Merge pull request #41 from mortonjt/case_study2

Adding case study2 notebook and data

README.md

@@ -19,12 +19,6 @@ To install this package, it is recommended to use conda as follows
 conda install -c biocore gneiss
 ```
 
-You can also install Gneiss via pip
-
-```
-pip install gneiss
-```
-
 To run through the tutorials, you'll need a few more packages, namely `seaborn`, `biom-format` and `h5py`.
 These packages can be installed with conda as follows
 ```
@@ -39,3 +33,4 @@ IPython notebooks demonstrating some of the modules in gneiss can be found as fo
 
 * [What are balances](https://github.com/biocore/gneiss/blob/master/ipynb/balance_trees.ipynb)
 * [Linear regression on balances in the 88 soils](https://github.com/biocore/gneiss/blob/master/ipynb/88soils.ipynb)
+* [Linear mixed effects models on balances in a CF study](https://github.com/biocore/gneiss/blob/master/ipynb/cfstudy.ipynb)

ipynb/88soils.ipynb

@@ -6,6 +6,8 @@
    "source": [
     "[Previous](https://github.com/biocore/gneiss/blob/master/ipynb/balance_trees.ipynb) \n",
     "\n",
+    "[Next](https://github.com/biocore/gneiss/blob/master/ipynb/88soils.ipynb) \n",
+    "\n",
     "In this study, there were 88 soil samples collected from North and South America.  Each of these soil samples had a pH measurement. From this [paper](http://www.ncbi.nlm.nih.gov/pubmed/19502440), it was observed that pH plays a primary role in community assemblage.  Here, we will show that pH by itself can actually predict the microbial abundances, using balance trees."
    ]
   },