minor updates to modules for first day

BenjaminLiuPenrose · Aug 13, 2018 · b7074eb · b7074eb
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diff --git a/modules/figure/orderedfac-1.png b/modules/figure/orderedfac-1.png
diff --git a/modules/figure/unnamed-chunk-17-1.png b/modules/figure/unnamed-chunk-17-1.png
diff --git a/modules/figure/unnamed-chunk-5-1.png b/modules/figure/unnamed-chunk-5-1.png
diff --git a/modules/figure/usedots-1.png b/modules/figure/usedots-1.png
diff --git a/modules/module0_induction.html b/modules/module0_induction.html
@@ -190,7 +190,7 @@ <h1>How we&#39;ll operate</h1>
 
 <p>Counselors will be available to help answer any questions you have (just wave to one of them), or feel free to just ask the presenter during the presentation. The counselors will also be monitoring the <a href="https://groups.google.com/a/lists.berkeley.edu/d/forum/r-bootcamp-2018">Google group Q&amp;A area</a>, so feel free to type in a question there (or send email to <a href="mailto:r-bootcamp-2018@lists.berkeley.edu">r-bootcamp-2018@lists.berkeley.edu</a>) and one of the counselors will answer the question. Or if you know the answer, help us out by answering it yourself or adding your thoughts. </p>
 
-<p>Your counseloRs are: Kellie Ottoboni (Statistics/BIDS), Nima Hejazi (Biostatistics), Sean Wu (Epidemiology), Hector Roux de Bezieux (Biostatistics), and Evan Muzzall (D-Lab).</p>
+<p>Your counseloRs are: Kellie Ottoboni (Statistics/BIDS), Nima Hejazi (Biostatistics), Sean Wu (Epidemiology), Hector Roux de Bezieux (Biostatistics), Dana Seidel (ESPM), and Evan Muzzall (D-Lab).</p>
 
 <h1>Suggestions on how to get the most out of the bootcamp</h1>
 

diff --git a/modules/module0_induction_slides.html b/modules/module0_induction_slides.html
diff --git a/modules/module2.Rda b/modules/module2.Rda
diff --git a/modules/module2_managingR.html b/modules/module2_managingR.html
@@ -281,7 +281,25 @@ <h1>Managing and saving the workspace</h1>
 ls()
 </code></pre>
 
-<pre><code>## [1] &quot;bioc&quot;   &quot;module&quot; &quot;source&quot;
+<pre><code>##  [1] &quot;a&quot;                &quot;D2R&quot;              &quot;deepExtract&quot;     
+##  [4] &quot;denslines&quot;        &quot;densplot&quot;         &quot;dim2&quot;            
+##  [7] &quot;ellipse.default&quot;  &quot;f.angdist&quot;        &quot;f.ciplot&quot;        
+## [10] &quot;f.dplot&quot;          &quot;f.ess&quot;            &quot;f.ess.old&quot;       
+## [13] &quot;f.flushplot&quot;      &quot;f.gm&quot;             &quot;f.grstat&quot;        
+## [16] &quot;f.identity&quot;       &quot;f.invlogit&quot;       &quot;f.logit&quot;         
+## [19] &quot;f.logmatern.euc&quot;  &quot;f.lonlat2eucl&quot;    &quot;f.matern.ang&quot;    
+## [22] &quot;f.matern.ang.cov&quot; &quot;f.matern.euc&quot;     &quot;f.merge&quot;         
+## [25] &quot;format_bytes&quot;     &quot;f.rdist.earth&quot;    &quot;f.sort&quot;          
+## [28] &quot;f.sort2&quot;          &quot;f.squexp&quot;         &quot;f.trimat&quot;        
+## [31] &quot;f.vecrep&quot;         &quot;getNcdf&quot;          &quot;im&quot;              
+## [34] &quot;indices&quot;          &quot;ls_sizes&quot;         &quot;machineName&quot;     
+## [37] &quot;makePoly&quot;         &quot;module&quot;           &quot;plot.ell&quot;        
+## [40] &quot;pmap&quot;             &quot;pmap2&quot;            &quot;pointsInPoly&quot;    
+## [43] &quot;pplot&quot;            &quot;pretty_size&quot;      &quot;print.closeR&quot;    
+## [46] &quot;q&quot;                &quot;R2&quot;               &quot;R2D&quot;             
+## [49] &quot;rcsv&quot;             &quot;rotate&quot;           &quot;sizes&quot;           
+## [52] &quot;source&quot;           &quot;temp.colors&quot;      &quot;thresh&quot;          
+## [55] &quot;tplot&quot;            &quot;tsplot&quot;           &quot;wcsv&quot;
 </code></pre>
 
 <p><strong>Challenge</strong>: how would I find all of my objects that have &#39;x&#39; in their names?</p>
@@ -360,13 +378,13 @@ <h3>Package namespaces</h3>
 <pre><code class="r">ls(&#39;package:stats&#39;)[1:20]
 </code></pre>
 
-<pre><code>##  [1] &quot;acf&quot;                  &quot;acf2AR&quot;               &quot;add.scope&quot;           
-##  [4] &quot;add1&quot;                 &quot;addmargins&quot;           &quot;aggregate&quot;           
+<pre><code>##  [1] &quot;acf&quot;                  &quot;acf2AR&quot;               &quot;add1&quot;                
+##  [4] &quot;addmargins&quot;           &quot;add.scope&quot;            &quot;aggregate&quot;           
 ##  [7] &quot;aggregate.data.frame&quot; &quot;aggregate.ts&quot;         &quot;AIC&quot;                 
 ## [10] &quot;alias&quot;                &quot;anova&quot;                &quot;ansari.test&quot;         
 ## [13] &quot;aov&quot;                  &quot;approx&quot;               &quot;approxfun&quot;           
-## [16] &quot;ar&quot;                   &quot;ar.burg&quot;              &quot;ar.mle&quot;              
-## [19] &quot;ar.ols&quot;               &quot;ar.yw&quot;
+## [16] &quot;ar&quot;                   &quot;ar.burg&quot;              &quot;arima&quot;               
+## [19] &quot;arima0&quot;               &quot;arima0.diag&quot;
 </code></pre>
 
 <pre><code class="r">lm &lt;- function(i) {
@@ -383,7 +401,7 @@ <h3>Package namespaces</h3>
 </code></pre>
 
 <pre><code>## y ~ x
-## &lt;environment: 0x55aa80a54468&gt;
+## &lt;environment: 0x43e4588&gt;
 </code></pre>
 
 <pre><code class="r">stats::lm(y ~ x)
@@ -395,7 +413,7 @@ <h3>Package namespaces</h3>
 ## 
 ## Coefficients:
 ## (Intercept)            x  
-##     -0.1505       0.1071
+##      0.3736       0.9397
 </code></pre>
 
 <pre><code class="r">rm(lm)
@@ -496,13 +514,14 @@ <h1>Reading &#39;foreign&#39; format data</h1>
 ## 3     2      1 female black 30-39    &lt;NA&gt;   &lt;NA&gt;    &lt;NA&gt; 30-44 30-39
 ## 4     2      1 female black 30-39    &lt;NA&gt;   &lt;NA&gt;    &lt;NA&gt; 30-44 30-39
 ## 5     2      1 female white 40-44    &lt;NA&gt;   &lt;NA&gt;    &lt;NA&gt; 30-44 40-49
+## 6     2      1 female white 30-39    &lt;NA&gt;   &lt;NA&gt;    &lt;NA&gt; 30-44 30-39
 ##   geocode sizeplac brnagain attend year region y
 ## 1       3    rural     &lt;NA&gt;   &lt;NA&gt; 2004      4 0
 ## 2       3    rural     &lt;NA&gt;   &lt;NA&gt; 2004      4 1
 ## 3       3    rural     &lt;NA&gt;   &lt;NA&gt; 2004      4 0
 ## 4       3    rural     &lt;NA&gt;   &lt;NA&gt; 2004      4 0
 ## 5       3    rural     &lt;NA&gt;   &lt;NA&gt; 2004      4 0
-##  [ reached getOption(&quot;max.print&quot;) -- omitted 1 row ]
+## 6       3    rural     &lt;NA&gt;   &lt;NA&gt; 2004      4 0
 </code></pre>
 
 <p>There are a number of other formats that we can handle for either reading or writing. Let&#39;s see <code>library(help = foreign)</code>.</p>
@@ -537,12 +556,12 @@ <h3>Writing out plots and tables</h3>
 
 <p><code>xtable()</code> formats tables for HTML and Latex (the default).</p>
 
-<pre><code class="r">require(xtable)
+<pre><code class="r">library(xtable)
 print(xtable(table(air$UniqueCarrier, air$Cancelled)), type = &quot;html&quot;)
 </code></pre>
 
-<pre><code>## &lt;!-- html table generated in R 3.5.1 by xtable 1.8-2 package --&gt;
-## &lt;!-- Thu Aug  9 18:02:29 2018 --&gt;
+<pre><code>## &lt;!-- html table generated in R 3.4.3 by xtable 1.8-2 package --&gt;
+## &lt;!-- Mon Aug 13 15:02:19 2018 --&gt;
 ## &lt;table border=1&gt;
 ## &lt;tr&gt; &lt;th&gt;  &lt;/th&gt; &lt;th&gt; 0 &lt;/th&gt; &lt;th&gt; 1 &lt;/th&gt;  &lt;/tr&gt;
 ##   &lt;tr&gt; &lt;td align=&quot;right&quot;&gt; AA &lt;/td&gt; &lt;td align=&quot;right&quot;&gt; 49222 &lt;/td&gt; &lt;td align=&quot;right&quot;&gt; 1033 &lt;/td&gt; &lt;/tr&gt;

diff --git a/modules/module2_managingR_slides.html b/modules/module2_managingR_slides.html
diff --git a/modules/module3_data.html b/modules/module3_data.html
diff --git a/modules/module3_data_slides.html b/modules/module3_data_slides.html
diff --git a/modules/module4_calc.html b/modules/module4_calc.html
diff --git a/modules/module4_calc_slides.html b/modules/module4_calc_slides.html
diff --git a/modules/module5_programming.html b/modules/module5_programming.html
diff --git a/modules/module5_programming_slides.html b/modules/module5_programming_slides.html
diff --git a/modules/myplot.pdf b/modules/myplot.pdf