Merge pull request #8 from tracykteal/gh-pages

updated data information

data.md → _extras/data.md

@@ -1,4 +1,9 @@
-# data-ecology
+---
+layout: page
+title: "Workshop data"
+permalink: /data/
+---
+
 All of the ecology lessons use the same data set throughout. The data is tabular (rows and columns), similar in structure to what you might have in a spreadsheet. 
 
 ## The Portal Project Teaching Database
@@ -15,6 +20,17 @@ This is a real dataset that has been used in over 100 publications. We've simpli
 it just a little bit for the workshop, but you can download the full dataset and work
 with it using exactly the same tools we'll learn about today.
 
+> ## Portal Project Teaching Dataset
+> The Portal Project Teaching Database is a simplified version of the Portal Project Database designed for teaching. It provides a real world example of life-history, population, and ecological data, with sufficient complexity to teach many aspects of data analysis and management, but with many complexities removed to allow students to focus on the core ideas and skills being taught.
+> 
+> The database is currently available in csv, json, and sqlite.
+> 
+> This database is not designed for research as it intentionally removes some of the real-world complexities. The original database is published at [Ecological Archives](http://esapubs.org/archive/ecol/E090/118/) and this version of the database should be used for research purposes. The Python code used for converting the original database to this teach version is included as 'create_portal_teach_dataset.py'. Suggested changes or additions to this dataset can be requested or contributed in the project GitHub repository [https://github.com/weecology/portal-teachingdb](https://github.com/weecology/portal-teachingdb).
+>
+> **CITATION:** Ernest, Morgan; Brown, James; Valone, Thomas; White, Ethan P. (2017): Portal Project Teaching Database. figshare. https://doi.org/10.6084/m9.figshare.1314459.v6
+{: .prereq}
+
+
 Files we use in this dataset:
 
 - [surveys.csv](https://ndownloader.figshare.com/files/2292172) - the survey data  

_includes/syllabus.html

@@ -2,6 +2,7 @@
   Display syllabus in tabular form.
   Days are displayed if at least one episode has 'start = true'.
 {% endcomment %}
+<!--
 <div class="syllabus">
   <h2 id="schedule">Schedule</h2>
 
@@ -76,3 +77,4 @@ <h2 id="schedule">Schedule</h2>
   </p>
 
 </div>
+-->

index.md

@@ -11,19 +11,31 @@ Data Carpentry's aim is to teach researchers basic concepts, skills, and tools f
 > There are no pre-requisites, and the materials assume no prior knowledge about the tools.
 {: .prereq}
 
-The workshop uses a single tabular data set that contains observations about adorable small mammals over a long period of time in Arizona. See [data.md](https://github.com/datacarpentry/ecology-workshop/blob/gh-pages/data.md) for more information about this data set, including the download location.
+> ## Data
+> 
+> The data for this workshop are is the [Portal Project Teaching Database](https://figshare.com/articles/Portal_Project_Teaching_Database/1314459) available on FigShare, with a CC-BY license available for reuse.
+>
+> The Portal Project Teaching Database is a simplified version of the Portal 
+> Project Database designed for teaching. It is a tabular dataset of observations
+> of small mammals in a desert ecosystem in Arizona, USA, collected over more than 40 years.
+> It provides a real world example of 
+> life-history, population, and ecological data, with sufficient complexity to 
+> teach many aspects of data analysis and management, but with many complexities
+> removed to allow students to focus on the core ideas and skills being taught.
+>
+> [More information on this dataset](data)
+{: .prereq}
 
-The workshop can be taught using R or python as the base language.
+The workshop can be taught using R or Python as the base language.
 
 Overview of the lessons:
 
-  1. Data organization in spreadsheets and data cleaning with OpenRefine
+  * Data organization in spreadsheets
+  * Data cleaning with OpenRefine
   * Introduction to R or python
   * Data analysis and visualization in R or python
   * SQL for data management
 
-An example of the ecology materials in the wild is this [Data Carpentry workshop at CalTech](http://www.datacarpentry.org/2015-11-23-caltech/) in 2015.
-
 ## Detailed structure
 
 ### Day 1 morning: Data organization & cleaning
@@ -33,14 +45,14 @@ There are two lessons in this section. The first is a spreadsheet lesson that te
   * [spreadsheet lesson](http://www.datacarpentry.org/spreadsheet-ecology-lesson/)
   * [spreadsheet repository](https://github.com/datacarpentry/spreadsheet-ecology-lesson)
 
-The second lesson uses a spreadsheet-like program called [OpenRefine](http://openrefine.org/) to teach data cleaning and filtering, and to introduce scripting, regular expressions and APIs (application programming interfaces).
+The second lesson uses a program called [OpenRefine](http://openrefine.org/) to teach data cleaning and filtering, and to introduce the idea scripting(application programming interfaces).
 
   * [OpenRefine lesson](http://www.datacarpentry.org/OpenRefine-ecology-lesson/)
   * [OpenRefine repository](https://github.com/datacarpentry/OpenRefine-ecology-lesson)
 
 ### Day 1 afternoon and Day 2 morning: Data analysis & visualization
 
-These lessons includes a basic information to R / python syntax, importing CSV data, subsetting and merging, data, and finishes with how to calculate summary statistics and create a simple plot.
+These lessons includes a basic information to R or Python syntax, importing CSV data, subsetting and merging, data, and finishes with how to do plotting.
 
   * [R lesson](http://www.datacarpentry.org/R-ecology-lesson/) and [python lesson](http://www.datacarpentry.org/python-ecology-lesson/)
   * [R repository](https://github.com/datacarpentry/R-ecology-lesson) and [python repository](https://github.com/datacarpentry/python-ecology-lesson)
@@ -58,6 +70,4 @@ This lesson introduces the concept of a database using SQLite, how to structure
 There are a number of other ecology lessons that are not part of the base workshop. Some of these are no longer taught, and some are only taught at extended workshops.
 
   * [shell-ecology](https://github.com/datacarpentry/shell-ecology)
-  * [R-dplyr-ecology-archived](https://github.com/datacarpentry/R-dplyr-ecology-archived)
-  * [scripting-ecology](https://github.com/datacarpentry/scripting-ecology)
-  * [R-ggplot2-ecology](https://github.com/datacarpentry/R-ggplot2-ecology)
+