Cleanup process and add Project file

.gitignore

@@ -1 +1,4 @@
 .ipynb_checkpoints/
+.Rproj.user
+.Rhistory
+.RData

prep/Preparation.Rmd

@@ -1,19 +1,14 @@
 ---
+title: "Preparation"
 output: html_document
 editor_options: 
   chunk_output_type: console
 ---
-# Lesson Prep
+See [Setup.Rmd](Setup.Rmd) for setting up RStudio environment..
 
-## Setup
+# R Ecology
 
-Update Tools with "Tools -\> Update" (do not pin) - takes a long time - don't do in class
-
-To have output go in console set in the config for the Rmd file set "chunk output in console"
-
-To view Rmd rendered (click Knit to html) in seprate windows select settings of the Rmd file and select "Preview in Window"
-
-Install Packages
+## Install Packages
 
 ```{r message=FALSE, warning=FALSE}
 options(repos = list(CRAN="http://cran.rstudio.com/"))
@@ -61,17 +56,3 @@ ggplot(data = complete_old, mapping = aes(x = weight, y = hindfoot_length))
 ggplot(data = complete_old, mapping = aes(x = weight, y = hindfoot_length)) +
   geom_point()
 ```
-## Presentatin Style
-
-Top/bottom
-```{r}
-1+2
-3+4
-print('Hello World')
-
-```
-
-
-
-
-

prep/Setup.Rmd

@@ -0,0 +1,41 @@
+---
+title: "Setup"
+output: html_document
+editor_options:
+  chunk_output_type: console
+---
+
+# Setup
+
+Update Tools with "Tools -> Update" (do not pin) - takes a long time - don't do in class.
+
+Use a "R Markdown" document (`output: html_document` in prolog).
+
+To have the output display in the console (not inline) set in the config for the Rmd file set "chunk output in console".
+
+To view Rmd rendered (click Knit to html) in separate windows select settings for the Rmd file (wheel) and select "Preview in Window"
+
+Prolog should look like this:
+```
+---
+title: "Setup"
+output: html_document
+editor_options:
+  chunk_output_type: console
+---
+```
+
+Notes:
+
+  * R Notebooks seem fragile and Caching output seems dangerous.  Use "Chunk Output Inline" for a more Notebook experence or use Juypter!
+  * R Markdown is a bit different (lists for example) than other markdown.
+  * With Rmd files I am a fan of using the console (chunk output in console) and use cmd-enter to run each line (opt-enter for not advancing cursor) for development.
+
+# Test
+
+Top/bottom
+```{r}
+1+2
+3+4
+print('Hello World')
+```

skc-workshop.Rproj

@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX