

{"id":12755,"date":"2020-05-19T17:31:39","date_gmt":"2020-05-19T22:31:39","guid":{"rendered":"https:\/\/rud.is\/b\/?p=12755"},"modified":"2020-05-19T17:31:39","modified_gmt":"2020-05-19T22:31:39","slug":"mining-r-4-0-0-changelog-for-nuggets-of-gold-1-stopifnot","status":"publish","type":"post","link":"https:\/\/rud.is\/b\/2020\/05\/19\/mining-r-4-0-0-changelog-for-nuggets-of-gold-1-stopifnot\/","title":{"rendered":"Mining R 4.0.0 Changelog for Nuggets of Gold: #1 stopifnot()"},"content":{"rendered":"<p>R 4.0.0 has been out for a while, now, and \u2014 apart from a case where <code>merge()<\/code> was slower than dirt \u2014 it&#8217;s been really stable for at least me (I use it daily on macOS, Linux, and Windows). Sure, it came with some headline-grabbing features\/upgrades, but I&#8217;ve started looking at what other useful nuggets might be in the <a href=\"https:\/\/cran.r-project.org\/doc\/manuals\/r-devel\/NEWS.html\">changelog<\/a> and decided to blog them as I find them.<\/p>\n<p>Today&#8217;s nugget is the venerable <code>stopifnot()<\/code> function which was significantly enhanced by <a href=\"https:\/\/bugs.r-project.org\/bugzilla\/show_bug.cgi?id=17688\">this PR by Neil Fultz<\/a>.<\/p>\n<p>Prior to R 4.0.0, if you wanted to use <code>stopifnot()<\/code> to perform some input validation (a.k.a. \u2014 in this case \u2014 [assertions])(https:\/\/en.wikipedia.org\/wiki\/Assertion_(software_development)) you&#8217;d do something like this (I&#8217;m borrowing from Neil&#8217;s example):<\/p>\n<pre><code class=\"language-r\">some_\u0192 &lt;- function(alpha, gradtol, steptol, interlim) {\n\n  stopifnot(\n    (is.numeric(alpha)),\n    (length(alpha) == 1),\n    (alpha &gt; 0),\n    (alpha &lt; 1),\n    (is.numeric(gradtol)),\n    (length(gradtol) == 1),\n    (gradtol &gt; 0),\n    (is.numeric(steptol)),\n    (length(steptol) == 1),\n    (steptol &gt; 0),\n    (is.numeric(interlim)),\n    (length(interlim) == 1),\n    (interlim &gt; 0)\n   )\n\n  message(\"Do something awesome\")\n\n}\n<\/code><\/pre>\n<p>When run with acceptable inputs we get:<\/p>\n<pre><code class=\"language-r\">some_\u0192(0.5, 3, 10, 100)\n## Do something awesome\n<\/code><\/pre>\n<p>But, when run with something out of kilter:<\/p>\n<pre><code class=\"language-r\">some_\u0192(\"a\", 3, 10, 100)\n##  Error in some_\u0192(\"a\", 3, 10, 100) : (is.numeric(alpha)) is not TRUE\n<\/code><\/pre>\n<p>we get a semi-useful, but somewhat unfriendly message back. Sure, it points to the right expression, but we&#8217;re supposed to be the kinder, friendlier data science (and general purpose) language who cares a bit more about our users. To that end, many folks switch to doing something like this:<\/p>\n<pre><code class=\"language-r\">some_\u0192 &lt;- function(alpha, gradtol, steptol, interlim) {\n\n  if (!is.numeric(alpha))   { stop('Error: alpha should be numeric') }\n  if (length(alpha) != 1)   { stop('Error: alpha should be a single value'); }\n  if (alpha &lt; 0)            { stop('Error: alpha is negative'); }\n  if (alpha &gt; 1)            { stop('Error: alpha is greater than one'); }\n  if (!is.numeric(gradtol)) { stop('Error: gradtol should be numeric') }\n  if (length(gradtol) != 1) { stop('Error: gradtol should be a single value'); }\n  if (gradtol &lt;= 0)         { stop('Error: gradtol should be positive'); }\n  if (!is.numeric(steptol)) { stop('Error: steptol should be numeric') }\n  if (length(steptol) != 1) { stop('Error: steptol should be a single value'); }\n  if (steptol &lt;= 0)         { stop('Error: steptol should be positive'); }\n  if (!is.numeric(iterlim)) { stop('Error: iterlim should be numeric') }\n  if (length(iterlim) != 1) { stop('Error: iterlim should be a single value'); }\n  if (iterlim &lt;= 0)         { stop('Error: iterlim should be positive'); }\n\n  message(\"Do something awesome\")\n\n}\n<\/code><\/pre>\n<p>which results in:<\/p>\n<pre><code class=\"language-r\">some_\u0192(\"a\", 3, 10, 100)\n##  Error in some_\u0192(\"a\", 3, 10, 100) : Error: alpha should be numeric\n<\/code><\/pre>\n<p>(you can make even better error messages than that).<\/p>\n<p>Neal thought there had to be a better way, and made one! The <code>...<\/code> expressions can be <em>named<\/em> and those names will become the error message:<\/p>\n<pre><code class=\"language-r\">some_\u0192 &lt;- function(alpha, gradtol, steptol, interlim) {\n\n  stopifnot(\n    'alpha should be numeric'          = (is.numeric(alpha)),\n    'alpha should be a single value'   = (length(alpha) == 1),\n    'alpha is negative'                = (alpha &gt; 0),\n    'alpha is greater than one'        = (alpha &lt; 1),\n    'gradtol should be numeric'        = (is.numeric(gradtol)),\n    'gradtol should be a single value' = (length(gradtol) == 1),\n    'gradtol should be positive'       = (gradtol &gt; 0),\n    'steptol should be numeric'        = (is.numeric(steptol)),\n    'steptol should be a single value' = (length(steptol) == 1),\n    'steptol should be positive'       = (steptol &gt; 0),\n    'iterlim should be numeric'        = (is.numeric(interlim)),\n    'iterlim should be a single value' = (length(interlim) == 1),\n    'iterlim should be positive'       = (interlim &gt; 0)\n   )\n\n  message(\"Do something awesome\")\n\n}\n\nsome_\u0192(\"a\", 3, 10, 100)\n\n##  Error in some_\u0192(\"a\", 3, 10, 100) : alpha should be numeric\n<\/code><\/pre>\n<p>Way easier to write and way more respectful to the caller.<\/p>\n<h3>Gratuitous Statistics<\/h3>\n<p>CRAN has ~2,600 packages that use <code>stopifnot()<\/code> in their package <code>\/R\/<\/code> code with the following selected distributions (charts are all log10 scale):<\/p>\n<p><a href=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?ssl=1\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"12757\" data-permalink=\"https:\/\/rud.is\/b\/2020\/05\/19\/mining-r-4-0-0-changelog-for-nuggets-of-gold-1-stopifnot\/stopoifnot-01\/\" data-orig-file=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?fit=2400%2C708&amp;ssl=1\" data-orig-size=\"2400,708\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"stopoifnot-01\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?fit=300%2C89&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?fit=510%2C150&amp;ssl=1\" src=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=510%2C150&#038;ssl=1\" alt=\"stopifnot usage: files using it per package\" width=\"510\" height=\"150\" class=\"aligncenter size-full wp-image-12757\" srcset=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?w=2400&amp;ssl=1 2400w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=300%2C89&amp;ssl=1 300w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=530%2C156&amp;ssl=1 530w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=150%2C44&amp;ssl=1 150w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=768%2C227&amp;ssl=1 768w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=1536%2C453&amp;ssl=1 1536w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=2048%2C604&amp;ssl=1 2048w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=500%2C148&amp;ssl=1 500w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=1200%2C354&amp;ssl=1 1200w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=400%2C118&amp;ssl=1 400w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=800%2C236&amp;ssl=1 800w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?resize=200%2C59&amp;ssl=1 200w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-01.png?w=1020&amp;ssl=1 1020w\" sizes=\"auto, (max-width: 510px) 100vw, 510px\" \/><\/a><\/p>\n<p>Here are the packages with 50 or more files using <code>stopifnot()<\/code>:<\/p>\n<pre><code class=\"language-r\">   pkg              n\n   &lt;chr&gt;        &lt;int&gt;\n 1 spatstat       252\n 2 pracma         145\n 3 QuACN           80\n 4 raster          74\n 5 spdep           61\n 6 lavaan          54\n 7 surveillance    53\n 8 copula          50\n<\/code><\/pre>\n<p><a href=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?ssl=1\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"12759\" data-permalink=\"https:\/\/rud.is\/b\/2020\/05\/19\/mining-r-4-0-0-changelog-for-nuggets-of-gold-1-stopifnot\/stopoifnot-02\/\" data-orig-file=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?fit=2400%2C708&amp;ssl=1\" data-orig-size=\"2400,708\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"stopoifnot-02\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?fit=300%2C89&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?fit=510%2C150&amp;ssl=1\" src=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=510%2C150&#038;ssl=1\" alt=\"stopifnot calls per-file\" width=\"510\" height=\"150\" class=\"aligncenter size-full wp-image-12759\" srcset=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?w=2400&amp;ssl=1 2400w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=300%2C89&amp;ssl=1 300w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=530%2C156&amp;ssl=1 530w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=150%2C44&amp;ssl=1 150w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=768%2C227&amp;ssl=1 768w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=1536%2C453&amp;ssl=1 1536w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=2048%2C604&amp;ssl=1 2048w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=500%2C148&amp;ssl=1 500w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=1200%2C354&amp;ssl=1 1200w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=400%2C118&amp;ssl=1 400w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=800%2C236&amp;ssl=1 800w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?resize=200%2C59&amp;ssl=1 200w, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2020\/05\/stopoifnot-02.png?w=1020&amp;ssl=1 1020w\" sizes=\"auto, (max-width: 510px) 100vw, 510px\" \/><\/a><\/p>\n<p>Here are the packages with one or more files that have 100 or more calls to <code>stopifnot()<\/code> in them:<\/p>\n<pre><code class=\"language-r\">   pkg                 fil                            ct\n   &lt;chr&gt;               &lt;chr&gt;                       &lt;int&gt;\n 1 ff                  ordermerge.R                  278\n 2 OneArmPhaseTwoStudy zzz.R                         142\n 3 bit64               integer64.R                   137\n 4 updog               rflexdog.R                    124\n 5 RNetCDF             RNetCDF.R                     123\n 6 Rlda                rlda.R                        105\n 7 aster2              transform.R                   105\n 8 ads                 fads.R                        104\n 9 georob              georob_exported_functions.R   104\n10 bit64               highlevel64.R                 101\n<\/code><\/pre>\n<p>O_O That&#8217;s quite a bit of checking!<\/p>\n<h3>FIN<\/h3>\n<p>If you&#8217;re working on switching to R 4.0.0 or have switched, this and many other new features await! Drop a note in the comments with your favorite new feature (or, even better, a link to a blog post on said feature!).<\/p>\n<p>As I get time to dig out some more nuggets I&#8217;ll add more posts to this series.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>R 4.0.0 has been out for a while, now, and \u2014 apart from a case where merge() was slower than dirt \u2014 it&#8217;s been really stable for at least me (I use it daily on macOS, Linux, and Windows). Sure, it came with some headline-grabbing features\/upgrades, but I&#8217;ve started looking at what other useful nuggets [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":3,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":""},"categories":[91],"tags":[],"class_list":["post-12755","post","type-post","status-publish","format-standard","hentry","category-r"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.2 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Mining R 4.0.0 Changelog for Nuggets of Gold: #1 stopifnot() - rud.is<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/rud.is\/b\/2020\/05\/19\/mining-r-4-0-0-changelog-for-nuggets-of-gold-1-stopifnot\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Mining R 4.0.0 Changelog for Nuggets of Gold: #1 stopifnot() - rud.is\" \/>\n<meta property=\"og:description\" content=\"R 4.0.0 has been out for a while, now, and \u2014 apart from a case where merge() was slower than dirt \u2014 it&#8217;s been really stable for at least me (I use it daily on macOS, Linux, and Windows). 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[Tim Smith](https:\/\/github.com\/tdsmith) fixed [a bug](https:\/\/github.com\/hrbrmstr\/iptools\/issues\/26) in `ip_in_range()` that occurred when the netmask was `\/32` (thanks,\u2026","rel":"","context":"In &quot;Cybersecurity&quot;","block_context":{"text":"Cybersecurity","link":"https:\/\/rud.is\/b\/category\/cybersecurity\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts\/12755","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/comments?post=12755"}],"version-history":[{"count":0,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts\/12755\/revisions"}],"wp:attachment":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/media?parent=12755"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/categories?post=12755"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/tags?post=12755"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}