(v1.3.0.9036) documentation fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.3.0.9035
+Version: 1.3.0.9036
-Date: 2020-09-29
+Date: 2020-09-30
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.3.0.9035
+# AMR 1.3.0.9036
-## <small>Last updated: 29 September 2020</small>
+## <small>Last updated: 30 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!
 

R/rsi.R

@@ -95,6 +95,11 @@
 #' @examples
 #' summary(example_isolates) # see all R/SI results at a glance
 #' 
+#' if (require("skimr")) {
+#'   # support for skim() too:
+#'   skim(example_isolates)
+#' }
+#' 
 #' # For INTERPRETING disk diffusion and MIC values -----------------------
 #'        
 #' # a whole data set, even with combined MIC values and disk zones
@@ -124,7 +129,7 @@
 #'   df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.rsi)
 #'   df %>% mutate(across(where(is.mic), as.rsi))
 #'   df %>% mutate_at(vars(AMP:TOB), as.rsi)
-#'   df %>% mutate(across(AMP:TOB), as.rsi)
+#'   df %>% mutate(across(AMP:TOB, as.rsi))
 #'  
 #'   df %>%
 #'     mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
@@ -168,7 +173,7 @@
 #'     
 #'   # note: from dplyr 1.0.0 on, this will be: 
 #'   # example_isolates %>%
-#'   #   mutate(across(is.rsi.eligible, as.rsi))
+#'   #   mutate(across(where(is.rsi.eligible), as.rsi))
 #' }
 #' }
 as.rsi <- function(x, ...) {

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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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-1309035" class="section level1">
+    <div id="amr-1309036" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9035">
+<h1 class="page-header" data-toc-text="1.3.0.9036">
-<a href="#amr-1309035" class="anchor"></a>AMR 1.3.0.9035<small> Unreleased </small>
+<a href="#amr-1309036" class="anchor"></a>AMR 1.3.0.9036<small> Unreleased </small>
 </h1>
-<div id="last-updated-29-september-2020" class="section level2">
+<div id="last-updated-30-september-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-29-september-2020" class="anchor"></a><small>Last updated: 29 September 2020</small>
+<a href="#last-updated-30-september-2020" class="anchor"></a><small>Last updated: 30 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="breaking" 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: 2020-09-29T21:35Z
+last_built: 2020-09-30T08:23Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
       </span>
     </div>
 
@@ -413,6 +413,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span>
 
+<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://docs.ropensci.org/skimr'>"skimr"</a></span>)) {
+  <span class='co'># support for skim() too:</span>
+  <span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span>(<span class='kw'>example_isolates</span>)
+}
+
 <span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
        
 <span class='co'># a whole data set, even with combined MIC values and disk zones</span>
@@ -442,7 +447,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
   <span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='as.mic.html'>is.mic</a></span>(<span class='kw'>x</span>) <span class='op'>|</span> <span class='fu'><a href='as.disk.html'>is.disk</a></span>(<span class='kw'>x</span>), <span class='kw'>as.rsi</span>)
   <span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>))
   <span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
-  <span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
+  <span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>, <span class='kw'>as.rsi</span>))
  
   <span class='kw'>df</span> <span class='op'>%&gt;%</span>
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>)
@@ -485,7 +490,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
     
   <span class='co'># note: from dplyr 1.0.0 on, this will be: </span>
   <span class='co'># example_isolates %&gt;%</span>
-  <span class='co'>#   mutate(across(is.rsi.eligible, as.rsi))</span>
+  <span class='co'>#   mutate(across(where(is.rsi.eligible), as.rsi))</span>
 }
 <span class='co'># }</span>
 </pre>

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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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">1.3.0.9035</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
       </span>
     </div>
 

man/as.rsi.Rd

@@ -156,6 +156,11 @@ On our website \url{https://msberends.github.io/AMR} you can find \href{https://
 \examples{
 summary(example_isolates) # see all R/SI results at a glance
 
+if (require("skimr")) {
+  # support for skim() too:
+  skim(example_isolates)
+}
+
 # For INTERPRETING disk diffusion and MIC values -----------------------
        
 # a whole data set, even with combined MIC values and disk zones
@@ -185,7 +190,7 @@ if (require("dplyr")) {
   df \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.rsi)
   df \%>\% mutate(across(where(is.mic), as.rsi))
   df \%>\% mutate_at(vars(AMP:TOB), as.rsi)
-  df \%>\% mutate(across(AMP:TOB), as.rsi)
+  df \%>\% mutate(across(AMP:TOB, as.rsi))
  
   df \%>\%
     mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
@@ -228,7 +233,7 @@ if (require("dplyr")) {
     
   # note: from dplyr 1.0.0 on, this will be: 
   # example_isolates \%>\%
-  #   mutate(across(is.rsi.eligible, as.rsi))
+  #   mutate(across(where(is.rsi.eligible), as.rsi))
 }
 }
 }

tests/testthat/test-_deprecated.R

@@ -18,3 +18,10 @@
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
+
+context("deprecated.R")
+
+test_that("deprecated functions work", {
+  skip_on_cran()
+  # if some functions get deprecated, put the tests here
+})

tests/testthat/test-_misc.R

@@ -19,7 +19,7 @@
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
-context("misc.R")
+context("aa_helper_functions.R")
 
 test_that("percentages works", {
   skip_on_cran()
@@ -50,3 +50,40 @@ test_that("looking up ab columns works", {
   expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
   expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
 })
+
+test_that("imports work", {
+  skip_on_cran()
+  
+  import_functions <- c(
+    "anti_join" = "dplyr",
+    "cur_column" = "dplyr",
+    "freq.default" = "cleaner",
+    "full_join" = "dplyr",
+    "has_internet" = "curl",
+    "html_attr" = "rvest",
+    "html_children" = "rvest",
+    "html_node" = "rvest",
+    "html_nodes" = "rvest",
+    "html_table" = "rvest",
+    "html_text" = "rvest",
+    "inline_hist" = "skimr",
+    "inner_join" = "dplyr",
+    "insertText" = "rstudioapi",
+    "left_join" = "dplyr",
+    "new_pillar_shaft_simple" = "pillar",
+    "peek_mask" = "dplyr",
+    "peek_vars" = "tidyselect",
+    "read_excel" = "readxl",
+    "read_html" = "xml2",
+    "right_join" = "dplyr",
+    "semi_join" = "dplyr",
+    "sfl" = "skimr",
+    "showQuestion" = "rstudioapi")
+  
+  for (i in seq_len(length(import_functions))) {
+    fn <- names(import_functions)[i]
+    pkg <- 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"))
+  }
+})

tests/testthat/test-deprecated.R

@@ -1,31 +0,0 @@
-# ==================================================================== #
-# 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.    #
-# ==================================================================== #
-
-context("deprecated.R")
-
-test_that("deprecated functions work", {
-  skip_on_cran()
-  expect_equal(suppressWarnings(portion_S(example_isolates$AMX)), proportion_S(example_isolates$AMX))
-  expect_equal(suppressWarnings(portion_SI(example_isolates$AMX)), proportion_SI(example_isolates$AMX))
-  expect_equal(suppressWarnings(portion_I(example_isolates$AMX)), proportion_I(example_isolates$AMX))
-  expect_equal(suppressWarnings(portion_IR(example_isolates$AMX)), proportion_IR(example_isolates$AMX))
-  expect_equal(suppressWarnings(portion_R(example_isolates$AMX)), proportion_R(example_isolates$AMX))
-})

tests/testthat/test-import_fn.R

@@ -1,49 +0,0 @@
-# ==================================================================== #
-# 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.    #
-# ==================================================================== #
-
-context("import_fn.R")
-
-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"))
-  }
-})

tests/testthat/test-mic.R

@@ -41,6 +41,7 @@ test_that("mic works", {
   expect_s3_class(unique(x[1], x[9]), "mic")
   expect_warning(as.mic("INVALID VALUE"))
   
+
   pdf(NULL) # prevent Rplots.pdf being created
   expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
   expect_silent(plot(as.mic(c(1, 2, 4, 8))))