updated root readme

README.md

@@ -1,56 +1,24 @@
-[Tutorial](http://mindymallory.github.io/research-project-template/intro-to-r/)
 
 <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" /></a><br />This
 work is licensed under a
 <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">Creative
 Commons Attribution-ShareAlike 4.0 International License</a>.
 
+**Attributions:**  
+[Mindy Mallory Research Project Template](https://github.com/mindymallory/research-project-template)  
+[Griffin Chure Reproducible Research](https://github.com/gchure/reproducible_research)  
+
 Research Project Template
 =========================
 
-This repository contains a template for a reproducible research project.
-The fundamental idea of reproducible research is that the steps that
-take your research from raw data to manuscript, thesis, or report should
-be fully automated. This way, your work can be checked by your adviser,
-mentors, collaborators, others working in your area, journal reviewers,
-and your future self.
-
-I became interested in reproducible research because I was tired of
-being terrified of my own analysis. I was constantly petrified someone
-would question my work and ask me to open the black box and verify what
-I did was correct; in some cases even being asked reproduce a result was
-terrifying because I knew the convoluted path of data prep and cleaning
-that I took in arriving at my result.
-
-I read the book [Reproducable Research with R and
-RStudio](http://www.amazon.com/Reproducible-Research-Studio-Chapman-Hall/dp/1466572841)
-by Christopher Gandrud (2013), and I read a lot of blog posts and
-tutorials by [Karl Broman](http://kbroman.org/pages/software.html) and
-[Carl
-Boettiger](http://www.carlboettiger.info/2012/05/06/research-workflow.html)
-and I struck out on my own path to execute a reproducible research
-project from start to finish. The repository for that project is
-[here](https://github.com/mindymallory/BBOBAS), while I was successful
-in learning the basics of how r, rmarkdown, knitr, and pandoc combine to
-make reproducible research possible, you can tell just by looking at the
-project's Github repository that I failed miserably at making the
-project reproducible. This is because the repository is totally
-unorganized, and I am pretty sure I am the only one who could reproduce
-the results from this project.
-
-But in that failure, I learned a lot about how a reproducible research
-project should be organized. I built this template for my future
-students and for my future self.
-
-R and RStudio are an excellent vehicle for conducting reproducible
-research. You write manuscripts and reports in `.rmarkdown` documents
-that includes code chunks that perform analysis. The code chunks are
-evaluated by `R` and incorporated in the document by the tools in the
-`knitr` package to produce a markdown `.md` document. From there a
-program called `pandoc` converts your markdown document to whatever file
-format you like: PDF (formatted with latex .csl files), html, or
-Microsoft Word. This all happens without the user really knowing what is
-going on, which makes it easy to get started.
+### Overview
+This repository sets out the skeleton of an organizational structure used for scientific research. It loosely follows what I have used for several of my research projects and I hope it inspires you to conduct your research in an open, reproducible, and honest manner.
+
+### How to Use
+To use this template for your research, fork this repository, change the name
+to something descriptive for your project, and adjust the licensing as you
+see fit.
+
 
 Getting Started
 ===============
@@ -74,6 +42,13 @@ the steps to generate the manuscript are automated and thus, not subject
 to the inconsistencies that go along with piece-wise data preparation
 and analysis.
 
+Working with R and RStudio
+-------------------------
+
+
+Here are some tutorials and resources:  
+- [Mindy Mallory]([Tutorial](http://mindymallory.github.io/research-project-template/intro-to-r/))  
+
 Generate the Manuscript with One Click
 ======================================