clean up declared dependencies

Author: JohnMount

DESCRIPTION

@@ -18,7 +18,8 @@ Suggests:
     knitr,
     parallel,
     rmarkdown,
-    dplyr
+    dplyr,
+    ggplot2
 LazyData: true
 VignetteBuilder: knitr
 RoxygenNote: 5.0.1

cran-comments.md

@@ -7,25 +7,8 @@
 * using R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
 * using platform: x86_64-apple-darwin14.5.0 (64-bit)
 
-There were no ERRORs, or WARNINGSs.
-
-There was one NOTE:
-
-  * checking for unstated dependencies in vignettes ... NOTE
-  '::' or ':::' import not declared from: ‘caret’
-  'library' or 'require' calls not declared from:
-    ‘caret’ ‘ggplot2’
-
-
-Both of the above calls are guarded by requireNamespace calls are are
-there to illustrate how a user can use the additional caret or ggplot2
-packages.  caret and ggplot2 are not used (even optionally) in the
-vtreat package, other than being also present in some unit tests
-(again optional and to test things for users using caret or
-data.table).  These packages are deliberately not in suggests as the
-vtreat package does not use them or even optionally alter its behavior
-if they are available.
-
+R CMD check results
+0 errors | 0 warnings | 0 notes
 
 
 Note_to_CRAN_maintainers

inst/doc/vtreat.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="John Mount, Nina Zumel" />
 
-<meta name="date" content="2016-06-27" />
+<meta name="date" content="2016-07-11" />
 
 <title>vtreat package</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">vtreat package</h1>
 <h4 class="author"><em>John Mount, Nina Zumel</em></h4>
-<h4 class="date"><em>2016-06-27</em></h4>
+<h4 class="date"><em>2016-07-11</em></h4>
 
 
 
@@ -138,13 +138,13 @@ <h2>A Categorical Outcome Example</h2>
 ## 3    c 30
 ## 4 &lt;NA&gt; NA</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">treatmentsC &lt;-<span class="st"> </span><span class="kw">designTreatmentsC</span>(dTrainC,<span class="kw">colnames</span>(dTrainC),<span class="st">'y'</span>,<span class="ot">TRUE</span>)</code></pre></div>
-<pre><code>## [1] &quot;desigining treatments Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;design var x Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;design var z Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;scoring treatments Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;have treatment plan Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;rescoring complex variables Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;done rescoring complex variables Mon Jun 27 08:57:28 2016&quot;</code></pre>
+<pre><code>## [1] &quot;desigining treatments Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;design var x Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;design var z Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;scoring treatments Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;have treatment plan Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;rescoring complex variables Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;done rescoring complex variables Mon Jul 11 10:06:51 2016&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">print</span>(treatmentsC)</code></pre></div>
 <pre><code>## $treatments
 ## $treatments[[1]]
@@ -184,15 +184,18 @@ <h2>A Categorical Outcome Example</h2>
 ## $outcomename
 ## [1] &quot;y&quot;
 ## 
+## $vtreatVersion
+## [1] '0.5.26'
+## 
+## $splitmethod
+## [1] &quot;oneway&quot;
+## 
 ## $outcomeTarget
 ## [1] TRUE
 ## 
 ## $outcomeType
 ## [1] &quot;Binary&quot;
 ## 
-## $vtreatVersion
-## [1] '0.5.26'
-## 
 ## attr(,&quot;class&quot;)
 ## [1] &quot;treatmentplan&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">print</span>(treatmentsC$treatments[[<span class="dv">1</span>]])</code></pre></div>
@@ -259,13 +262,13 @@ <h2>A Numeric Outcome Example</h2>
 ## 3    c 30
 ## 4 &lt;NA&gt; NA</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">treatmentsN =<span class="st"> </span><span class="kw">designTreatmentsN</span>(dTrainN,<span class="kw">colnames</span>(dTrainN),<span class="st">'y'</span>)</code></pre></div>
-<pre><code>## [1] &quot;desigining treatments Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;design var x Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;design var z Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;scoring treatments Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;have treatment plan Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;rescoring complex variables Mon Jun 27 08:57:28 2016&quot;
-## [1] &quot;done rescoring complex variables Mon Jun 27 08:57:28 2016&quot;</code></pre>
+<pre><code>## [1] &quot;desigining treatments Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;design var x Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;design var z Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;scoring treatments Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;have treatment plan Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;rescoring complex variables Mon Jul 11 10:06:51 2016&quot;
+## [1] &quot;done rescoring complex variables Mon Jul 11 10:06:51 2016&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">print</span>(treatmentsN)</code></pre></div>
 <pre><code>## $treatments
 ## $treatments[[1]]
@@ -310,12 +313,15 @@ <h2>A Numeric Outcome Example</h2>
 ## $outcomename
 ## [1] &quot;y&quot;
 ## 
-## $outcomeType
-## [1] &quot;Numeric&quot;
-## 
 ## $vtreatVersion
 ## [1] '0.5.26'
 ## 
+## $splitmethod
+## [1] &quot;oneway&quot;
+## 
+## $outcomeType
+## [1] &quot;Numeric&quot;
+## 
 ## attr(,&quot;class&quot;)
 ## [1] &quot;treatmentplan&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dTrainNTreated &lt;-<span class="st"> </span><span class="kw">prepare</span>(treatmentsN,dTrainN,

inst/doc/vtreatCrossFrames.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="John Mount, Nina Zumel" />
 
-<meta name="date" content="2016-06-27" />
+<meta name="date" content="2016-07-11" />
 
 <title>vtreat cross frames</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">vtreat cross frames</h1>
 <h4 class="author"><em>John Mount, Nina Zumel</em></h4>
-<h4 class="date"><em>2016-06-27</em></h4>
+<h4 class="date"><em>2016-07-11</em></h4>
 
 
 
@@ -117,16 +117,16 @@ <h2>The Wrong Way</h2>
                                         <span class="st">'y'</span>,<span class="ot">TRUE</span>,
   <span class="dt">rareCount=</span><span class="dv">0</span> <span class="co"># Note: usually want rareCount&gt;0, setting to zero to illustrate problem</span>
 )</code></pre></div>
-<pre><code>## [1] &quot;desigining treatments Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xBad1 Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xBad2 Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xBad3 Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xGood1 Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xGood2 Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;scoring treatments Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;have treatment plan Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;rescoring complex variables Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;done rescoring complex variables Mon Jun 27 08:57:29 2016&quot;</code></pre>
+<pre><code>## [1] &quot;desigining treatments Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xBad1 Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xBad2 Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xBad3 Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xGood1 Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xGood2 Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;scoring treatments Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;have treatment plan Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;rescoring complex variables Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;done rescoring complex variables Mon Jul 11 10:06:52 2016&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dTrainTreated &lt;-<span class="st"> </span>vtreat::<span class="kw">prepare</span>(treatments,dTrain,
   <span class="dt">pruneSig=</span><span class="kw">c</span>() <span class="co"># Note: usually want pruneSig to be a small fraction, setting to null to illustrate problems</span>
 )
@@ -195,16 +195,16 @@ <h2>The Right Way: A Calibration Set</h2>
                                         <span class="st">'y'</span>,<span class="ot">TRUE</span>,
   <span class="dt">rareCount=</span><span class="dv">0</span> <span class="co"># Note: usually want rareCount&gt;0, setting to zero to illustrate problem</span>
 )</code></pre></div>
-<pre><code>## [1] &quot;desigining treatments Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xBad1 Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xBad2 Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xBad3 Mon Jun 27 08:57:29 2016&quot;
-## [1] &quot;design var xGood1 Mon Jun 27 08:57:30 2016&quot;
-## [1] &quot;design var xGood2 Mon Jun 27 08:57:30 2016&quot;
-## [1] &quot;scoring treatments Mon Jun 27 08:57:30 2016&quot;
-## [1] &quot;have treatment plan Mon Jun 27 08:57:30 2016&quot;
-## [1] &quot;rescoring complex variables Mon Jun 27 08:57:30 2016&quot;
-## [1] &quot;done rescoring complex variables Mon Jun 27 08:57:30 2016&quot;</code></pre>
+<pre><code>## [1] &quot;desigining treatments Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xBad1 Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xBad2 Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xBad3 Mon Jul 11 10:06:52 2016&quot;
+## [1] &quot;design var xGood1 Mon Jul 11 10:06:53 2016&quot;
+## [1] &quot;design var xGood2 Mon Jul 11 10:06:53 2016&quot;
+## [1] &quot;scoring treatments Mon Jul 11 10:06:53 2016&quot;
+## [1] &quot;have treatment plan Mon Jul 11 10:06:53 2016&quot;
+## [1] &quot;rescoring complex variables Mon Jul 11 10:06:53 2016&quot;
+## [1] &quot;done rescoring complex variables Mon Jul 11 10:06:53 2016&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dTrainTreated &lt;-<span class="st"> </span>vtreat::<span class="kw">prepare</span>(treatments,dTrain,
   <span class="dt">pruneSig=</span>pruneSig)
 newvars &lt;-<span class="st"> </span><span class="kw">setdiff</span>(<span class="kw">colnames</span>(dTrainTreated),<span class="st">'y'</span>)

inst/doc/vtreatGrouping.R

@@ -2,6 +2,9 @@
 knitr::opts_chunk$set(fig.width = 7)
 
 ## ----echo=FALSE, message=FALSE, warning=FALSE----------------------------
+library(vtreat)
+set.seed(23255)
+
 have_ggplot = requireNamespace("ggplot2", quietly=TRUE)
 have_dplyr = requireNamespace("dplyr", quietly=TRUE)
 if(have_ggplot) {
@@ -11,11 +14,7 @@ if(have_dplyr) {
   library(dplyr)
 }
 
-
-library(vtreat)
-set.seed(23255)
-
-## ----functions, echo=FALSE-----------------------------------------------
+## ----echo=FALSE, message=FALSE, warning=FALSE----------------------------
 #
 # takes the frame (d) and the outcome column (d$conc)
 # from the global environment
@@ -49,8 +48,6 @@ showGroupingBehavior = function(groupcol, title) {
   }
 }
 
-
-
 ## ----data----------------------------------------------------------------
 # panel data for concentration in multiple subjects 
 d <- datasets::Theoph

inst/doc/vtreatGrouping.Rmd

@@ -14,6 +14,9 @@ knitr::opts_chunk$set(fig.width = 7)
 ```
 
 ```{r echo=FALSE, message=FALSE, warning=FALSE}
+library(vtreat)
+set.seed(23255)
+
 have_ggplot = requireNamespace("ggplot2", quietly=TRUE)
 have_dplyr = requireNamespace("dplyr", quietly=TRUE)
 if(have_ggplot) {
@@ -22,15 +25,9 @@ if(have_ggplot) {
 if(have_dplyr) {
   library(dplyr)
 }
-
-
-library(vtreat)
-set.seed(23255)
 ```
 
-This vignette shows an example use of _y_-stratified sampling with a grouping restriction in `vtreat`.
-
-```{r functions, echo=FALSE}
+```{r echo=FALSE, message=FALSE, warning=FALSE}
 #
 # takes the frame (d) and the outcome column (d$conc)
 # from the global environment
@@ -63,10 +60,10 @@ showGroupingBehavior = function(groupcol, title) {
     print(plt)
   }
 }
-
-
 ```
 
+This vignette shows an example use of _y_-stratified sampling with a grouping restriction in `vtreat`.
+
 For this example, we will use the `Theosph` dataset: data from an experiment on the pharmacokinetics of theophylline. We will demonstrate the desired effects of _y_-stratification while also respecting a grouping constraint. 
 
 ## The Data

inst/doc/vtreatGrouping.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="John Mount, Nina Zumel" />
 
-<meta name="date" content="2016-06-27" />
+<meta name="date" content="2016-07-11" />
 
 <title>vtreat overfit</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">vtreat overfit</h1>
 <h4 class="author"><em>John Mount, Nina Zumel</em></h4>
-<h4 class="date"><em>2016-06-27</em></h4>
+<h4 class="date"><em>2016-07-11</em></h4>
 
 
 
@@ -96,12 +96,12 @@ <h2>Bad Practice: Using the same data to treat and to train</h2>
 treatments &lt;-<span class="st"> </span>vtreat::<span class="kw">designTreatmentsC</span>(dTrain,<span class="st">'x'</span>,<span class="st">'y'</span>,<span class="ot">TRUE</span>,
   <span class="dt">rareCount=</span><span class="dv">0</span> <span class="co"># Note: usually want rareCount&gt;0, setting to zero to illustrate problem</span>
 )</code></pre></div>
-<pre><code>## [1] &quot;desigining treatments Mon Jun 27 08:57:33 2016&quot;
-## [1] &quot;design var x Mon Jun 27 08:57:33 2016&quot;
-## [1] &quot;scoring treatments Mon Jun 27 08:57:33 2016&quot;
-## [1] &quot;have treatment plan Mon Jun 27 08:57:33 2016&quot;
-## [1] &quot;rescoring complex variables Mon Jun 27 08:57:33 2016&quot;
-## [1] &quot;done rescoring complex variables Mon Jun 27 08:57:33 2016&quot;</code></pre>
+<pre><code>## [1] &quot;desigining treatments Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;design var x Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;scoring treatments Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;have treatment plan Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;rescoring complex variables Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;done rescoring complex variables Mon Jul 11 10:06:56 2016&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dTrainTreated &lt;-<span class="st"> </span>vtreat::<span class="kw">prepare</span>(treatments,dTrain,
   <span class="dt">pruneSig=</span><span class="kw">c</span>() <span class="co"># Note: usually want pruneSig to be a small fraction, setting to null to illustrate problem</span>
 )
@@ -193,12 +193,12 @@ <h2>Correct Practice: Use different data to treat and train</h2>
                                         <span class="dt">rareCount=</span><span class="dv">0</span>,  <span class="co"># Note set this to something larger, like 5</span>
                                         <span class="dt">rareSig=</span><span class="kw">c</span>() <span class="co"># Note set this to something like 0.3</span>
 )</code></pre></div>
-<pre><code>## [1] &quot;desigining treatments Mon Jun 27 08:57:33 2016&quot;
-## [1] &quot;design var x Mon Jun 27 08:57:33 2016&quot;
-## [1] &quot;scoring treatments Mon Jun 27 08:57:34 2016&quot;
-## [1] &quot;have treatment plan Mon Jun 27 08:57:34 2016&quot;
-## [1] &quot;rescoring complex variables Mon Jun 27 08:57:34 2016&quot;
-## [1] &quot;done rescoring complex variables Mon Jun 27 08:57:34 2016&quot;</code></pre>
+<pre><code>## [1] &quot;desigining treatments Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;design var x Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;scoring treatments Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;have treatment plan Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;rescoring complex variables Mon Jul 11 10:06:56 2016&quot;
+## [1] &quot;done rescoring complex variables Mon Jul 11 10:06:56 2016&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dTrainTreated &lt;-<span class="st"> </span>vtreat::<span class="kw">prepare</span>(treatments,dTrain,
                                  <span class="dt">pruneSig=</span><span class="kw">c</span>() <span class="co"># Note: set this to filter, like 0.05 or 1/nvars</span>
 )

inst/doc/vtreatOverfit.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Win-Vector LLC" />
 
-<meta name="date" content="2016-06-27" />
+<meta name="date" content="2016-07-11" />
 
 <title>vtreat scale mode</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">vtreat scale mode</h1>
 <h4 class="author"><em>Win-Vector LLC</em></h4>
-<h4 class="date"><em>2016-06-27</em></h4>
+<h4 class="date"><em>2016-07-11</em></h4>
 
 
 

inst/doc/vtreatScaleMode.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="John Mount, Nina Zumel" />
 
-<meta name="date" content="2016-06-27" />
+<meta name="date" content="2016-07-11" />
 
 <title>vtreat significance</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">vtreat significance</h1>
 <h4 class="author"><em>John Mount, Nina Zumel</em></h4>
-<h4 class="date"><em>2016-06-27</em></h4>
+<h4 class="date"><em>2016-07-11</em></h4>
 
 
 
@@ -119,13 +119,13 @@ <h4 class="date"><em>2016-06-27</em></h4>
 ## 2   FALSE      lev002       lev002F
 ## 252 FALSE      lev002       lev002F</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">treatmentsC &lt;-<span class="st"> </span>vtreat::<span class="kw">designTreatmentsC</span>(d,<span class="kw">c</span>(<span class="st">'catVarNoise'</span>,<span class="st">'catVarPerfect'</span>),<span class="st">'y'</span>,<span class="ot">TRUE</span>)</code></pre></div>
-<pre><code>## [1] &quot;desigining treatments Mon Jun 27 08:57:35 2016&quot;
-## [1] &quot;design var catVarNoise Mon Jun 27 08:57:35 2016&quot;
-## [1] &quot;design var catVarPerfect Mon Jun 27 08:57:35 2016&quot;
-## [1] &quot;scoring treatments Mon Jun 27 08:57:35 2016&quot;
-## [1] &quot;have treatment plan Mon Jun 27 08:57:35 2016&quot;
-## [1] &quot;rescoring complex variables Mon Jun 27 08:57:35 2016&quot;
-## [1] &quot;done rescoring complex variables Mon Jun 27 08:57:35 2016&quot;</code></pre>
+<pre><code>## [1] &quot;desigining treatments Mon Jul 11 10:06:57 2016&quot;
+## [1] &quot;design var catVarNoise Mon Jul 11 10:06:57 2016&quot;
+## [1] &quot;design var catVarPerfect Mon Jul 11 10:06:57 2016&quot;
+## [1] &quot;scoring treatments Mon Jul 11 10:06:57 2016&quot;
+## [1] &quot;have treatment plan Mon Jul 11 10:06:57 2016&quot;
+## [1] &quot;rescoring complex variables Mon Jul 11 10:06:57 2016&quot;
+## [1] &quot;done rescoring complex variables Mon Jul 11 10:06:58 2016&quot;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Estimate effect significance (not coeficient significance).</span>
 estSigGLM &lt;-<span class="st"> </span>function(xVar,yVar,<span class="dt">numberOfHiddenDegrees=</span><span class="dv">0</span>) {
   d &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">x=</span>xVar,<span class="dt">y=</span>yVar,<span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)