Merge pull request #728 from ethanwhite/knitr-update

Rework knitr demo for smoother flow

materials/knitr.md

@@ -14,104 +14,109 @@ language: R
 
 ### Getting started
 
-* Open RStudio
+* `install.packages("rmarkdown")` in console for permanence
 * `File` -> `New File` -> `R Markdown`
     * Enter a title and author(s).
     * Choose 'Default Output Format' as `HTML`.
 * Generates a basic stub of a `.Rmd` document
-    * Customize "front matter" at the top of the document between the `---`. 
-* Press `Knit` to create an `HTML` from the document
-    * 1st time may ask you to install some packages
-    * `install.packages("rmarkdown")` in console for permanence
-* Runs the code in the code chunks and prints their output along with the
-  markdown formatted text
-* Can also create `PDF` & Word versions of our files
-    * `PDF` Requires `pandoc` and `TeX` installation
-    * Use the `Knit` dropdown or change `output: pdf_document`
-* R Notebook
-    * `output: html_notebook`
-    * "Interactive R Markdown" 
-        * execute individual code chunks
-        * output in editor pane  
+    * Customize "front matter" at the top of the document between the `---`.
+* Delete everything below the second `---`
 
 ### Markdown
 
 * Basic approach to formatting text
 * Let's you do
+    * `# Headers`
     * `*italics*`
     * `**bold**`
     * `[links](http://google.com)`
     * Lists
         * `*`
         * `1.`
-    * `# Header`
+
+
+<pre><code>
+## Concept
+
+Exploration of population dynamic patterns at **The Portal Project**.
+How do counts of rodents like *Dipodomys* species change through time?
+
+In this document I will:
+
+1. Load data from the [Portal Project Teaching Database](http://figshare.com/articles/Portal_Project_Teaching_Database/1314459)
+2. Process it into population time series
+3. And make initial visualizations
+</code></pre>
+
 * Easy to read for humans
 * Easy to convert into other things for computers
-* Common on lots of websites
+
+* Press `Knit` to create `HTML` from the document
+* Can also create `PDF` & Word versions of our files
+    * `PDF` Requires `pandoc` and `TeX` installation
+    * Use the `Knit` dropdown or change `output: pdf_document`
+
+* Markdown is common on lots of websites
 * Used to create all of the exercises and lectures in this course
 * Github will automatically render it
     * [https://github.com/ethanwhite/CV/blob/master/CV.md](https://github.com/ethanwhite/CV/blob/master/CV.md)
 
-<pre><code>Explore patterns in population dynamics at Portal.
+### R chunks 
 
-## Required Libraries</code></pre>
+* R Markdown allows you to include code to run in the document
+* Click on `Insert` and choose R
 
-### R chunks 
+<pre><code>
+## Required Packages
 
-* Set R code inside a set of <code>```</code> with the `{r}` designation
+```{r}
+library(dplyr)
+library(ggplot2)
+```
+</code></pre>
 
-<pre><code>```{r}
-```</code></pre>
 
-* Code that you write inside chunks gets executed during the "knit" process and 
-the results are shown below.
+* Knitting runs the code and prints its output
 
-<pre><code>```{r}
-library(dplyr)
-```</code></pre>
+<pre><code>
+## Data
+
+```{r}
+data <- read.csv("https://ndownloader.figshare.com/files/2292172")
+head(data)
+```
+</code></pre>
+
+
+### Chunk options
 
 * Chunks have lots of useful options
   * Options are described at: [http://yihui.name/knitr/options/](http://yihui.name/knitr/options/)
   * Options will be listed in RStudio if you press tab inside
       the `{r}` brackets at the top of the chunk
 
-<pre><code>```{r, message=FALSE}
-library(dplyr)
-```</code></pre>
-
 <pre><code>```{r, message=FALSE}
 library(dplyr)
 library(ggplot2)
 ```</code></pre>
 
-<pre><code>```{r, message=FALSE, warning=FALSE}
-library(dplyr)
-library(ggplot2)
+* `cache=TRUE` reuses results of the code chunk in subsequent "knits". Save time
+re-calculating or re-downloading it each time.
+
+<pre><code>```{r, cache=TRUE}
+data <- read.csv("https://ndownloader.figshare.com/files/2292172")
+head(data)
 ```</code></pre>
 
 * You can run code inside your text, too:
-    * <code>`r cos(pi)`</code> turns into `-1` when you press the `Knit` button.
-    * We will see and example of this later.
-
-### Analysis Report Example
-
-* Here's a text segment linked to a code chunk that begins an analysis report.
 
-<pre><code>## Data
-
-Data is from the [Portal project teaching database](http://figshare.com/articles/Portal_Project_Teaching_Database/1314459) 
-published on Figshare. We need the surveys table for our analysis:
-
-```{r, cache=TRUE}
-download.file("https://ndownloader.figshare.com/files/2292172", 
-              "surveys.csv")
-data <- read.csv("surveys.csv")
-```</code></pre>
+```
+The data includes `r length(unique(data$species_id))` species.
+```
 
-* Setting `cache=TRUE` lets you reuse the results of this code chunk in
-subsequent "knits" instead of re-calculating or re-downloading it each time.
+### Analysis Example
 
-<pre><code>## Analyze population time-series
+<pre><code>## Analysis
 
 Get the time-series of counts for all species.
 
@@ -120,6 +125,7 @@ time_series <-
   data %>%
   group_by(species_id, year) %>%
   summarize(count = n()) %>%
+  filter(species_id %in% c('DM', 'DO', 'DS')) %>%
   na.omit()
 
 head(time_series)
@@ -133,31 +139,19 @@ head(time_series)
 ggplot(time_series, aes(x = year, y = count)) +
   geom_point() +
   geom_line() +
-  facet_wrap(~species_id) +
-  scale_x_continuous(breaks = pretty_breaks(n=2))
-```
+  geom_smooth() +
+  facet_wrap(~species_id)
+```</pre></code>
 
-## A simple model
+### Notebook
 
-```{r, echo=FALSE}
-model <- data %>% group_by(year) %>% 
-  summarize(count = n()) %>% 
-  lm(count ~ year, data = .)
+* In RStudio run chunks using `Ctrl-Shift-Enter` or `Cmd-Shift-Enter`
+* Displays results in the editor
 
-results <- anova(model)
-```</code></pre>
-
-* Here's the example of an inline code chunk.
+* Notebook
 
-<pre><code>We found a marginally significant linear relationship between the
-total count and year (p = `r round(results[["Pr(>F)"]][1], 3)`; see
-Table 1 for more details)
+* `output: html_notebook` or File -> New File -> R Notebook
 
-```{r, echo=FALSE}
-knitr::kable(results, caption = "Table 1")
-```</code></pre>
-
-* `knitr::kable()` is a handy way to make nice-looking tables from data frames.
 
 ### R Presentations
 
@@ -173,6 +167,7 @@ author:
 date: 
 autosize: true
 
+
 First Slide
 ========================================================