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02b_eth_outcomes_checks_eth5.do
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02b_eth_outcomes_checks_eth5.do
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/*==============================================================================
DO FILE NAME: 02b_outcomes_checks_eth5
PROJECT: Ethnicity and COVID-19
DATE: 14 July 2020
AUTHOR: R Mathur
adapted from A Schultze
DESCRIPTION OF FILE: Produce a table of baseline characteristics, by ethnicity
Generalised to produce same columns as levels of eth5
Output to a textfile for further formatting
DATASETS USED: $Tempdir\analysis_dataset.dta
DATASETS CREATED: None
OTHER OUTPUT: Results in txt: $Tabfigdir\table1.txt
Log file: $Logdir\05_eth_table1_descriptives
USER-INSTALLED ADO:
(place .ado file(s) in analysis folder)
Notes:
Table 1 population is people who are alive on indexdate
It does not exclude anyone who experienced any outcome prior to indexdate
change the analysis_dataset to exlucde people with any of the following as of Feb 1st 2020:
COVID identified in primary care
COVID test result via SGSS
A&E admission for COVID-19
ICU admission for COVID-19
==============================================================================*/
global outcomes "tested positivetest hes onscoviddeath ons_noncoviddeath onsdeath"
* Open a log file
capture log close
log using ./logs/02b_outcomes_checks_eth5.log, replace t
/* PROGRAMS TO AUTOMATE TABULATIONS===========================================*/
********************************************************************************
* All below code from K Baskharan
* Generic code to output one row of table
cap prog drop generaterow
program define generaterow
syntax, variable(varname) condition(string)
qui cou
local overalldenom=r(N)
sum `variable' if `variable' `condition'
file write tablecontent (r(max)) _tab
qui cou if `variable' `condition'
local rowdenom = r(N)
local colpct = 100*(r(N)/`overalldenom')
file write tablecontent %9.0gc (`rowdenom') (" (") %3.1f (`colpct') (")") _tab
forvalues i=1/6{
qui cou if eth5 == `i'
local rowdenom = r(N)
qui cou if eth5 == `i' & `variable' `condition'
local pct = 100*(r(N)/`rowdenom')
file write tablecontent %9.0gc (r(N)) (" (") %3.1f (`pct') (")") _tab
}
file write tablecontent _n
end
* Output one row of table for co-morbidities and meds
cap prog drop generaterow2
program define generaterow2
syntax, variable(varname) condition(string)
qui cou
local overalldenom=r(N)
qui cou if `variable' `condition'
local rowdenom = r(N)
local colpct = 100*(r(N)/`overalldenom')
file write tablecontent %9.0gc (`rowdenom') (" (") %3.1f (`colpct') (")") _tab
forvalues i=1/6{
qui cou if eth5 == `i'
local rowdenom = r(N)
qui cou if eth5 == `i' & `variable' `condition'
local pct = 100*(r(N)/`rowdenom')
file write tablecontent %9.0gc (r(N)) (" (") %3.1f (`pct') (")") _tab
}
file write tablecontent _n
end
/* Explanatory Notes
defines a program (SAS macro/R function equivalent), generate row
the syntax row specifies two inputs for the program:
a VARNAME which is your variable
a CONDITION which is a string of some condition you impose
the program qui counts if variable and condition and returns the qui counts
column percentages are then automatically generated
this is then written to the text file 'tablecontent'
the number followed by space, brackets, formatted pct, end bracket and then tab
the format %3.1f specifies length of 3, followed by 1 dp.
*/
********************************************************************************
* Generic code to output one section (varible) within table (calls above)
cap prog drop tabulatevariable
prog define tabulatevariable
syntax, variable(varname) min(real) max(real) [missing]
local lab: variable label `variable'
file write tablecontent ("`lab'") _n
forvalues varlevel = `min'/`max'{
generaterow, variable(`variable') condition("==`varlevel'")
}
if "`missing'"!="" generaterow, variable(`variable') condition("== 12")
end
********************************************************************************
/* Explanatory Notes
defines program tabulate variable
syntax is :
- a VARNAME which you stick in variable
- a numeric minimum
- a numeric maximum
- optional missing option, default value is .
forvalues lowest to highest of the variable, manually set for each var
run the generate row program for the level of the variable
if there is a missing specified, then run the generate row for missing vals
*/
********************************************************************************
* Generic code to qui summarize a continous variable
cap prog drop summarizevariable
prog define summarizevariable
syntax, variable(varname)
local lab: variable label `variable'
file write tablecontent ("`lab'") _n
qui summarize `variable', d
file write tablecontent ("Mean (SD)") _tab
file write tablecontent %3.1f (r(mean)) (" (") %3.1f (r(sd)) (")") _tab
forvalues i=1/6{
qui summarize `variable' if eth5 == `i', d
file write tablecontent %3.1f (r(mean)) (" (") %3.1f (r(sd)) (")") _tab
}
file write tablecontent _n
qui summarize `variable', d
file write tablecontent ("Median (IQR)") _tab
file write tablecontent %3.1f (r(p50)) (" (") %3.1f (r(p25)) ("-") %3.1f (r(p75)) (")") _tab
forvalues i=1/6{
qui summarize `variable' if eth5 == `i', d
file write tablecontent %3.1f (r(p50)) (" (") %3.1f (r(p25)) ("-") %3.1f (r(p75)) (")") _tab
}
file write tablecontent _n
end
/* INVOKE PROGRAMS FOR TABLE 1================================================*/
*Set up output file
cap file close tablecontent
file open tablecontent using ./output/table0_outcomes_eth5.txt, write text replace
file write tablecontent ("Table 0: Outcome qui counts by ethnic group") _n
* eth5 labelled columns
local lab1: label eth5 1
local lab2: label eth5 2
local lab3: label eth5 3
local lab4: label eth5 4
local lab5: label eth5 5
local lab6: label eth5 6
file write tablecontent _tab ("Total") _tab ///
("`lab1'") _tab ///
("`lab2'") _tab ///
("`lab3'") _tab ///
("`lab4'") _tab ///
("`lab5'") _tab ///
("`lab6'") _n
/*STEP 1: NO CARE HOMES*/
use ./output/analysis_dataset.dta, clear
keep if carehome==0
*Denominator
file write tablecontent ("Main population: no care homes") _n
gen byte cons=1
file write tablecontent ("N") _tab
generaterow2, variable(cons) condition("==1")
file write tablecontent _n
*Outcomes
foreach var of global outcomes {
file write tablecontent ("`var'") _tab
generaterow2, variable(`var') condition("==1")
}
*icu outcomes
local p" "any_resp_support_flag" "basic_resp_support_flag" "advanced_resp_support_flag" "
foreach var of local p {
file write tablecontent ("`var'") _tab
generaterow2, variable(`var') condition("==1")
}
/* STEP 2: CAREHOMES*/
use ./output/analysis_dataset.dta, clear
keep if carehome==1
gen byte cons=1
*Denominator
file write tablecontent ("Care home population") _n
file write tablecontent ("N") _tab
generaterow2, variable(cons) condition("==1")
file write tablecontent _n
*Outcomes
foreach var of global outcomes {
file write tablecontent ("`var'") _tab
generaterow2, variable(`var') condition("==1")
}
*icu outcomes
local p" "any_resp_support_flag" "basic_resp_support_flag" "advanced_resp_support_flag" "
foreach var of local p {
file write tablecontent ("`var'") _tab
generaterow2, variable(`var') condition("==1")
}
file close tablecontent
* Close log file
log close