Update docs

Author: jamesmulhall

docs/readme.md

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+# Overview of how to re-run the full analysis.
+
+### 1. Pre-process data in QGIS to generate updated_GIS_output_cleaned file
+This is covered in the related publication (preprint link to be added here shortly). Please feel free to reach out to the ALLFED team for more information or assistance here.  <br />
+
+### 2. Run `scripts/run_monte_carlo.ipynb`
+The parameters currently selected are the ones used in the publication, but feel free to change these to fit your assumptions or context.  <br />
+
+### 3. Run `scripts/key_results.ipynb`
+This will output the most important findings in terms of who can access water at what resolutions and by walking/cycling/using non-piped sources.  <br />
+
+### 4. Run postprocessing scripts to format data for QGIS visualisation
+You can generate TIF files for making result maps by doing the following:
+* Run`/scripts/Data_Manipulation_Scripts/parquet_process.py` to find the median/5th/95th runs
+* Rename the identified run files to “zone_simulation_result_median.parquet”, “zone_simulation_result_5th_percentile.parquet”, and “zone_simulation_result_95th_percentile.parquet”
+* Run `/scripts/Data_Manipulation_Scripts/export_results_with_centroids`
+* Run `/scripts/Data_Manipulation_Scripts/rasterize_results`: this will provide unsmoothed results for mapping which are better for high-resolution analysis of results
+* Run `/scripts/Data_Manipulation_Scripts/rasterize_and_smooth_results`: this will provide smoothed results which can look better for a global-scale map
+* Put output into QGIS
+* Reproject TIF files into chosen map project (Winkel Tripel was used for our publication)
+* Update symbology as desired (we used singleband pseudocolor with Magma reversed as the colormap)