updating readme links

R/py_int/README_seeding.md

@@ -9,18 +9,18 @@ We ranked each of the MSOAs in Devon according to their:
 	* Index of multiple deprivation (less deprived = greater exposure)
 	* Transport connectivity (more connected = greater exposure)
 
-MSOAs in the top tertile for all three categories were considered to be the areas where COVID was mostly likely to initially be seeded. Within these MSOAs we randomly seed the infection on the first day in a given number of individuals that spend > 30% outside their own home.
+MSOAs in the top tertile for all three categories were considered to be high risk areas where COVID initially found in the region. Within these MSOAs we filter out individuals that spend <30% time outside their home and then randomly seed the infection on the first day to a given number of the remaining individuals.
 
-Code for calculating the risk levels of MSOAs is found in R/py_int/msoa_high_risk.R
+Code for calculating the risk levels of MSOAs is found in R/py_int/msoa_high_risk.R . Prior to using this code the code in R/py_int/msoa_pop_density.R and R/py_int/msoa_connectedness.R must be run in order to create the population density and connectedness scores for each MSOA.
 
 
 Population density:
 
 	Code in R/py_int/msoa_pop_density.R
 	Resulting data in devon_data/population_density_msoas.csv
 
-	In order to calculate population density we downloaded MSOA shapefile from (XXXX) and LSOA population data from (https://www.ons.gov.uk/file?uri=/peoplepopulationandcommunity/populationandmigration/populationestimates/datasets/lowersuperoutputareamidyearpopulationestimates/mid2018sape21dt1a/sape21dt1amid2018on2019lalsoasyoaestimatesformatted.zip).
-	We aggregated the population data to MSOA level using (XXXX), calculated the areas of each MSOA  in the shapefile, and then used these values to calculate population density.	
+	In order to calculate population density we downloaded MSOA shapefile from [here](https://opendata.arcgis.com/datasets/826dc85fb600440889480f4d9dbb1a24_0.zip?outSR=%7B%22latestWkid%22%3A27700%2C%22wkid%22%3A27700%7D) and LSOA population data from [here](https://www.ons.gov.uk/file?uri=/peoplepopulationandcommunity/populationandmigration/populationestimates/datasets/lowersuperoutputareamidyearpopulationestimates/mid2018sape21dt1a/sape21dt1amid2018on2019lalsoasyoaestimatesformatted.zip).
+	We aggregated the population data to MSOA level using and then calculated the areas of each MSOA in the shapefile, and then used these values to calculate population density.	
 
 Connectedness: 
 
@@ -42,9 +42,9 @@ Index of Multiple Deprivation:
 	Code in R/py_int/msoa_high_risk.R
 	Resulting data in init_data/msoa_danger_fn.csv
 
-	We downloaded the Index of Multiple Deprivation Rank data from here: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/833970/File_1_-_IMD2019_Index_of_Multiple_Deprivation.xlsx
+	We downloaded the Index of Multiple Deprivation Rank data from [here](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/833970/File_1_-_IMD2019_Index_of_Multiple_Deprivation.xlsx)
 
-	This was available at LSOA level, we averaged the LSOA ranks to give a MSOA rank. 
+	This was available at LSOA level, we averaged the LSOA ranks to give an MSOA average rank.