generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
401_redacted_tables_allpts.do
95 lines (81 loc) · 3.37 KB
/
401_redacted_tables_allpts.do
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
version 16
/*==============================================================================
DO FILE NAME: redacted output tables
PROJECT: EIA OpenSAFELY project
DATE: 07/03/2022
AUTHOR: J Galloway / M Russell
adapted from C Rentsch
DESCRIPTION OF FILE: redacted output table
DATASETS USED: main data file
DATASETS CREATED: redacted output table
OTHER OUTPUT: logfiles, printed to folder $Logdir
USER-INSTALLED ADO:
(place .ado file(s) in analysis folder)
==============================================================================*/
**Set filepaths
*global projectdir "C:\Users\k1754142\OneDrive\PhD Project\OpenSAFELY\Github Practice"
*global projectdir "C:\Users\Mark\OneDrive\PhD Project\OpenSAFELY\Github Practice"
global projectdir `c(pwd)'
di "$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/redacted_tables_allpts.log", replace
**Set Ado file path
adopath + "$projectdir/analysis/extra_ados"
set scheme plotplainblind
**Set index dates ===========================================================*/
global year_preceding = "01/04/2018"
global start_date = "01/04/2019"
global appt_date = "01/04/2021"
global end_date = "01/04/2022"
*Descriptive statistics======================================================================*/
**Baseline table for reference population
clear *
save "$projectdir/output/data/table_1_rounded_allpts.dta", replace emptyok
use "$projectdir/output/data/file_eia_allpts.dta", clear
codebook chronic_resp_disease
set type double
codebook chronic_resp_disease
generate double chronic_r_disease = chronic_resp_disease
codebook chronic_r_disease
lab define chronic_r_disease 0 "No" 1 "Yes", modify
lab val chronic_r_disease chronic_r_disease
lab var chronic_r_disease "Chronic resp disease"
foreach var of varlist ckd chronic_liver_disease chronic_r_disease chronic_resp_disease cancer stroke chronic_cardiac_disease diabcatm hypertension smoke bmicat imd ethnicity male agegroup {
preserve
contract `var'
local v : variable label `var'
gen variable = `"`v'"'
decode `var', gen(categories)
egen total_un = total(_freq)
egen non_missing_un=sum(_freq) if categories!="Not Known"
gen missing_un=(total_un-non_missing_un)
drop if categories=="Not Known"
gen count = round(_freq, 5)
gen total = round(total_un, 5)
gen missing = round(missing_un, 5)
gen non_missing = round(non_missing_un, 5)
gen percent = round((count/non_missing)*100, 0.1)
order variable, first
order categories, after(variable)
order count, after(categories)
order percent, after(count)
order total, after(percent)
order missing, after(total)
list variable categories count percent total missing
keep variable categories count percent total missing
append using "$projectdir/output/data/table_1_rounded_allpts.dta"
save "$projectdir/output/data/table_1_rounded_allpts.dta", replace
restore
}
use "$projectdir/output/data/table_1_rounded_allpts.dta", clear
export excel "$projectdir/output/tables/table_1_rounded_allpts.xls", replace keepcellfmt firstrow(variables)
*Output tables as CSVs
import excel "$projectdir/output/tables/table_1_rounded_allpts.xls", clear
export delimited using "$projectdir/output/tables/table_1_rounded_allpts.csv" , novarnames replace
log close