To run WinBugs within Stata, please follow the instructions here: https://www.stata-press.com/data/bas.html Name of the project: Geographical patterns of the loss in life expectancy and crude probability of death for cancer patients Description: This is a collaborative work of Yuliya Leontyeva and Yuxin Huang. The purpose of the project is to estimate the loss in life expectancy and crude probability of death using full Bayesian flexible parametric relative survival spatial model. The paper uses a publicly available simulated datasets Date: 2023-03-31 Created by: Yuliya Leontyeva, PhD student at MEB Questions / comments regarding Stata code should be addressed yo Yuliya Leontyeva email: yuliya.leontyeva@ki.se Questions / comments regarding R code should be addressed Yuxin Huang email: yuxin.huang@hdr.qut.edu.au -------------------------------------------------------------- This document provides explanations regarding the folders included on GitHub -------------------------------------------------------------- FOLDERS: 1. Data This folder includes: - cancer.dta - contains simulated data to represent a hypothetical gender-specific cancer Data columns: cancer.txt (15051 records) ==================================================================================== id Unique identifier for each case. sex All values are 2 (one gender). year Year of diagnosis. Ranges from 1997 to 2007. site10group All values are 1 (hypothetical cancer). dx_date Date of diagnosis (DDMMMYYYY). dth_date Date of death (DDMMMYYYY). age Age at diagnosis (years). bagegroup Broad age group at diagnosis (1=0-49 years, 2=50-69 years, 3=70-89 years). Missing means age was 90+ years. grid Represents the geographical area of residence at diagnosis (values 1 to 478). fu_date Date of censoring (31Dec2007) or date of death (DDMMMYYYY). exit Same as fu_date (DDMMMYYYY). - pop_dths.txt - contains simulated data to represent hypothetical population mortality files Data columns: pop_dths.txt (99902 records) ===================================================================================== year Ranges from 1997 to 2007. sex All values are 2 (one gender). agegroup Values from 1 to 19 representing 5-year age groups (0-4,5-9...,90+). grid Represents the geographical area of residence at diagnosis (values 1 to 478). count Number of deaths (all causes). pop Population size. - model.txt - a file, which contains the likelihood of the FPRM used in the analysis. It contains also all prior distributions for all parameters in the model - 1259030002_sla06aaust_shape - zip file dowloaded from Australian Statistiska bureur (archive) Data columns: (478 records) ==================================================================================== _ID_orig Unique identifier for SLA _CX_orig x-coordinate of SLA _CY_orig y-coordinate of SLA STATE_CODE_orig State code. For all recordes it is 3 SLA_CODE06_orig SLA_CODE SLA_NAME06_orig SLA_NAME SLA_5DIGIT_orig 5-digit code for SLA grid_orig Order number of SLA from 1-478 adj_grid_orig The number of neigbours for each SLA - adj_matrix - contains the index of SLA and adjacent areas for each SLA. 18 SLAs without neigbours were assigned to the nearest SLAs by geographical proximity and using relevant locality-specific information. Number of observations = 2724 2. Programs This folder includes Stata & R programs In Stata folder there are the following do files: - set_winbugs - Set WinBugs on your computer - master.do - the master file where all the below-mentioned do files are run in the order - adjm - Create weignening matrix W based on the common border and corner - popmort.do - creates population mortality rates file in Stata format, where the information from SLAs neigbours is used - winbugs - runs Bayesian analysis in WinBugs and saves the estimates - lle_est - obtains estimates for the Loss in Life Expectancy - cr_est - obtains estimates for the crude mortality
StocholmJulia/Bayesian_spatial_estimates
This is a collaborative work of Yuliya Leontyeva and Yuxin Huang
Stata