(v1.2.0.9024) AMR calculation speed improvement

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.2.0.9023
+Version: 1.2.0.9024
-Date: 2020-07-02
+Date: 2020-07-03
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.2.0.9023
+# AMR 1.2.0.9024
-## <small>Last updated: 02-Jul-2020</small>
+## <small>Last updated: 03-Jul-2020</small>
 
 ### New
 * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@@ -19,7 +19,10 @@
 * Added Monuril as trade name for fosfomycin
 
 ### Changed
-* Using unexisting columns in all `count_*()`, `proportion_*()`, `susceptibility()` and `resistance()` functions wil now return an error instead of dropping them silently. Using variables for column names (as well as `dplyr::all_of()`) now works again.
+* Improvements for `susceptibility()` and `resistance()` and all `count_*()`, `proportion_*()` functions:
+  * 95% speed improvement (!) by using other base R functions for calculation
+  * Using unexisting columns wil now return an error instead of dropping them silently
+  * Using variables for column names (as well as `dplyr::all_of()`) now works again
 * Improvements for `as.ab()`:
   * Dramatic improvement of the algorithm behind `as.ab()`, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more
   * Added progress bar

R/rsi_calc.R

@@ -101,7 +101,7 @@ rsi_calc <- function(...,
   if (is.data.frame(x)) {
     rsi_integrity_check <- character(0)
     for (i in seq_len(ncol(x))) {
-      # check integrity of columns: force rsi class
+      # check integrity of columns: force <rsi> class
       if (!is.rsi(x[, i, drop = TRUE])) {
         rsi_integrity_check <- c(rsi_integrity_check, as.character(x[, i, drop = TRUE]))
         x[, i] <- suppressWarnings(as.rsi(x[, i, drop = TRUE])) # warning will be given later
@@ -113,22 +113,16 @@ rsi_calc <- function(...,
       rsi_integrity_check <- as.rsi(rsi_integrity_check)
     }
 
+    x_transposed <- as.list(as.data.frame(t(x)))
     if (only_all_tested == TRUE) {
-      # THE NUMBER OF ISOLATES WHERE *ALL* ABx ARE S/I/R
+      # no NAs in any column
-      x <- apply(X = as.data.frame(lapply(x, as.integer), stringsAsFactors = FALSE),
+      numerator <- sum(sapply(x_transposed, function(y) !any(is.na(y)) & any(y %in% ab_result, na.rm = TRUE)))
-                 MARGIN = 1,
+      denominator <- sum(sapply(x_transposed, function(y) !(any(is.na(y)))))
-                 FUN = base::min)
-      numerator <- sum(as.integer(x) %in% as.integer(ab_result), na.rm = TRUE)
-      denominator <- length(x) - sum(is.na(x))
-      
     } else {
-      # THE NUMBER OF ISOLATES WHERE *ANY* ABx IS S/I/R
+      # may contain NAs in any column
       other_values <- base::setdiff(c(NA, levels(ab_result)), ab_result)
-      other_values_filter <- base::apply(x, 1, function(y) {
+      numerator <- sum(sapply(x_transposed, function(y) any(y %in% ab_result, na.rm = TRUE)))
-        base::all(y %in% other_values) & base::any(is.na(y))
+      denominator <- sum(sapply(x_transposed, function(y) !(all(y %in% other_values) & any(is.na(y)))))
-      })
-      numerator <- sum(as.logical(by(x, seq_len(nrow(x)), function(row) any(unlist(row) %in% ab_result, na.rm = TRUE))))
-      denominator <- nrow(x[!other_values_filter, , drop = FALSE])
     }
   } else {
     # x is not a data.frame
@@ -153,7 +147,7 @@ rsi_calc <- function(...,
     if (data_vars != "") {
       data_vars <- paste(" for", data_vars)
     }
-    warning("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` was set to ", minimum, ").", call. = FALSE)
+    warning("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` = ", minimum, ").", call. = FALSE)
     fraction <- NA
   } else {
     fraction <- numerator / denominator

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">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</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">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</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">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</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">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</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">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</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">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</span>
       </span>
     </div>
 
@@ -229,13 +229,13 @@
       <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209023" class="section level1">
+    <div id="amr-1209024" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9023">
+<h1 class="page-header" data-toc-text="1.2.0.9024">
-<a href="#amr-1209023" class="anchor"></a>AMR 1.2.0.9023<small> Unreleased </small>
+<a href="#amr-1209024" class="anchor"></a>AMR 1.2.0.9024<small> Unreleased </small>
 </h1>
-<div id="last-updated-02-jul-2020" class="section level2">
+<div id="last-updated-03-jul-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-02-jul-2020" class="anchor"></a><small>Last updated: 02-Jul-2020</small>
+<a href="#last-updated-03-jul-2020" class="anchor"></a><small>Last updated: 03-Jul-2020</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@@ -262,7 +262,13 @@
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
 <ul>
-<li>Using unexisting columns in all <code>count_*()</code>, <code>proportion_*()</code>, <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> functions wil now return an error instead of dropping them silently. Using variables for column names (as well as <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again.</li>
+<li>Improvements for <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> and all <code>count_*()</code>, <code>proportion_*()</code> functions:
+<ul>
+<li>95% speed improvement (!) by using other base R functions for calculation</li>
+<li>Using unexisting columns wil now return an error instead of dropping them silently</li>
+<li>Using variables for column names (as well as <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again</li>
+</ul>
+</li>
 <li>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:
 <ul>
 <li>Dramatic improvement of the algorithm behind <code><a href="../reference/as.ab.html">as.ab()</a></code>, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more</li>

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-07-02T19:12Z
+last_built: 2020-07-03T08:50Z
 urls:
   reference: https://msberends.gitlab.io/AMR/reference
   article: https://msberends.gitlab.io/AMR/articles

docs/reference/ab_from_text.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">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</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">1.2.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9024</span>
       </span>
     </div>