Baseline data tables

analysis/000_baseline_data_reference.do

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+version 16
+
+/*==============================================================================
+DO FILE NAME:			Incidence graphs
+PROJECT:				OpenSAFELY Disease Incidence project
+DATE: 					23/08/2024
+AUTHOR:					J Galloway / M Russell									
+DESCRIPTION OF FILE:	Baseline data for full cohort
+DATASETS USED:			Dataset definition
+OTHER OUTPUT: 			logfiles, printed to folder $Logdir
+USER-INSTALLED ADO: 	 
+  (place .ado file(s) in analysis folder)						
+==============================================================================*/
+
+*Set filepaths
+*global projectdir "C:\Users\Mark\OneDrive\PhD Project\OpenSAFELY Incidence\disease_incidence"
+*global projectdir "C:\Users\k1754142\OneDrive\PhD Project\OpenSAFELY Incidence\disease_incidence"
+global projectdir `c(pwd)'
+di "$projectdir"
+
+capture mkdir "$projectdir/output/data"
+capture mkdir "$projectdir/output/tables"
+capture mkdir "$projectdir/output/figures"
+
+global logdir "$projectdir/logs"
+di "$logdir"
+
+*Open a log file
+cap log close
+log using "$logdir/baseline_data_reference.log", replace
+
+*Set Ado file path
+adopath + "$projectdir/analysis/extra_ados"
+
+set type double
+
+global start_date = "01/04/2016"
+
+*Import dataset
+import delimited "$projectdir/output/dataset_definition_2016.csv", clear
+
+set scheme plotplainblind
+
+*Create and label variables ===========================================================*/
+
+**Age
+lab var age "Age"
+rename age_band age_band_old
+encode age_band_old, gen(age_band)
+drop age_band_old
+lab var age_band "Age band, years"
+
+label define age_band		1 "0 to 9"  ///
+							2 "10 to 19" ///
+							3 "20 to 29" ///
+							4 "30 to 39" ///
+							5 "40 to 49" ///
+							6 "50 to 59" ///
+							7 "60 to 69" ///
+							8 "70 to 79" ///
+							9 "80 or above", modify
+lab val age_band age_band
+
+**Sex
+gen gender = 1 if sex == "female"
+replace gender = 2 if sex == "male"
+lab var gender "Gender"
+lab define gender 1 "Female" 2 "Male", modify
+lab val gender gender
+tab gender, missing
+keep if gender == 1 | gender == 2
+drop sex
+
+**Ethnicity
+gen ethnicity_n = 1 if ethnicity == "White"
+replace ethnicity_n = 2 if ethnicity == "Asian or Asian British"
+replace ethnicity_n = 3 if ethnicity == "Black or Black British"
+replace ethnicity_n = 4 if ethnicity == "Mixed"
+replace ethnicity_n = 5 if ethnicity == "Chinese or Other Ethnic Groups"
+replace ethnicity_n = 6 if ethnicity == "Unknown"
+
+
+label define ethnicity_n	1 "White"  						///
+							2 "Asian or Asian British"		///
+							3 "Black or Black British"  	///
+							4 "Mixed"						///
+							5 "Chinese or Other Ethnic Groups" ///
+							6 "Unknown", modify
+
+label values ethnicity_n ethnicity_n
+lab var ethnicity_n "Ethnicity"
+tab ethnicity_n, missing
+drop ethnicity
+rename ethnicity_n ethnicity
+
+**IMD
+gen imd = 1 if imd_quintile == "1 (most deprived)"
+replace imd = 2 if imd_quintile == "2"
+replace imd = 3 if imd_quintile == "3"
+replace imd = 4 if imd_quintile == "4"
+replace imd = 5 if imd_quintile == "5 (least deprived)"
+replace imd = 6 if imd_quintile == "Unknown"
+
+label define imd 1 "1 (most deprived)" 2 "2" 3 "3" 4 "4" 5 "5 (least deprived)" 6 "Unknown", modify
+label values imd imd 
+lab var imd "Index of multiple deprivation"
+tab imd, missing
+drop imd_quintile
+
+save "$projectdir/output/data/reference_data_processed.dta", replace
+
+/*Tables================================================================*/
+
+use "$projectdir/output/data/reference_data_processed.dta", clear
+
+**Baseline table for reference population
+preserve
+table1_mc, total(before) onecol nospacelowpercent missing iqrmiddle(",")  ///
+	vars(age contn %5.1f \ ///
+		 age_band cat %5.1f \ ///
+		 gender cat %5.1f \ ///
+		 ethnicity cat %5.1f \ ///
+		 imd cat %5.1f \ ///
+		 )
+restore
+
+**Rounded and redacted baseline table for ref population
+clear *
+save "$projectdir/output/data/reference_table_rounded.dta", replace emptyok
+use "$projectdir/output/data/reference_data_processed.dta", clear
+
+foreach var of varlist imd ethnicity gender age_band  {
+	preserve
+	contract `var'
+	local v : variable label `var' 
+	gen variable = `"`v'"'
+    decode `var', gen(categories)
+	gen count = round(_freq, 5)
+	egen total = total(count)
+	gen percent = round((count/total)*100, 0.1)
+	order total, before(percent)
+	replace percent = . if count<=7
+	replace total = . if count<=7
+	replace count = . if count<=7
+	gen cohort = "All"
+	order cohort, first
+	format percent %14.4f
+	format count total %14.0f
+	list cohort variable categories count total percent
+	keep cohort variable categories count total percent
+	append using "$projectdir/output/data/reference_table_rounded.dta"
+	save "$projectdir/output/data/reference_table_rounded.dta", replace
+	restore
+}
+use "$projectdir/output/data/reference_table_rounded.dta", clear
+export excel "$projectdir/output/tables/reference_table_rounded.xls", replace sheet("Overall") keepcellfmt firstrow(variables)
+
+/*
+**Baseline table for individual diagnoses - tagged to above excel
+use "$projectdir/output/data/reference_data_processed.dta", clear
+
+local index=1
+foreach disease in $diseases {
+	clear *
+	save "$projectdir/output/data/baseline_table_rounded_`disease'.dta", replace emptyok
+	local index = `index' + 16
+
+use "$projectdir/output/data/baseline_data_processed.dta", clear
+
+foreach var of varlist imd ethnicity gender {
+	preserve
+	keep if `disease'==1
+	contract `var'
+	local v : variable label `var' 
+	gen variable = `"`v'"'
+    decode `var', gen(categories)
+	gen count = round(_freq, 5)
+	egen total = total(count)
+	gen percent = round((count/total)*100, 0.1)
+	order total, before(percent)
+	replace percent = . if count<=7
+	replace total = . if count<=7
+	replace count = . if count<=7
+	gen cohort = "`disease'"
+	order cohort, first
+	format percent %14.4f
+	format count total %14.0f
+	list cohort variable categories count total percent
+	keep cohort variable categories count total percent
+	append using "$projectdir/output/data/baseline_table_rounded_`disease'.dta"
+	save "$projectdir/output/data/baseline_table_rounded_`disease'.dta", replace
+	restore
+}
+
+use "$projectdir/output/data/baseline_table_rounded_`disease'", clear
+export excel "$projectdir/output/tables/baseline_table_rounded.xls", sheet("Overall", modify) cell("A`index'") keepcellfmt firstrow(variables)
+}
+*/
+
+*Table of mean age for reference population
+clear *
+save "$projectdir/output/data/reference_mean_age_rounded.dta", replace emptyok
+use "$projectdir/output/data/reference_data_processed.dta", clear
+
+foreach var of varlist age  {
+	preserve
+	collapse (count) count=patient_id (mean) mean_age=age (sd) stdev_age=age
+	gen cohort = "All"
+	rename *count freq
+	gen count = round(freq, 5)
+	replace stdev_age = . if count<=7
+	replace mean_age = . if count<=7
+	replace count = . if count<=7
+	order count, first
+	order cohort, first
+	format mean_age stdev_age %14.4f
+	format count %14.0f
+	list cohort count mean_age stdev_age
+	keep cohort count mean_age stdev_age
+	append using "$projectdir/output/data/reference_mean_age_rounded.dta"
+	save "$projectdir/output/data/reference_mean_age_rounded.dta", replace
+	restore
+}
+use "$projectdir/output/data/reference_mean_age_rounded.dta", clear
+export excel "$projectdir/output/tables/reference_mean_age_rounded.xls", replace sheet("Overall") keepcellfmt firstrow(variables)
+
+/*		 
+**Table of mean age at diagnosis, by disease - tagged to the above
+use "$projectdir/output/data/baseline_data_processed.dta", clear
+
+foreach disease in $diseases {
+	preserve
+	keep if `disease'==1
+	collapse (count) count=`disease' (mean) mean_age=`disease'_age (sd) stdev_age=`disease'_age
+	gen cohort ="`disease'"
+	rename *count freq
+	gen count = round(freq, 5)
+	gen countstr = string(count)
+	replace stdev_age = . if count<=7
+	replace mean_age = . if count<=7
+	replace count = . if count<=7
+	order count, first
+	order cohort, first
+	format mean_age stdev_age %14.4f
+	format count %14.0f
+	list cohort count mean_age stdev_age
+	keep cohort count mean_age stdev_age
+	append using "$projectdir/output/data/table_mean_age_rounded.dta"
+	save "$projectdir/output/data/table_mean_age_rounded.dta", replace	
+	restore
+}	
+
+use "$projectdir/output/data/table_mean_age_rounded.dta", clear
+export excel "$projectdir/output/tables/table_mean_age_rounded.xls", replace keepcellfmt firstrow(variables)
+*/
+
+***Output tables as CSVs		 
+import excel "$projectdir/output/tables/reference_table_rounded.xls", clear
+export delimited using "$projectdir/output/tables/reference_table_rounded.csv", novarnames  replace
+
+import excel "$projectdir/output/tables/reference_mean_age_rounded.xls", clear
+export delimited using "$projectdir/output/tables/reference_mean_age_rounded.csv", novarnames  replace	
+
+/*Graphs================================================================*/
+
+use "$projectdir/output/data/baseline_data_processed.dta", clear
+
+*Graph of (count) diagnoses by month, by disease
+foreach disease in $diseases {
+	preserve
+	keep if `disease'==1 //would need to remove this if calculating incidence
+	collapse (count) total_diag_un=`disease', by(`disease'_moyear) 
+	gen total_diag = round(total_diag_un, 5)
+	drop total_diag_un
+
+	outsheet * using "$projectdir/output/tables/incidence_count_`disease'.csv" , comma replace
+	export delimited using "$projectdir/output/tables/incidence_count_`disease'.csv", datafmt replace
+
+	**Label diseases
+	local dis_full = strproper(subinstr("`disease'", "_", " ",.)) 
+	if "`dis_full'" == "Rheumatoid" local dis_full "Rheumatoid Arthritis"
+	if "`dis_full'" == "Copd" local dis_full "COPD"
+	if "`dis_full'" == "Crohns Disease" local dis_full "Crohn's Disease"
+	if "`dis_full'" == "Dm Type2" local dis_full "Type 2 Diabetes Mellitus"
+	if "`dis_full'" == "Chd" local dis_full "Coronary Heart Disease"
+	if "`dis_full'" == "Ckd" local dis_full "Chronic Kidney Disease"
+	if "`dis_full'" == "Coeliac" local dis_full "Coeliac Disease"
+	if "`dis_full'" == "Pmr" local dis_full "Polymyalgia Rheumatica"
+
+	twoway connected total_diag `disease'_moyear, ytitle("Monthly count of diagnoses", size(med)) color(gold%35) msymbol(circle) lstyle(solid) lcolor(gold) ylabel(, nogrid labsize(small)) xtitle("Date of diagnosis", size(medium) margin(medsmall)) xlabel(671 "2016" 683 "2017" 695 "2018" 707 "2019" 719 "2020" 731 "2021" 743 "2022" 755 "2023" 767 "2024" 779 "2025", nogrid labsize(small)) xline(722) title("`dis_full'", size(medium) margin(b=2)) name(`disease'_count, replace) saving("$projectdir/output/figures/count_inc_`disease'.gph", replace)
+		graph export "$projectdir/output/figures/count_inc_`disease'.svg", replace
+
+	restore
+}
+
+log close