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https://github.com/sjoerdvanalten/UKBWeightsFinal

All codes necessary to reproduce the results for necessary to reproduce the results ``The costs of non-reprsenative data: reweighting the UK Biobank corrects for pervasive selection bias due to volunteering'' by Sjoerd van Alten, Ben Domingue, Titus Galama and Andries Marees.
https://github.com/sjoerdvanalten/UKBWeightsFinal

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All codes necessary to reproduce the results for necessary to reproduce the results ``The costs of non-reprsenative data: reweighting the UK Biobank corrects for pervasive selection bias due to volunteering'' by Sjoerd van Alten, Ben Domingue, Titus Galama and Andries Marees.

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README 

        
This folder contains all the codes necessary to reproduce the results if "van Alten, S., Domingue, B. W., Faul, J., Galama, T., & Marees, A. T. (2024). Reweighting UK Biobank corrects for pervasive selection bias due to volunteering. International Journal of Epidemiology, 53(3), dyae054."



NOTE: Access the (restricted) UK Census data is necessary to reproduce these results. If your purpose is to use the weights in your own UKB work, these can be requested directly from the UKB returns catalogue, with application ID 55154 (https://biobank.ndph.ox.ac.uk/ukb/app.cgi?id=55154).

Currently, the weights can only be requested when using the UKB Research Access Portal. If you wish to create weights on already existing UKB data, contact the author directly: [email protected] 



It is important to run each file from the directory in which it is stored.



Ensure that all data is available in the following folders:



PrepareCensus/DATA/RAW:



"recodev12.csv": This file is available from UK Data Service (under condition of safeguarded access), and contains the England & Wales 5% Local Authority Safeguarded Microdata

Place all files provied by UK Data Services for the 2011 Census Microdata Individual Safeguarded Sample (Local Authority): Scotland in a new subfolder called ScotlandCensus



-Create a subfolder called "LADMap1991": Place in this folder the geometry of the census 1991. These shapefiles can be downloaded at 

https://borders.ukdataservice.ac.uk/easy_download_data.html?data=England_dt_1991 and https://borders.ukdataservice.ac.uk/easy_download_data.html?data=Wales_dt_1991

The names of the files that one needs to download are england_dt_1991.dbf/prj/shp/shx and wales_dt_1991.dbf/prj/shp/shx 

- The file CensusLAGeo.geojson contains the geometry of the census 2011

local authority regions and can be found at

https://ons-inspire.esriuk.com/arcgis/rest/services/Census_Boundaries/Census_Merged_Local_Authority_Districts_December_2011_Boundaries/MapServer/0/query?where=1%3D1&outFields=*&outSR=4326&f=geojson

-Create a subfolder called "LSOA2011" and downlload England and WALES LSOA geometries in it, as well as scotland LAS gometries. These are called england_lsoa_2011.dbf/prj/shp/shx, wales_lsoa_2011.dbf/prj/shp/shx  

and scotland_oa_2011/dbf/prj/shp/shx, and can be downloaded from the following sources:

https://borders.ukdataservice.ac.uk/easy_download_data.html?data=England_lsoa_2011

https://borders.ukdataservice.ac.uk/easy_download_data.html?data=Wales_lsoa_2011

https://borders.ukdataservice.ac.uk/easy_download_data.html?data=Scotland_oa_2011

-Create a subfolder called ScotlandCAMap2001 that contains the geometry of scottish council areas in 2001. These files are called scotland_ca_2001.dbf/prj/shp/shx and can be downloaded from 

https://borders.ukdataservice.ac.uk/easy_download_data.html?data=Scotland_ca_2001

- Download Mid-2011 population count by lower super output area from:

https://www.ons.gov.uk/peoplepopulationandcommunity/populationandmigration/populationestimates/datasets/lowersuperoutputareamidyearpopulationestimates

the relevant file is called mid-2011-lsoa-quinary-estimates.xls



To reproduce all results in the paper, use the following procedure:

 

First, run Main.sh in the PrepareCensus/CODE folder on a linux system. 

Next, open Main.txt in the UKB/CODE folder and run all bash files in order.



- The csv file LACodesToLaNames.csv shows how the England & Wales Microdata grouped

local authorities map into the actual local authorities. The information in this file

is obtained from the Appendix of the 2011 Census Microdata Individual Safeguarded 

Samples - User Guide