Update README.md

README.md

@@ -1,4 +1,4 @@
-These scripts run the model and generate output from: 
+## These scripts run the model and generate output from: 
 
 Estimated effectiveness of symptom and risk screening to prevent the spread of COVID-19
 Authors: Gostic, Gomez, Mumah, Kucharski, Lloyd-Smith.
@@ -9,8 +9,19 @@ This code by K. Gostic, adapted from a previous version implemented by A. Kuchar
 
 Model and methods adapted from  Gostic KM, Kucharski AJ, Lloyd-Smith JO. (2015) eLife 4:e05564.
 
+
+## Repository contents:
 All code runs in R.
-See script nCov_manuscript_plots.R for all analysis and plotting code.
-See https://lloyd-smithlab.shinyapps.io/travelScreeningModel/ for an interactive version of the model.
-Code for the shiny app is hosted elsewhere. These scripts generate figures shown in the manuscript.
+* The nCov_manuscript_plots.R script runs all analyses and generates all plots and data outputs.
+    * .RData files contain raw, simulated data.
+        * "a" indicates outputs generated based on arrival screening only. "d" indicates departure screening only. "ad" indicates both. 
+        * "flat" indicates outputs generated assuming a stable epidemic. Outputs without the "flat" flag were generated assuming a growing source epidemic.
+  * 2002_nCoV/ contains all plot and source data outputs.
+      * Source data .csv files contain processed data frames used to generate the corresponding plot.
+      * Plot names corresond to their ID in the manuscript (e.g. Fig. 3, Fig 3S1).
+
+## See https://lloyd-smithlab.shinyapps.io/travelScreeningModel/ for an interactive Shiny app.
+Code for the shiny app is hosted elsewhere. These scripts here generate figures shown in the manuscript.
+
+------
 contact: kgostic [at] uchicago.edu