.mo <- function(object, ...) {
   top <- as.data.frame(table(x), responseName = "n", stringsAsFactors = FALSE)
   top_3 <- top[order(-top$n), 1][1:3]
   value <- c("Class" = "mo",
-    "<NA>" = length(x[is.na(x)]),
-    "Unique" = n_distinct(x[!is.na(x)]),
-    "#1" = top_3[1],
-    "#2" = top_3[2],
-    "#3" = top_3[3])
+             "<NA>" = length(x[is.na(x)]),
+             "Unique" = n_distinct(x[!is.na(x)]),
+             "#1" = top_3[1],
+             "#2" = top_3[2],
+             "#3" = top_3[3])
   class(value) <- c("summaryDefault", "table")
   value
 }

R/rsi.R

@@ -670,24 +670,42 @@ exec_as.rsi <- function(method,
             class =  c("rsi", "ordered", "factor"))
 }
 
-#' @method pillar_shaft rsi
-#' @export 
+# will be exported using s3_register() in R/zzz.R
 pillar_shaft.rsi <- function(x, ...) {
   out <- trimws(format(x))
   out[is.na(x)] <- font_grey(" NA")
-  out[x == "S"] <- font_green_bg(font_white(" S "))
-  out[x == "I"] <- font_yellow_bg(font_black(" I "))
-  out[x == "R"] <- font_red_bg(font_white(" R "))
-  new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
-  new_pillar_shaft_simple(out, align = "left", width = 3)
+  out[x == "S"] <- font_green_bg(font_white("  S  "))
+  out[x == "I"] <- font_yellow_bg(font_black("  I  "))
+  out[x == "R"] <- font_red_bg(font_white("  R  "))
+  create_pillar_column(out, align = "left", width = 5)
 }
 
-#' @method type_sum rsi
-#' @export
+# will be exported using s3_register() in R/zzz.R
 type_sum.rsi <- function(x, ...) {
   "rsi"
 }
 
+# will be exported using s3_register() in R/zzz.R
+freq.rsi <- function(x, ...) {
+  x_name <- deparse(substitute(x))
+  x_name <- gsub(".*[$]", "", x_name)
+  ab <- suppressMessages(suppressWarnings(as.ab(x_name)))
+  freq.default <- import_fn("freq.default", "cleaner", error_on_fail = FALSE)
+  digits <- list(...)$digits
+  if (is.null(digits)) {
+    digits <- 2
+  }
+  if (!is.na(ab)) {
+    freq.default(x = x, ...,
+                 .add_header = list(Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", ab_atc(ab), ")"),
+                                    `Drug group` = ab_group(ab, language = NULL),
+                                    `%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE), digits = digits)))
+  } else {
+    freq.default(x = x, ...,
+                 .add_header = list(`%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE), digits = digits)))
+  }
+}
+
 #' @method print rsi
 #' @export
 #' @noRd

R/zzz.R

@@ -29,6 +29,7 @@
          envir = asNamespace("AMR"))
   
   # support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
+  # without the need to depend on other packages
   s3_register("pillar::pillar_shaft", "ab")
   s3_register("tibble::type_sum", "ab")
   s3_register("pillar::pillar_shaft", "mo")
@@ -39,9 +40,10 @@
   s3_register("tibble::type_sum", "mic")
   s3_register("pillar::pillar_shaft", "disk")
   s3_register("tibble::type_sum", "disk")
+  # support for frequency tables
+  s3_register("cleaner::freq", "mo")
+  s3_register("cleaner::freq", "rsi")
 }
-pillar_shaft <- import_fn("pillar_shaft", "pillar", error_on_fail = FALSE)
-type_sum <- import_fn("type_sum", "tibble", error_on_fail = FALSE)
 
 .onAttach <- function(...) {
   if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) {
@@ -66,9 +68,9 @@ create_MO_lookup <- function() {
   MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, 
                                                    MO_lookup$species,
                                                    MO_lookup$subspecies)))
-  MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname), "fullname_lower"] <- tolower(trimws(MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname), 
-                                                                                                                             "fullname"]))
-  MO_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower)
+  ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname)
+  MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
+  MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower))
   
   # add a column with only "e coli" like combinations
   MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower)
@@ -79,54 +81,11 @@ create_MO_lookup <- function() {
 
 create_MO.old_lookup <- function() {
   MO.old_lookup <- AMR::microorganisms.old
-  MO.old_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname)))
+  MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
   
-  # add a column with only "e coli" like combinations
-  MO.old_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower)
+  # add a column with only "e coli"-like combinations
+  MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
   
   # so arrange data on prevalence first, then full name
   MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
 }
-
-# copied from vctrs::s3_register
-s3_register <- function(generic, class, method = NULL) {
-  stopifnot(is.character(generic), length(generic) == 1)
-  stopifnot(is.character(class), length(class) == 1)
-  pieces <- strsplit(generic, "::")[[1]]
-  stopifnot(length(pieces) == 2)
-  package <- pieces[[1]]
-  generic <- pieces[[2]]
-  caller <- parent.frame()
-  get_method_env <- function() {
-    top <- topenv(caller)
-    if (isNamespace(top)) {
-      asNamespace(environmentName(top))
-    }
-    else {
-      caller
-    }
-  }
-  get_method <- function(method, env) {
-    if (is.null(method)) {
-      get(paste0(generic, ".", class), envir = get_method_env())
-    }
-    else {
-      method
-    }
-  }
-  method_fn <- get_method(method)
-  stopifnot(is.function(method_fn))
-  setHook(packageEvent(package, "onLoad"), function(...) {
-    ns <- asNamespace(package)
-    method_fn <- get_method(method)
-    registerS3method(generic, class, method_fn, envir = ns)
-  })
-  if (!isNamespaceLoaded(package)) {
-    return(invisible())
-  }
-  envir <- asNamespace(package)
-  if (exists(generic, envir)) {
-    registerS3method(generic, class, method_fn, envir = envir)
-  }
-  invisible()
-}

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 
@@ -236,18 +236,19 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1309009" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9009">
-<a href="#amr-1309009" class="anchor"></a>AMR 1.3.0.9009<small> Unreleased </small>
+    <div id="amr-1309010" class="section level1">
+<h1 class="page-header" data-toc-text="1.3.0.9010">
+<a href="#amr-1309010" class="anchor"></a>AMR 1.3.0.9010<small> Unreleased </small>
 </h1>
-<div id="last-updated-26-august-2020" class="section level2">
+<div id="last-updated-28-august-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-26-august-2020" class="anchor"></a><small>Last updated: 26 August 2020</small>
+<a href="#last-updated-28-august-2020" class="anchor"></a><small>Last updated: 28 August 2020</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h3>
 <ul>
+<li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
 <li>
 <p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
 <p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
@@ -297,7 +298,7 @@
 <li><p>Overall speed improvement by tweaking joining functions</p></li>
 <li><p>Function <code><a href="../reference/mo_property.html">mo_shortname()</a></code> now returns the genus for input where the species is unknown</p></li>
 <li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
-<li><p>Support for coloured <code>tibble</code> printing of classes <code>ab</code>, <code>mo</code>, <code>rsi</code>, <code>mic</code> and <code>disk</code></p></li>
+<li><p>Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: <code>tibble</code> printing support for classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;ab&gt;</code> and <code>&lt;mo&gt;</code>. When using <code>tibble</code>s containing antimicrobial columns (class <code>&lt;rsi&gt;</code>), “S” will print in green, “I” will print in yellow and “R” will print in red. Microbial IDs (class <code>&lt;mo&gt;</code>) will emphasise on the genus and species, not on the kingdom.</p></li>
 </ul>
 </div>
 </div>
@@ -399,8 +400,8 @@
 <p>Negative effects of this change are:</p>
 <ul>
 <li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
-<li>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</li>
-<li>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</li>
+<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
+<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
 <li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
 </ul>
 </li>

docs/pkgdown.yml

@@ -2,7 +2,7 @@ pandoc: 2.7.3
 pkgdown: 1.5.1.9000
 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
 articles: []
-last_built: 2020-08-26T14:13Z
+last_built: 2020-08-28T19:54Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

docs/reference/antibiotic_class_selectors.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/reference/as.mo.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/reference/bug_drug_combinations.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/reference/eucast_rules.html

@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/reference/microorganisms.codes.html

@@ -82,7 +82,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9009</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9010</span>
       </span>
     </div>
 

tests/testthat/test-import_fn.R

@@ -0,0 +1,47 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+#                                                                      #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
+# ==================================================================== #
+
+test_that("imports work", {
+  skip_on_cran()
+  
+  import_functions <- c(
+    cleaner = "freq.default",
+    curl = "has_internet",
+    dplyr = "cur_column",
+    dplyr = "peek_mask",
+    readxl = "read_excel",
+    rstudioapi = "showQuestion",
+    rvest = "html_attr",
+    rvest = "html_children",
+    rvest = "html_node",
+    rvest = "html_nodes",
+    rvest = "html_table",
+    rvest = "html_text",
+    tidyselect = "peek_vars",
+    xml2 = "read_html")
+  
+  for (i in seq_len(length(import_functions))) {
+    pkg <- names(import_functions)[i]
+    fn <- unname(import_functions[i])
+    expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
+           failure_message = paste0("Function ", pkg, "::", fn, "() does not exist"))
+  }
+})