title: Plot size and resolution with R markdown, knitr, pandoc, beamer
body: <p>Doesn't fit on the slide by default, doesn't even print by any other means.</p>
  
  <p>Here's the .Rmd: <strong>Edit: it seems you have to use plot() in every chunk.  Second plot now prints.</strong></p>
  
  <pre><code># Plot should show at high resolution
  
  ```{r echo=FALSE, comment = ""}
  # load some data
  require(plyr)
  rbi &lt;- ddply(baseball, .(year), summarise,  
    mean_rbi = mean(rbi, na.rm = TRUE))
  ```
  
  ```{r}
  # plot
  plot(mean_rbi ~ year, type = "l", data = rbi)
  ```
  
  # Second attempt
  ```{r, fig.width = 2, fig.height = 2}
  plot(mean_rbi ~ year, type = "l", data = rbi)
  ```
  
  # Third attempt
  ```{r, out.width = 2, out.height = 2}
  plot(mean_rbi ~ year, type = "l", data = rbi)
  ```
  
  # Fourth attempt
  ```{r, out.width = '200px', out.height = '200px'}
  plot(mean_rbi ~ year, type = "l", data = rbi)
  ```
  
  # Fifth attempt
  ```{r, out.width = '\\maxwidth'}
  plot(mean_rbi ~ year, type = "l", data = rbi)
  ```
  </code></pre>
  
  <p>Save that as <code>test.Rmd</code>
  Then compile to tex using beamer:</p>
  
  <pre><code>knit("test.Rmd")
  system("pandoc -s -t beamer --slide-level 1 test.md -o test.tex")
  </code></pre>
  
  <p>Open <code>test.tex</code> in RStudio and click "Compile PDF".</p>
  
  <p>I've read Yihui's <a href="http://yihui.name/knitr/options#chunk_options">documentation</a> and hope I haven't missed something really obvious.</p>
  
  <p><strong>Edit</strong> new code incorporating Yihui's suggestions.</p>
  
  <pre><code>```{r setup, include=FALSE}
  opts_chunk$set(dev = 'pdf')
  ```
  
  # Plot should show at high resolution
  
  ```{r echo=FALSE, comment = ""}
  # load some data
  require(plyr)
  rbi &lt;- ddply(baseball, .(year), summarise,  
    mean_rbi = mean(rbi, na.rm = TRUE))
  ```
  
  ```{r}
  # plot
  plot(mean_rbi ~ year, type = "l", data = rbi)
  ```
  
  # Second attempt
  ```{r, fig.width = 4, fig.height = 4}
  plot(mean_rbi ~ year, type = "l", data = rbi)
  ```
  </code></pre>
  
  <p><code>sessionInfo()</code></p>
  
  <pre><code> R version 3.0.1 (16/05/2013)
  Platform: x86_64-pc-linux-gnu (64-bit)
  
  Local:
   [1] LC_CTYPE = en_US.UTF-8 LC_NUMERIC = C LC_TIME = C LC_COLLATE = C        
   [5] LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C           
   [9] LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
  [1] plyr_1.8       markdown_0.6   knitr_1.2      rCharts_0.3.51 slidify_0.3.52
  
  loaded via a namespace (and not attached):
   [1] RJSONIO_1.0-3   codetools_0.2-8 digest_0.6.3    evaluate_0.4.3  formatR_0.8    
   [6] grid_3.0.1      lattice_0.20-15 stringr_0.6.2   tools_3.0.1     whisker_0.3-2  
  [11] yaml_2.1.7  
  </code></pre>