generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
300_box_plots.do
289 lines (219 loc) · 14.9 KB
/
300_box_plots.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
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
version 16
/*==============================================================================
DO FILE NAME: Box plots
PROJECT: EIA OpenSAFELY project
DATE: 07/03/2022
AUTHOR: J Galloway / M Russell
adapted from C Rentsch
DESCRIPTION OF FILE: Box plots
DATASETS USED: main data file
DATASETS CREATED: Box plots and outputs
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 "$projectdir/output/figures"
capture mkdir "$projectdir/output/tables"
global logdir "$projectdir/logs"
di "$logdir"
**Open a log file
cap log close
log using "$logdir/box_plots.log", replace
**Set Ado file path
adopath + "$projectdir/analysis/extra_ados"
**Use cleaned data from previous step
use "$projectdir/output/data/file_eia_all.dta", clear
set scheme plotplainblind
/*GP referral performance by region, all years===========================================================================*/
***Restrict all analyses below to patients with rheum appt, GP appt and 12m follow-up and registration
keep if has_12m_post_appt==1
preserve
gen qs1_0 =1 if time_gp_rheum_ref_appt<=3 & time_gp_rheum_ref_appt!=.
recode qs1_0 .=0 if time_gp_rheum_ref_appt!=.
gen qs1_1 =1 if time_gp_rheum_ref_appt>3 & time_gp_rheum_ref_appt<=7 & time_gp_rheum_ref_appt!=.
recode qs1_1 .=0 if time_gp_rheum_ref_appt!=.
gen qs1_2 = 1 if time_gp_rheum_ref_appt>7 & time_gp_rheum_ref_appt!=.
recode qs1_2 .=0 if time_gp_rheum_ref_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs1_0 (mean) qs1_1 (mean) qs1_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 days" 2 "Within 7 days" 3 "More than 7 days")) title("Time to rheumatology referral") name(regional_qs1_bar, replace)
graph export "$projectdir/output/figures/regional_qs1_bar_overall.svg", replace
restore
/*GP referral performance by region, Apr 2019 to Apr 2020===========================================================================*/
preserve
keep if appt_year==1
gen qs1_0 =1 if time_gp_rheum_ref_appt<=3 & time_gp_rheum_ref_appt!=.
recode qs1_0 .=0 if time_gp_rheum_ref_appt!=.
gen qs1_1 =1 if time_gp_rheum_ref_appt>3 & time_gp_rheum_ref_appt<=7 & time_gp_rheum_ref_appt!=.
recode qs1_1 .=0 if time_gp_rheum_ref_appt!=.
gen qs1_2 = 1 if time_gp_rheum_ref_appt>7 & time_gp_rheum_ref_appt!=.
recode qs1_2 .=0 if time_gp_rheum_ref_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs1_0 (mean) qs1_1 (mean) qs1_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 days" 2 "Within 7 days" 3 "More than 7 days")) title("Time to rheumatology referral") name(regional_qs1_bar, replace)
graph export "$projectdir/output/figures/regional_qs1_bar_2019.svg", replace
restore
/*GP referral performance by region, Apr 2020 to Apr 2021===========================================================================*/
preserve
keep if appt_year==2
gen qs1_0 =1 if time_gp_rheum_ref_appt<=3 & time_gp_rheum_ref_appt!=.
recode qs1_0 .=0 if time_gp_rheum_ref_appt!=.
gen qs1_1 =1 if time_gp_rheum_ref_appt>3 & time_gp_rheum_ref_appt<=7 & time_gp_rheum_ref_appt!=.
recode qs1_1 .=0 if time_gp_rheum_ref_appt!=.
gen qs1_2 = 1 if time_gp_rheum_ref_appt>7 & time_gp_rheum_ref_appt!=.
recode qs1_2 .=0 if time_gp_rheum_ref_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs1_0 (mean) qs1_1 (mean) qs1_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 days" 2 "Within 7 days" 3 "More than 7 days")) title("Time to rheumatology referral") name(regional_qs1_bar, replace)
graph export "$projectdir/output/figures/regional_qs1_bar_2020.svg", replace
restore
/*
*Regional GP referral performance
preserve
graph hbox qs1, over(nuts_region) blabel(bar, color(black) position(inside) format(%9.4f)) title("Quality Standard 1: GP referral within 3 days") ytitle(Proportion meeting standard) saving("$projectdir/output/figures/regional_gpref_box.gph", replace) name(regional_gpref_box, replace)
restore
*/
*Rheum ref to appt performance by region, all years==========================================================================*/
preserve
gen qs2_0 =1 if time_ref_rheum_appt<=21 & time_ref_rheum_appt!=.
recode qs2_0 .=0 if time_ref_rheum_appt!=.
gen qs2_1 =1 if time_ref_rheum_appt>21 & time_ref_rheum_appt<=42 & time_ref_rheum_appt!=.
recode qs2_1 .=0 if time_ref_rheum_appt!=.
gen qs2_2 = 1 if time_ref_rheum_appt>42 & time_ref_rheum_appt!=.
recode qs2_2 .=0 if time_ref_rheum_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs2_0 (mean) qs2_1 (mean) qs2_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 weeks" 2 "Within 6 weeks" 3 "More than 6 weeks")) title("Time from rheumatology referral to assessment") name(regional_qs2_bar, replace)
graph export "$projectdir/output/figures/regional_qs2_bar_overall.svg", replace
restore
*Rheum ref to appt performance by region, Apr 2019 to Apr 2020==========================================================================*/
preserve
keep if appt_year==1
gen qs2_0 =1 if time_ref_rheum_appt<=21 & time_ref_rheum_appt!=.
recode qs2_0 .=0 if time_ref_rheum_appt!=.
gen qs2_1 =1 if time_ref_rheum_appt>21 & time_ref_rheum_appt<=42 & time_ref_rheum_appt!=.
recode qs2_1 .=0 if time_ref_rheum_appt!=.
gen qs2_2 = 1 if time_ref_rheum_appt>42 & time_ref_rheum_appt!=.
recode qs2_2 .=0 if time_ref_rheum_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs2_0 (mean) qs2_1 (mean) qs2_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 weeks" 2 "Within 6 weeks" 3 "More than 6 weeks")) title("Time from rheumatology referral to assessment") name(regional_qs2_bar, replace)
graph export "$projectdir/output/figures/regional_qs2_bar_2019.svg", replace
restore
*Rheum ref to appt performance by region, Apr 2020 to Apr 2021==========================================================================*/
preserve
keep if appt_year==2
gen qs2_0 =1 if time_ref_rheum_appt<=21 & time_ref_rheum_appt!=.
recode qs2_0 .=0 if time_ref_rheum_appt!=.
gen qs2_1 =1 if time_ref_rheum_appt>21 & time_ref_rheum_appt<=42 & time_ref_rheum_appt!=.
recode qs2_1 .=0 if time_ref_rheum_appt!=.
gen qs2_2 = 1 if time_ref_rheum_appt>42 & time_ref_rheum_appt!=.
recode qs2_2 .=0 if time_ref_rheum_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs2_0 (mean) qs2_1 (mean) qs2_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 weeks" 2 "Within 6 weeks" 3 "More than 6 weeks")) title("Time from rheumatology referral to assessment") name(regional_qs2_bar, replace)
graph export "$projectdir/output/figures/regional_qs2_bar_2020.svg", replace
restore
*Last GP to rheum appt performance by region, all years==========================================================================*/
preserve
gen qs2_0 =1 if time_gp_rheum_appt<=21 & time_gp_rheum_appt!=.
recode qs2_0 .=0 if time_gp_rheum_appt!=.
gen qs2_1 =1 if time_gp_rheum_appt>21 & time_gp_rheum_appt<=42 & time_gp_rheum_appt!=.
recode qs2_1 .=0 if time_gp_rheum_appt!=.
gen qs2_2 = 1 if time_gp_rheum_appt>42 & time_gp_rheum_appt!=.
recode qs2_2 .=0 if time_gp_rheum_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs2_0 (mean) qs2_1 (mean) qs2_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 weeks" 2 "Within 6 weeks" 3 "More than 6 weeks")) title("Time from referral to rheumatology assessment, overall") name(regional_qs2_bar_GP, replace)
graph export "$projectdir/output/figures/regional_qs2_bar_GP_overall.svg", replace
restore
//for output checking tables for boxplot - see output/tables/referral_byregion_rounded.csv
*Last GP to rheum appt performance by region, Apr 2019 to Apr 2020==========================================================================*/
preserve
keep if appt_year==1
gen qs2_0 =1 if time_gp_rheum_appt<=21 & time_gp_rheum_appt!=.
recode qs2_0 .=0 if time_gp_rheum_appt!=.
gen qs2_1 =1 if time_gp_rheum_appt>21 & time_gp_rheum_appt<=42 & time_gp_rheum_appt!=.
recode qs2_1 .=0 if time_gp_rheum_appt!=.
gen qs2_2 = 1 if time_gp_rheum_appt>42 & time_gp_rheum_appt!=.
recode qs2_2 .=0 if time_gp_rheum_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs2_0 (mean) qs2_1 (mean) qs2_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 weeks" 2 "Within 6 weeks" 3 "More than 6 weeks")) title("Time from referral to rheumatology assessment, Apr 2019 to Apr 2020") name(regional_qs2_bar_GP, replace)
graph export "$projectdir/output/figures/regional_qs2_bar_GP_2019.svg", replace
restore
//for output checking tables for boxplot - see output/tables/referral_byregion_rounded.csv
*Last GP to rheum appt performance by region, Apr 2020 to Apr 2021==========================================================================*/
preserve
keep if appt_year==2
gen qs2_0 =1 if time_gp_rheum_appt<=21 & time_gp_rheum_appt!=.
recode qs2_0 .=0 if time_gp_rheum_appt!=.
gen qs2_1 =1 if time_gp_rheum_appt>21 & time_gp_rheum_appt<=42 & time_gp_rheum_appt!=.
recode qs2_1 .=0 if time_gp_rheum_appt!=.
gen qs2_2 = 1 if time_gp_rheum_appt>42 & time_gp_rheum_appt!=.
recode qs2_2 .=0 if time_gp_rheum_appt!=.
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) qs2_0 (mean) qs2_1 (mean) qs2_2, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 weeks" 2 "Within 6 weeks" 3 "More than 6 weeks")) title("Time from referral to rheumatology assessment, Apr 2020 to Apr 2021") name(regional_qs2_bar_GP, replace)
graph export "$projectdir/output/figures/regional_qs2_bar_GP_2020.svg", replace
restore
//for output checking tables for boxplot - see output/tables/referral_byregion_rounded.csv
*csDMARD shared care performance by region prescriptions, all years==========================================================================*/
*As above, all patients must have 1) rheum appt 2) 12m+ follow-up after rheum appt 3) 12m+ of registration after appt
**For RA, PsA and Undiff IA patients combined (not including AxSpA)
keep if (ra_code==1 | psa_code==1 | undiff_code==1)
preserve
gen csdmard_0 =1 if time_to_csdmard<=90 & time_to_csdmard!=.
recode csdmard_0 .=0
gen csdmard_1 =1 if time_to_csdmard>90 & time_to_csdmard<=180 & time_to_csdmard!=.
recode csdmard_1 .=0
gen csdmard_2 = 1 if time_to_csdmard>180 & time_to_csdmard<=365 & time_to_csdmard!=.
recode csdmard_2 .=0
gen csdmard_3 = 1 if time_to_csdmard>365 | time_to_csdmard==.
recode csdmard_3 .=0
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) csdmard_0 (mean) csdmard_1 (mean) csdmard_2 (mean) csdmard_3, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 months" 2 "Within 6 months" 3 "Within 12 months" 4 "None within 12 months")) title("Time to first csDMARD in primary care, overall") name(regional_csdmard_bar, replace)
graph export "$projectdir/output/figures/regional_csdmard_bar_overall.svg", replace
//for output checking table for boxplot - see output/tables/drug_byyearandregion_rounded.csv
restore
*csDMARD shared care performance by region prescriptions, Apr 2019 to Apr 2020==========================================================================*/
preserve
keep if appt_year==1
gen csdmard_0 =1 if time_to_csdmard<=90 & time_to_csdmard!=.
recode csdmard_0 .=0
gen csdmard_1 =1 if time_to_csdmard>90 & time_to_csdmard<=180 & time_to_csdmard!=.
recode csdmard_1 .=0
gen csdmard_2 = 1 if time_to_csdmard>180 & time_to_csdmard<=365 & time_to_csdmard!=.
recode csdmard_2 .=0
gen csdmard_3 = 1 if time_to_csdmard>365 | time_to_csdmard==.
recode csdmard_3 .=0
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) csdmard_0 (mean) csdmard_1 (mean) csdmard_2 (mean) csdmard_3, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 months" 2 "Within 6 months" 3 "Within 12 months" 4 "None within 12 months")) title("Time to first csDMARD in primary care, Apr 2019 to Apr 2020") name(regional_csdmard_bar, replace)
graph export "$projectdir/output/figures/regional_csdmard_bar_2019.svg", replace
restore
//for output checking table for boxplot - see output/tables/drug_byyearandregion_rounded.csv
*csDMARD shared care performance by region prescriptions, Apr 2020 to Apr 2021==========================================================================*/
preserve
keep if appt_year==2
gen csdmard_0 =1 if time_to_csdmard<=90 & time_to_csdmard!=.
recode csdmard_0 .=0
gen csdmard_1 =1 if time_to_csdmard>90 & time_to_csdmard<=180 & time_to_csdmard!=.
recode csdmard_1 .=0
gen csdmard_2 = 1 if time_to_csdmard>180 & time_to_csdmard<=365 & time_to_csdmard!=.
recode csdmard_2 .=0
gen csdmard_3 = 1 if time_to_csdmard>365 | time_to_csdmard==.
recode csdmard_3 .=0
expand=2, gen(copy)
replace nuts_region = 0 if copy==1
graph hbar (mean) csdmard_0 (mean) csdmard_1 (mean) csdmard_2 (mean) csdmard_3, over(nuts_region, relabel(1 "National")) stack ytitle(Proportion of patients) ytitle(, size(small)) ylabel(0.0 "0" 0.2 "0.2" 0.4 "0.4" 0.6 "0.6" 0.8 "0.8" 1.0 "1.0") legend(order(1 "Within 3 months" 2 "Within 6 months" 3 "Within 12 months" 4 "None within 12 months")) title("Time to first csDMARD in primary care, Apr 2020 to Apr 2021") name(regional_csdmard_bar, replace)
graph export "$projectdir/output/figures/regional_csdmard_bar_2020.svg", replace
restore
//for output checking table for boxplot - see output/tables/drug_byyearandregion_rounded.csv
log close