add readme about aline study code

notebooks/aline/README.md

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+# Reproducing the indwelling arterial catheter study (aline study)
+
+This folder contains code for reproducing a study on indwelling arterial catheters:
+
+> Hsu DJ, Feng M, Kothari R, Zhou H, Chen KP, Celi LA. The association between indwelling arterial catheters and mortality in hemodynamically stable patients with respiratory failure: a propensity score analysis. CHEST Journal. 2015 Dec 1;148(6):1470-6.
+
+The study showed, in the MIMIC-II database, that after adjustment for various confounders, indwelling arterial catheters were not associated with a mortality benefit.
+
+The code here reproduces this study in the MIMIC-III database. This involved many technical changes due to schema differences and data differences between MIMIC-II and MIMIC-III. As MIMIC-III covers four additional years, the cohort extracted here is larger than that reported in the study.
+
+# Requirements
+
+There are a number of prerequesites to running this code:
+
+* an installation of MIMIC-III in a PostgreSQL database
+* Python 2.7 with the numpy, pandas, matplotlib, and psycopg2 packages
+* Jupyter with a Python 2 kernel
+* R with the Matching library
+
+# Running the study
+
+The study can be reproduced by:
+
+1. Running the `aline.ipynb` file - this notebook generates the data (using the SQL files in this directory) and saves a single dataframe to CSV
+2. Running the `aline_propensity_score.Rmd` file - this R markdown file uses the above CSV to create a propensity score and calculate the mortality difference between matched pairs
+
+# Slight modifications
+
+There are a few minor differences between our reproduction and the original study.
+
+* the original study subselected variables using a genetic algorithm, whereas we simply use the final set of variables they report
+* we did not include PO2 and PCO2 in the propensity score
+* we removed patients based on hospital service, not ICU service
+*