(v0.7.1.9028) predict update

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.7.1.9027
+Version: 0.7.1.9028
 Date: 2019-08-07
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
@@ -68,7 +68,7 @@ Suggests:
 VignetteBuilder: knitr
 URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
 BugReports: https://gitlab.com/msberends/AMR/issues
-License: GPL-2
+License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.1.9027
+# AMR 0.7.1.9028
 
 ### Breaking
 * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured  a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.

R/resistance_predict.R

@@ -61,7 +61,7 @@
 #' @importFrom dplyr %>% pull mutate mutate_at n group_by_at summarise filter filter_at all_vars n_distinct arrange case_when n_groups transmute ungroup
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)
+#' x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010, model = "binomial")
 #' plot(x)
 #' ggplot_rsi_predict(x)
 #'
@@ -70,7 +70,7 @@
 #' x <- septic_patients %>%
 #'   filter_first_isolate() %>%
 #'   filter(mo_genus(mo) == "Staphylococcus") %>%
-#'   resistance_predict("PEN")
+#'   resistance_predict("PEN", model = "binomial")
 #' plot(x)
 #'
 #'
@@ -86,6 +86,7 @@
 #'     filter(mo == as.mo("E. coli")) %>%
 #'     resistance_predict(col_ab = "AMX",
 #'                        col_date = "date",
+#'                        model = "binomial",
 #'                        info = FALSE,
 #'                        minimum = 15)
 #'

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
       </span>
     </div>
 

docs/authors.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </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">0.7.1.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
       </span>
     </div>
 
@@ -377,7 +377,9 @@
 <div class="license">
 <h2>License</h2>
 <ul class="list-unstyled">
-<li><a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a></li>
+<li>
+<a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a> | file <a href="LICENSE-text.html">LICENSE</a>
+</li>
 </ul>
 </div>
 <div class="developers">

docs/news/index.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
       </span>
     </div>
 
@@ -225,9 +225,9 @@
       
     </div>
 
-    <div id="amr-0-7-1-9027" class="section level1">
+    <div id="amr-0-7-1-9028" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9027" class="anchor"></a>AMR 0.7.1.9027<small> Unreleased </small>
+<a href="#amr-0-7-1-9028" class="anchor"></a>AMR 0.7.1.9028<small> Unreleased </small>
 </h1>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
@@ -1218,7 +1218,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0-7-1-9027">0.7.1.9027</a></li>
+        <li><a href="#amr-0-7-1-9028">0.7.1.9028</a></li>
         <li><a href="#amr-0-7-1">0.7.1</a></li>
         <li><a href="#amr-0-7-0">0.7.0</a></li>
         <li><a href="#amr-0-6-1">0.6.1</a></li>

docs/reference/index.html

@@ -78,7 +78,7 @@
       </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">0.7.1.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
       </span>
     </div>
 

docs/reference/resistance_predict.html

@@ -80,7 +80,7 @@
       </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">0.7.1.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9028</span>
       </span>
     </div>
 
@@ -342,7 +342,7 @@
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><span class='co'># NOT RUN {</span>
-<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>resistance_predict</span>(<span class='no'>septic_patients</span>, <span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>)
+<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>resistance_predict</span>(<span class='no'>septic_patients</span>, <span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
 <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>)
 <span class='fu'>ggplot_rsi_predict</span>(<span class='no'>x</span>)
 
@@ -351,7 +351,7 @@
 <span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
   <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%&gt;%</span>
-  <span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>)
+  <span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>)
 <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>)
 
 
@@ -367,6 +367,7 @@
     <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
     <span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
                        <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
+                       <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"binomial"</span>,
                        <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
                        <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>15</span>)
 

man/resistance_predict.Rd

@@ -80,7 +80,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 }
 
 \examples{
-x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)
+x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010, model = "binomial")
 plot(x)
 ggplot_rsi_predict(x)
 
@@ -89,7 +89,7 @@ library(dplyr)
 x <- septic_patients \%>\%
   filter_first_isolate() \%>\%
   filter(mo_genus(mo) == "Staphylococcus") \%>\%
-  resistance_predict("PEN")
+  resistance_predict("PEN", model = "binomial")
 plot(x)
 
 
@@ -105,6 +105,7 @@ if (!require(ggplot2)) {
     filter(mo == as.mo("E. coli")) \%>\%
     resistance_predict(col_ab = "AMX",
                        col_date = "date",
+                       model = "binomial",
                        info = FALSE,
                        minimum = 15)