Prep completed for ecology lessons

.gitignore

@@ -3,3 +3,5 @@
 .Rhistory
 .RData
 *.html
+Test.*
+data/

ReadMe.md

@@ -3,12 +3,21 @@
 ## Lessons
 
 Lessons (Day 1):
+
   * https://datacarpentry.org/R-ecology-lesson-alternative/index.html
   * https://datacarpentry.org/R-ecology-lesson-alternative/introduction-r-rstudio.html
   * https://datacarpentry.org/R-ecology-lesson-alternative/visualizing-ggplot.html
   * https://datacarpentry.org/R-ecology-lesson-alternative/how-r-thinks-about-data.html
 
 Lessons (Day 2):
+
   * https://datacarpentry.org/R-ecology-lesson-alternative/working-with-data.html
   * https://datacarpentry.org/R-ecology-lesson/05-r-and-databases.html
 
+
+## Hints
+
+RStudio keyboard:
+
+  * cmd-r/ctrl-r - Run a line and move to the next
+  * option-r/alt-r - Run a single line and stay on that line

prep/Instructor.Rmd

@@ -46,6 +46,7 @@ git config push.default simple
   * 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.
+  * You can auto-install packages in a Rmd file.  Need to figure out proper pedegody for this.
 
 # Test
 

prep/Preparation-RNotebook.ipynb

@@ -0,0 +1,117 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "9dd1774e-6446-4f7f-b3ee-3ac0dcd5a027",
+   "metadata": {},
+   "source": [
+    "# R Notebook Prep\n",
+    "\n",
+    "This produces a large graphics.  Clear all outputs before saving."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "03dca8c7-f3a4-48c4-8a9e-17b6701ce59b",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "## Setup system - run only once\n",
+    "\n",
+    "# Configure mirror\n",
+    "options(repos = list(CRAN=\"http://cran.rstudio.com/\"))\n",
+    "\n",
+    "# Install basic packages\n",
+    "install.packages(c(\"tidyverse\", \"lubridate\", \"ratdat\"))\n",
+    "\n",
+    "# Install plotting packages\n",
+    "install.packages(\"ggplot2\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "942ae10c-eec7-4ca0-be76-c268872c150f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "library(tidyverse)\n",
+    "library(lubridate)\n",
+    "library(ratdat)\n",
+    "library(ggplot2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7ade46ad-0ce2-4106-b0cd-5377e84d51b4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ggplot(data = complete_old, mapping = aes(x = weight, y = hindfoot_length)) +\n",
+    "  geom_point()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6605dcea-b970-4591-82eb-7928512fcc4f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "myplot <- ggplot(data = complete_old, mapping = aes(x = plot_type, y = hindfoot_length)) +\n",
+    "  geom_jitter(aes(color = plot_type), alpha = 0.2) +\n",
+    "  geom_boxplot(outlier.shape = NA, fill = NA)\n",
+    "\n",
+    "myplot\n",
+    "\n",
+    "myplot +\n",
+    "  theme_bw() +\n",
+    "  theme(axis.title = element_text(size = 14), \n",
+    "        legend.position = \"none\", \n",
+    "        panel.grid.major.x = element_blank()) +\n",
+    "  labs(title = \"Rodent size by plot type\",\n",
+    "       x = \"Plot type\",\n",
+    "       y = \"Hindfoot length (mm)\",\n",
+    "       color = \"Plot type\") +\n",
+    "  facet_wrap(vars(sex), ncol = 1)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b65f2312-4e9e-4e36-895e-e591f7c9db9b",
+   "metadata": {},
+   "source": [
+    "This produces a large graphics.  Clear all outputs before saving."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c26e0424-4115-48b2-a0d9-97dabee03875",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "4.3.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

prep/Preparation-RStudio.Rmd

@@ -5,6 +5,8 @@ editor_options:
 ---
 # R Ecology
 
+Test the technology prep (not show notes)
+
 ## Install Packages
 
 Run the (Setup.Rmd)[Setup.Rmd] RStudio notebook once.
@@ -17,7 +19,7 @@ library(lubridate)
 library(ratdat)
 ```
 
-## Lessons Snippits
+## Plotting
 
 ```{r}
 #install.packages("ggplot2")
@@ -71,3 +73,32 @@ myplot +
 
 ```
 
+## Understanding Data
+
+```{r}
+class(complete_old)
+head(complete_old)
+
+# provide a summary
+summary(complete_old)
+```
+
+## Working with Data
+
+Download Data (once)
+```{r}
+dir.create('data/cleaned', recursive = TRUE)
+download.file('https://www.michaelc-m.com/Rewrite-R-ecology-lesson/data/cleaned/surveys_complete_77_89.csv', 'data/cleaned/surveys_complete_77_89.csv')
+```
+
+Load data
+```{r}
+surveys <- read_csv("data/cleaned/surveys_complete_77_89.csv")
+class(surveys)
+select(surveys, plot_id, species_id, hindfoot_length)
+```
+
+Write Data
+```{r}
+write_csv(surveys, "data/cleaned/test.csv")
+```