(v1.2.0.9001) filter_ab_class() update

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.2.0.9000
+Version: 1.2.0.9001
-Date: 2020-06-02
+Date: 2020-06-03
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NAMESPACE

@@ -114,6 +114,7 @@ export(filter_first_weighted_isolate)
 export(filter_fluoroquinolones)
 export(filter_glycopeptides)
 export(filter_macrolides)
+export(filter_penicillins)
 export(filter_tetracyclines)
 export(first_isolate)
 export(full_join_microorganisms)

NEWS.md

@@ -1,9 +1,12 @@
-# AMR 1.2.0.9000
+# AMR 1.2.0.9001
-## <small>Last updated: 02-Jun-2020</small>
+## <small>Last updated: 03-Jun-2020</small>
 
 ### Changed
 * Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
+* All `*_join_microorganisms()` functions now return the original data class (e.g. tibbles and data.tables)
 * Fixed a bug where `as.ab()` would return an error on invalid input values
+* Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*)
+* Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()`
 
 # AMR 1.2.0
 
@@ -20,7 +23,7 @@
 
 ### Changed
 * Taxonomy:
-  * Updated the taxonomy of microorganisms tot May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). **Note:** a taxonomic update may always impact determination of first isolates (using `first_isolate()`), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.
+  * Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). **Note:** a taxonomic update may always impact determination of first isolates (using `first_isolate()`), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.
   * Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string)
 * EUCAST rules:
   * The `eucast_rules()` function no longer applies "other" rules at default that are made available by this package (like setting ampicillin = R when ampicillin + enzyme inhibitor = R). The default input value for `rules` is now `c("breakpoints", "expert")` instead of `"all"`, but this can be changed by the user. To return to the old behaviour, set `options(AMR.eucast_rules = "all")`.

R/filter_ab_class.R

@@ -21,14 +21,14 @@
 
 #' Filter isolates on result in antimicrobial class
 #'
-#' Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
+#' Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.
 #' @inheritSection lifecycle Stable lifecycle
 #' @param x a data set
 #' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics]
 #' @param result an antibiotic result: S, I or R (or a combination of more of them)
 #' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
 #' @param ... parameters passed on to `filter_at` from the `dplyr` package
-#' @details The `group` column in [antibiotics] data set will be searched for `ab_class` (case-insensitive). If no results are found, the `atc_group1` and `atc_group2` columns will be searched. Next, `x` will be checked for column names with a value in any abbreviations, codes or official names found in the [antibiotics] data set.
+#' @details The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched for the input given in `ab_class` (case-insensitive). Next, `x` will be checked for column names with a value in any abbreviation, code or official name found in the [antibiotics] data set.
 #' @rdname filter_ab_class
 #' @export
 #' @examples
@@ -36,6 +36,7 @@
 #' library(dplyr)
 #'
 #' # filter on isolates that have any result for any aminoglycoside
+#' example_isolates %>% filter_ab_class("aminoglycoside")
 #' example_isolates %>% filter_aminoglycosides()
 #'
 #' # this is essentially the same as (but without determination of column names):
@@ -45,7 +46,7 @@
 #'
 #'
 #' # filter on isolates that show resistance to ANY aminoglycoside
-#' example_isolates %>% filter_aminoglycosides("R")
+#' example_isolates %>% filter_aminoglycosides("R", "any")
 #'
 #' # filter on isolates that show resistance to ALL aminoglycosides
 #' example_isolates %>% filter_aminoglycosides("R", "all")
@@ -76,13 +77,14 @@ filter_ab_class <- function(x,
   
   # save to return later
   x_class <- class(x)
+  x.bak <- x
   x <- as.data.frame(x, stringsAsFactors = FALSE)
   
   scope <- scope[1L]
   if (is.null(result)) {
     result <- c("S", "I", "R")
   }
-  # make result = "SI" work too:
+  # make result = "SI" works too:
   result <- unlist(strsplit(result, ""))
   
   if (!all(result %in% c("S", "I", "R"))) {
@@ -92,16 +94,30 @@ filter_ab_class <- function(x,
     stop("`scope` must be one of: any, all", call. = FALSE)
   }
   
-  # get only columns with class ab, mic or disk - those are AMR results
+  # get all columns in data with names that resemble antibiotics
-  vars_df <- colnames(x)[sapply(x, function(y) is.rsi(y) | is.mic(y) | is.disk(y))]
+  ab_in_data <- suppressMessages(get_column_abx(x))
-  vars_df_ab <- suppressWarnings(as.ab(vars_df))
+  if (length(ab_in_data) == 0) {
-  # get the columns with a group names in the chosen ab class
+    message(font_blue("NOTE: no antimicrobial agents found, data left unchanged."))
-  vars_df <- vars_df[which(ab_group(vars_df_ab) %like% ab_class | 
+    return(x.bak)
-                             ab_atc_group1(vars_df_ab) %like% ab_class |
+  }
-                             ab_atc_group2(vars_df_ab) %like% ab_class)]
+  # get reference data
+  ab_class <- gsub("[^a-zA-Z0-9]+", ".*", ab_class)
+  ab_class <- gsub("(ph|f)", "(ph|f)", ab_class)
+  ab_class <- gsub("(t|th)", "(t|th)", ab_class)
+  ab_reference <- subset(antibiotics,
+                         group %like% ab_class | 
+                           atc_group1 %like% ab_class | 
+                           atc_group2 %like% ab_class)
   ab_group <- find_ab_group(ab_class)
+  # get the columns with a group names in the chosen ab class
+  agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
+  if (length(agents) == 0) {
+    message(font_blue(paste0("NOTE: no antimicrobial agents of class ", ab_group, 
+                             " found (such as ", find_ab_names(ab_class, 2), 
+                             "), data left unchanged.")))
+    return(x.bak)
+  }
   
-  if (length(vars_df) > 0) {
   if (length(result) == 1) {
     operator <- " is "
   } else {
@@ -113,25 +129,27 @@ filter_ab_class <- function(x,
   } else {
     scope_txt <- " and "
     scope_fn <- all
-      if (length(vars_df) > 1) {
+    if (length(agents) > 1) {
       operator <- gsub("is", "are", operator)
     }
   }
-    if (length(vars_df) > 1) {
+  if (length(agents) > 1) {
     scope <- paste(scope, "of columns ")
   } else {
     scope <- "column "
   }
+  
+  # sort columns on official name
+  agents <- agents[order(ab_name(names(agents), language = NULL))]
+  
   message(font_blue(paste0("Filtering on ", ab_group, ": ", scope,
-                             paste0(font_bold(paste0("`", vars_df, "`"), collapse = NULL), collapse = scope_txt), operator, toString(result))))
+                           paste(paste0("`", font_bold(agents, collapse = NULL),
-    filtered <<- as.logical(by(x, seq_len(nrow(x)),
+                                        "` (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
-                              function(row) scope_fn(unlist(row[, vars_df]) %in% result, na.rm = TRUE)))
+                                 collapse = scope_txt),
+                           operator, toString(result))))
+  filtered <- as.logical(by(x, seq_len(nrow(x)),
+                            function(row) scope_fn(unlist(row[, agents]) %in% result, na.rm = TRUE)))
   x <- x[which(filtered), , drop = FALSE]
-  } else {
-    message(font_blue(paste0("NOTE: no antimicrobial agents of class ", ab_group, 
-                             " (such as ", find_ab_names(ab_group), 
-                             ") found, data left unchanged.")))
-  }
   class(x) <- x_class
   x
 }
@@ -279,6 +297,19 @@ filter_macrolides <- function(x,
                   ...)
 }
 
+#' @rdname filter_ab_class
+#' @export
+filter_penicillins <- function(x,
+                               result = NULL,
+                               scope = "any",
+                               ...) {
+  filter_ab_class(x = x,
+                  ab_class = "penicillin",
+                  result = result,
+                  scope = scope,
+                  ...)
+}
+
 #' @rdname filter_ab_class
 #' @export
 filter_tetracyclines <- function(x,
@@ -312,9 +343,9 @@ find_ab_group <- function(ab_class) {
   )
 }
 
-find_ab_names <- function(ab_group) {
+find_ab_names <- function(ab_group, n = 3) {
   drugs <- antibiotics[which(antibiotics$group %like% ab_group), "name"]
-  paste0(ab_name(sample(drugs, size = min(4, length(drugs)), replace = FALSE),
+  paste0(sort(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
-                 tolower = TRUE, language = NULL), 
+                      tolower = TRUE, language = NULL)), 
          collapse = ", ")
 }

R/guess_ab_col.R

@@ -160,6 +160,11 @@ get_column_abx <- function(x,
     x <- x[!is.na(x)]
   }
 
+  if (length(x) == 0) {
+    message(font_blue("No columns found."))
+    return(x)
+  }
+  
   # sort on name
   x <- x[order(names(x), x)]
   duplicates <- c(x[base::duplicated(x)], x[base::duplicated(names(x))]) 
@@ -167,7 +172,7 @@ get_column_abx <- function(x,
   x <- c(x[!names(x) %in% names(duplicates)], duplicates)
   x <- x[order(names(x), x)]
   
-  # succeeded with aut-guessing
+  # succeeded with auto-guessing
   message(font_blue("OK."))
 
   for (i in seq_len(length(x))) {

R/join_microorganisms.R

@@ -55,7 +55,9 @@
 #' }
 inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   check_dataset_integrity()
+  check_groups_before_join(x, "inner_join_microorganisms")
   checked <- joins_check_df(x, by)
+  x_class <- class(x)
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
@@ -64,6 +66,7 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   if (NROW(join) > NROW(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
   }
+  class(join) <- x_class
   join
 }
 
@@ -71,7 +74,9 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
 #' @export
 left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   check_dataset_integrity()
+  check_groups_before_join(x, "left_join_microorganisms")
   checked <- joins_check_df(x, by)
+  x_class <- class(x)
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
@@ -80,6 +85,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   if (NROW(join) > NROW(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
   }
+  class(join) <- x_class
   join
 }
 
@@ -87,7 +93,9 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
 #' @export
 right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   check_dataset_integrity()
+  check_groups_before_join(x, "right_join_microorganisms")
   checked <- joins_check_df(x, by)
+  x_class <- class(x)
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
@@ -96,6 +104,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   if (NROW(join) > NROW(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
   }
+  class(join) <- x_class
   join
 }
 
@@ -103,7 +112,9 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
 #' @export
 full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   check_dataset_integrity()
+  check_groups_before_join(x, "full_join_microorganisms")
   checked <- joins_check_df(x, by)
+  x_class <- class(x)
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
@@ -112,6 +123,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   if (NROW(join) > NROW(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
   }
+  class(join) <- x_class
   join
 }
 
@@ -119,24 +131,32 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
 #' @export
 semi_join_microorganisms <- function(x, by = NULL, ...) {
   check_dataset_integrity()
+  check_groups_before_join(x, "semi_join_microorganisms")
+  x_class <- class(x)
   checked <- joins_check_df(x, by)
   x <- checked$x
   by <- checked$by
-  suppressWarnings(
+  join <- suppressWarnings(
     semi_join(x = x, y = microorganisms, by = by, ...)
   )
+  class(join) <- x_class
+  join
 }
 
 #' @rdname join
 #' @export
 anti_join_microorganisms <- function(x, by = NULL, ...) {
   check_dataset_integrity()
+  check_groups_before_join(x, "anti_join_microorganisms")
   checked <- joins_check_df(x, by)
+  x_class <- class(x)
   x <- checked$x
   by <- checked$by
-  suppressWarnings(
+  join <- suppressWarnings(
     anti_join(x = x, y = microorganisms, by = by, ...)
   )
+  class(join) <- x_class
+  join
 }
 
 joins_check_df <- function(x, by) {
@@ -146,6 +166,7 @@ joins_check_df <- function(x, by) {
       by <- "mo"
     }
   }
+  x <- as.data.frame(x, stringsAsFactors = FALSE)
   if (is.null(by)) {
     # search for column with class `mo` and return first one found
     by <- colnames(x)[lapply(x, is.mo) == TRUE][1]
@@ -168,3 +189,9 @@ joins_check_df <- function(x, by) {
   list(x = x,
        by = joinby)
 }
+
+check_groups_before_join <- function(x, fn) {
+  if (is.data.frame(x) && !is.null(attributes(x)$groups)) {
+    warning("Groups are dropped, since the ", fn, "() function relies on merge() from base R, not on join() from dplyr.", call. = FALSE)
+  }
+}

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</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">1.2.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</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">1.2.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</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">1.2.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</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">1.2.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</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">1.2.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
       </span>
     </div>
 
@@ -229,20 +229,24 @@
       <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209000" class="section level1">
+    <div id="amr-1209001" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9000">
+<h1 class="page-header" data-toc-text="1.2.0.9001">
-<a href="#amr-1209000" class="anchor"></a>AMR 1.2.0.9000<small> Unreleased </small>
+<a href="#amr-1209001" class="anchor"></a>AMR 1.2.0.9001<small> Unreleased </small>
 </h1>
-<div id="last-updated-02-jun-2020" class="section level2">
+<div id="last-updated-03-jun-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-02-jun-2020" class="anchor"></a><small>Last updated: 02-Jun-2020</small>
+<a href="#last-updated-03-jun-2020" class="anchor"></a><small>Last updated: 03-Jun-2020</small>
 </h2>
 <div id="changed" class="section level3">
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
 <ul>
 <li>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</li>
+<li>All <code>*_join_microorganisms()</code> functions now return the original data class (e.g. tibbles and data.tables)</li>
 <li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
+<li>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</li>
+<li>Added official antimicrobial names to all <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> functions, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code>
+</li>
 </ul>
 </div>
 </div>
@@ -274,7 +278,7 @@
 <ul>
 <li>Taxonomy:
 <ul>
-<li>Updated the taxonomy of microorganisms tot May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). <strong>Note:</strong> a taxonomic update may always impact determination of first isolates (using <code><a href="../reference/first_isolate.html">first_isolate()</a></code>), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.</li>
+<li>Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). <strong>Note:</strong> a taxonomic update may always impact determination of first isolates (using <code><a href="../reference/first_isolate.html">first_isolate()</a></code>), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.</li>
 <li>Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string)</li>
 </ul>
 </li>

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-06-02T14:04Z
+last_built: 2020-06-03T09:44Z
 urls:
   reference: https://msberends.gitlab.io/AMR/reference
   article: https://msberends.gitlab.io/AMR/articles

docs/reference/filter_ab_class.html

@@ -49,7 +49,7 @@
   <script src="../extra.js"></script>
 
 <meta property="og:title" content="Filter isolates on result in antimicrobial class — filter_ab_class" />
-<meta property="og:description" content="Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
+<meta property="og:description" content="Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs." />
 <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
 
 
@@ -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">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
       </span>
     </div>
 
@@ -232,7 +232,7 @@
     </div>
 
     <div class="ref-description">
-    <p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.</p>
+    <p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.</p>
     </div>
 
     <pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='no'>x</span>, <span class='no'>ab_class</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
@@ -259,6 +259,8 @@
 
 <span class='fu'>filter_macrolides</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
 
+<span class='fu'>filter_penicillins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
+
 <span class='fu'>filter_tetracyclines</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -288,7 +290,7 @@
 
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>The <code>group</code> column in <a href='antibiotics.html'>antibiotics</a> data set will be searched for <code>ab_class</code> (case-insensitive). If no results are found, the <code>atc_group1</code> and <code>atc_group2</code> columns will be searched. Next, <code>x</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
+    <p>The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched for the input given in <code>ab_class</code> (case-insensitive). Next, <code>x</code> will be checked for column names with a value in any abbreviation, code or official name found in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
     <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
 
     
@@ -302,6 +304,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
 
 <span class='co'># filter on isolates that have any result for any aminoglycoside</span>
+<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_ab_class</span>(<span class='st'>"aminoglycoside"</span>)
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>()
 
 <span class='co'># this is essentially the same as (but without determination of column names):</span>
@@ -311,7 +314,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 
 
 <span class='co'># filter on isolates that show resistance to ANY aminoglycoside</span>
-<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>)
+<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>)
 
 <span class='co'># filter on isolates that show resistance to ALL aminoglycosides</span>
 <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)

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">1.2.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
       </span>
     </div>
 
@@ -421,7 +421,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
+          <p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
         </td>
         <td><p>Filter isolates on result in antimicrobial class</p></td>
       </tr><tr>

man/filter_ab_class.Rd

@@ -13,6 +13,7 @@
 \alias{filter_fluoroquinolones}
 \alias{filter_glycopeptides}
 \alias{filter_macrolides}
+\alias{filter_penicillins}
 \alias{filter_tetracyclines}
 \title{Filter isolates on result in antimicrobial class}
 \usage{
@@ -40,6 +41,8 @@ filter_glycopeptides(x, result = NULL, scope = "any", ...)
 
 filter_macrolides(x, result = NULL, scope = "any", ...)
 
+filter_penicillins(x, result = NULL, scope = "any", ...)
+
 filter_tetracyclines(x, result = NULL, scope = "any", ...)
 }
 \arguments{
@@ -54,10 +57,10 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
 \item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package}
 }
 \description{
-Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
+Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.
 }
 \details{
-The \code{group} column in \link{antibiotics} data set will be searched for \code{ab_class} (case-insensitive). If no results are found, the \code{atc_group1} and \code{atc_group2} columns will be searched. Next, \code{x} will be checked for column names with a value in any abbreviations, codes or official names found in the \link{antibiotics} data set.
+The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched for the input given in \code{ab_class} (case-insensitive). Next, \code{x} will be checked for column names with a value in any abbreviation, code or official name found in the \link{antibiotics} data set.
 }
 \section{Stable lifecycle}{
 
@@ -72,6 +75,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
 library(dplyr)
 
 # filter on isolates that have any result for any aminoglycoside
+example_isolates \%>\% filter_ab_class("aminoglycoside")
 example_isolates \%>\% filter_aminoglycosides()
 
 # this is essentially the same as (but without determination of column names):
@@ -81,7 +85,7 @@ example_isolates \%>\%
 
 
 # filter on isolates that show resistance to ANY aminoglycoside
-example_isolates \%>\% filter_aminoglycosides("R")
+example_isolates \%>\% filter_aminoglycosides("R", "any")
 
 # filter on isolates that show resistance to ALL aminoglycosides
 example_isolates \%>\% filter_aminoglycosides("R", "all")

tests/testthat/test-join_microorganisms.R

@@ -56,4 +56,8 @@ test_that("joins work", {
   expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
   expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
   
+  library(dplyr)
+  x <- tibble(bact = as.mo("E.coli"))
+  expect_warning(left_join_microorganisms(x %>% group_by(bact), "bact"))
+
 })