From 05c9544a794546489694dc6a874ea4c7de4d4935 Mon Sep 17 00:00:00 2001 From: Alistair Johnson Date: Tue, 16 May 2017 18:59:28 -0400 Subject: [PATCH] add readme about aline study code --- notebooks/aline/README.md | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 notebooks/aline/README.md diff --git a/notebooks/aline/README.md b/notebooks/aline/README.md new file mode 100644 index 0000000..c50e5b2 --- /dev/null +++ b/notebooks/aline/README.md @@ -0,0 +1,34 @@ +# 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 +*