(v1.3.0.9032) support skimr

.github/workflows/codecovr.yaml

@@ -63,5 +63,5 @@ jobs:
         shell: Rscript {0}
 
       - name: Test coverage
-        run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_functions_dplyr.R"), quiet = FALSE)
+        run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_pm_functions.R", "R/zzz.R"), quiet = FALSE)
         shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.3.0.9031
+Version: 1.3.0.9032
-Date: 2020-09-26
+Date: 2020-09-28
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -51,6 +51,7 @@ Suggests:
     rmarkdown,
     rstudioapi,
     rvest,
+    skimr,
     testthat,
     tidyr,
     xml2

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.3.0.9031
+# AMR 1.3.0.9032
-## <small>Last updated: 26 September 2020</small>
+## <small>Last updated: 28 September 2020</small>
 
 Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
 
@@ -18,6 +18,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th
   #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"   
   ```
 * Support for veterinary ATC codes
+* Support for skimming classes `<rsi>`, `<mic>`, `<disk>` and `<mo>` with the `skimr` package 
 
 ### Changed
 * Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.

R/disk.R

@@ -186,3 +186,17 @@ unique.disk <- function(x, incomparables = FALSE, ...) {
   attributes(y) <- attributes(x)
   y
 }
+
+# will be exported using s3_register() in R/zzz.R
+get_skimmers.disk <- function(column) {
+  sfl <- import_fn("sfl", "skimr", error_on_fail = FALSE)
+  inline_hist <- import_fn("inline_hist", "skimr", error_on_fail = FALSE)
+  sfl(
+    skim_type = "disk",
+    smallest = ~min(as.double(.), na.rm = TRUE),
+    largest = ~max(as.double(.), na.rm = TRUE),
+    median = ~stats::median(as.double(.), na.rm = TRUE),
+    n_unique = n_unique,
+    hist = ~inline_hist(stats::na.omit(as.double(.)))
+  )
+}

R/mic.R

@@ -296,3 +296,17 @@ unique.mic <- function(x, incomparables = FALSE, ...) {
   attributes(y) <- attributes(x)
   y
 }
+
+# will be exported using s3_register() in R/zzz.R
+get_skimmers.mic <- function(column) {
+  sfl <- import_fn("sfl", "skimr", error_on_fail = FALSE)
+  inline_hist <- import_fn("inline_hist", "skimr", error_on_fail = FALSE)
+  sfl(
+    skim_type = "mic",
+    min = ~as.character(sort(na.omit(.))[1]),
+    max = ~as.character(sort(stats::na.omit(.))[length(stats::na.omit(.))]),
+    median = ~as.character(stats::na.omit(.)[as.double(stats::na.omit(.)) == median(as.double(stats::na.omit(.)))])[1],
+    n_unique = n_unique,
+    hist_log2 = ~inline_hist(log2(as.double(stats::na.omit(.))))
+  )
+}

R/mo.R

@@ -1637,11 +1637,24 @@ freq.mo <- function(x, ...) {
                                                                   decimal.mark = "."),
                                                            " (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), digits = digits),
                                                            ")"),
-                                  `No. of genera` = pm_n_distinct(mo_genus(x_noNA, language = NULL)),
+                                  `Nr. of genera` = pm_n_distinct(mo_genus(x_noNA, language = NULL)),
-                                  `No. of species` = pm_n_distinct(paste(mo_genus(x_noNA, language = NULL),
+                                  `Nr. of species` = pm_n_distinct(paste(mo_genus(x_noNA, language = NULL),
                                                                          mo_species(x_noNA, language = NULL)))))
 }
 
+# will be exported using s3_register() in R/zzz.R
+get_skimmers.mo <- function(column) {
+  sfl <- import_fn("sfl", "skimr", error_on_fail = FALSE)
+  sfl(
+    skim_type = "mo",
+    unique_total = n_unique,
+    gram_negative = ~sum(mo_gramstain(stats::na.omit(.), language = NULL) == "Gram-negative", na.rm = TRUE),
+    gram_positive = ~sum(mo_gramstain(stats::na.omit(.), language = NULL) == "Gram-positive", na.rm = TRUE),
+    top_genus = ~names(sort(-table(mo_genus(stats::na.omit(.), language = NULL))))[1L],
+    top_species = ~names(sort(-table(mo_name(stats::na.omit(.), language = NULL))))[1L]
+  )
+}
+
 #' @method print mo
 #' @export
 #' @noRd

R/rsi.R

@@ -743,6 +743,43 @@ freq.rsi <- function(x, ...) {
   }
 }
 
+
+# will be exported using s3_register() in R/zzz.R
+get_skimmers.rsi <- function(column) {
+  # a bit of a crazy hack to get the variable name
+  name_call <- function(.data, name = deparse(substitute(column))) {
+    vars <- tryCatch(eval(parse(text = ".data$skim_variable"), envir = sys.frame(2)), 
+                     error = function(e) NULL)
+    calls <- sys.calls()
+    i <- tryCatch(attributes(calls[[length(calls)]])$position, 
+                  error = function(e) NULL)
+    if (is.null(vars) | is.null(i)) {
+      NA_character_
+    } else{
+      lengths <- sapply(vars, length)
+      lengths <-  sum(lengths[!names(lengths) == "rsi"])
+      var <- vars$rsi[i - lengths]
+      if (var == "data") {
+        NA_character_
+      } else{
+        ab_name(var)
+      }
+    }
+  }
+  
+  sfl <- import_fn("sfl", "skimr", error_on_fail = FALSE)
+  sfl(
+    skim_type = "rsi",
+    name = name_call,
+    count_R = count_R,
+    count_S = count_susceptible,
+    count_I = count_I,
+    prop_R = ~proportion_R(., minimum = 0),
+    prop_S = ~susceptibility(., minimum = 0),
+    prop_I = ~proportion_I(., minimum = 0)
+  )
+}
+
 #' @method print rsi
 #' @export
 #' @noRd

R/rsi_calc.R

@@ -151,9 +151,10 @@ rsi_calc <- function(...,
       data_vars <- paste(" for", data_vars)
     }
     warning("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` = ", minimum, ").", call. = FALSE)
-    fraction <- NA
+    fraction <- NA_real_
   } else {
     fraction <- numerator / denominator
+    fraction[is.nan(fraction)] <- NA_real_
   }
   
   if (as_percent == TRUE) {

R/zzz.R

@@ -49,9 +49,14 @@
   s3_register("tibble::type_sum", "mic")
   s3_register("pillar::pillar_shaft", "disk")
   s3_register("tibble::type_sum", "disk")
-  # support for frequency tables
+  # support for frequency tables from the cleaner package
   s3_register("cleaner::freq", "mo")
   s3_register("cleaner::freq", "rsi")
+  # support from skim from the skimr package
+  s3_register("skimr::get_skimmers", "mo")
+  s3_register("skimr::get_skimmers", "rsi")
+  s3_register("skimr::get_skimmers", "mic")
+  s3_register("skimr::get_skimmers", "disk")
 }
 
 .onAttach <- function(...) {

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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</span>
       </span>
     </div>
 
@@ -236,13 +236,13 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1309031" class="section level1">
+    <div id="amr-1309032" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9031">
+<h1 class="page-header" data-toc-text="1.3.0.9032">
-<a href="#amr-1309031" class="anchor"></a>AMR 1.3.0.9031<small> Unreleased </small>
+<a href="#amr-1309032" class="anchor"></a>AMR 1.3.0.9032<small> Unreleased </small>
 </h1>
-<div id="last-updated-26-september-2020" class="section level2">
+<div id="last-updated-28-september-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-26-september-2020" class="anchor"></a><small>Last updated: 26 September 2020</small>
+<a href="#last-updated-28-september-2020" class="anchor"></a><small>Last updated: 28 September 2020</small>
 </h2>
 <p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p>
 <div id="new" class="section level3">
@@ -264,6 +264,7 @@
 </pre></div>
 </li>
 <li><p>Support for veterinary ATC codes</p></li>
+<li><p>Support for skimming classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and <code>&lt;mo&gt;</code> with the <code>skimr</code> package</p></li>
 </ul>
 </div>
 <div id="changed" class="section level3">

docs/pkgdown.yml

@@ -2,7 +2,7 @@ pandoc: 2.7.3
 pkgdown: 1.5.1.9000
 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
 articles: []
-last_built: 2020-09-26T14:51Z
+last_built: 2020-09-27T23:07Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</span>
       </span>
     </div>
 

docs/reference/as.rsi.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">1.3.0.9029</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</span>
       </span>
     </div>
 

docs/reference/join.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">1.3.0.9029</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</span>
       </span>
     </div>
 

docs/reference/mo_matching_score.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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</span>
       </span>
     </div>
 

docs/reference/mo_property.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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</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">1.3.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9032</span>
       </span>
     </div>
 

tests/testthat/test-join_microorganisms.R

@@ -45,7 +45,6 @@ test_that("joins work", {
   expect_true(nrow(unjoined) < nrow(right))
   expect_true(nrow(unjoined) < nrow(full))
 
-
   expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI")), 1)
   expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI", by = c("mo" = "mo"))), 1)
 

tests/testthat/test-rsi.R

@@ -28,7 +28,6 @@ test_that("rsi works", {
   expect_true(as.rsi("I") < as.rsi("R"))
   expect_true(is.rsi(as.rsi("S")))
   
-  
   x <- example_isolates$AMX
   expect_s3_class(x[1], "rsi")
   expect_s3_class(x[[1]], "rsi")
@@ -70,6 +69,14 @@ test_that("rsi works", {
   
   expect_error(get_guideline("this one does not exist"))
   
+  expect_s3_class(example_isolates %>%
+                    mutate(m = as.mic(2),
+                           d = as.disk(20)) %>% 
+                    skimr::skim(),
+                  "data.frame")
+  expect_s3_class(skimr::skim(example_isolates),
+                  "data.frame")
+
 })