generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
dummy_data.R
276 lines (261 loc) · 9.84 KB
/
dummy_data.R
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
######################################
# This script:
# - creates dummy data for study_definition_vax.py
######################################
library(tidyverse)
library(lubridate)
library(glue)
source(here::here("analysis", "lib", "dummy_data_functions.R"))
# input_vax <- arrow::read_feather(
# here::here("output", "input_vax.feather")
# )
set.seed(5476)
# date vars
# set these to have occured ever during lifetime
date_vars_ever <- c("chronic_cardiac_disease_date",
"heart_failure_date",
"other_heart_disease_date",
"diabetes_date",
"dialysis_date",
"chronic_liver_disease_date",
"current_copd_date",
"ld_inc_ds_and_cp_date",
"cystic_fibrosis_date",
"other_respiratory_date",
"lung_cancer_date",
"haematological_cancer_date",
"cancer_excl_lung_and_haem_date",
"chemo_or_radio_date",
"solid_organ_transplantation_date",
"bone_marrow_transplant_date",
"sickle_cell_disease_date",
"permanant_immunosuppression_date",
"temporary_immunosuppression_date",
"asplenia_date",
"dmards_date",
"dementia_date",
"other_neuro_conditions_date",
"psychosis_schiz_bipolar_date")
# set these to have occured since start of pandemic
date_vars_recent <- c("positive_test_0_date",
"primary_care_covid_case_0_date",
"primary_care_suspected_covid_0_date",
"covidadmitted_0_date",
"death_date",
"longres_date",
"endoflife_date",
"midazolam_date",
"coviddeath_date",
"dereg_date")
jcvi_group_patterns <- readr::read_csv(here::here("output", "lib", "jcvi_groups.csv")) %>%
mutate(across(definition, ~str_extract(.x, "age_. >=\\d{2}"))) %>%
# add dummy conditions for groups 1 and 6, as longres and atrisk data not available here (done correctly in real data)
mutate(across(definition, ~case_when(group=="01" ~ "age_1 >=85",
group=="06" ~ "age_1 >=62",
!is.na(.x) ~ .x,
TRUE ~ "TRUE")))
# conditions for eligibility dates
elig_date_patterns <- readr::read_csv(here::here("output", "lib", "elig_dates.csv")) %>%
mutate(across(description, ~str_replace_all(.x, "p=", "p=="))) %>%
mutate(across(description, ~str_replace_all(.x, "OR", "|"))) %>%
mutate(across(description, ~str_replace_all(.x, "AND", "&"))) %>%
mutate(across(description, ~str_replace_all(.x, "DEFAULT", "TRUE")))
dummy_data_elig <- tibble(patient_id = 1:n) %>%
mutate(age_1 = as.integer(runif(nrow(.), 16, 90), 0),
age_2 = age_1,
imd_0 = sample(
x = seq(100L,32100L,100L),
size = n,
replace = TRUE)) %>%
var_category(sex, categories = c("F", "M")) %>%
var_category(ethnicity_6,
categories = c(as.character(1:5), NA_character_),
ratios = c(rep(0.99/5,5), 0.01)) %>%
var_category(ethnicity_6_sus,
categories = c(as.character(1:5), NA_character_),
ratios = c(rep(0.99/5,5), 0.01)) %>%
var_category(region_0, categories = regions$region, ratios = regions$ratio) %>%
# binary vars for exclusion criteria
mutate(hscworker = rbernoulli(n = nrow(.), p=0.01)) %>%
# jcvi_group
var_category(
name = jcvi_group,
categories = jcvi_group_patterns$group,
conditions = jcvi_group_patterns$definition
) %>%
# elig_date
var_category(
name = elig_date,
categories = elig_date_patterns$date,
conditions = elig_date_patterns$description)
# fix vaccine dates so that they have roughly correct distribution
dummy_data_vax <- dummy_data_elig %>%
mutate(
covid_vax_pfizer_1_date = as.Date(elig_date) + days(round(rnorm(nrow(.), mean = 10, sd = 3))),
covid_vax_az_1_date = as.Date(elig_date) + days(round(rnorm(nrow(.), mean = 10, sd = 3))),
covid_vax_moderna_1_date = as.Date(elig_date) + days(round(rnorm(nrow(.), mean = 10, sd = 3)))) %>%
mutate(
vaccine_1_type = sample(
x = c("pfizer", "az", "moderna", "none"),
size = nrow(.),
replace = TRUE,
prob = c(0.4, 0.4, 0.1, 0.1)
),
missing_pfizer_2 = rbernoulli(nrow(.), p=0.05),
missing_az_2 = rbernoulli(nrow(.), p=0.05),
missing_moderna_2 = rbernoulli(nrow(.), p=0.05),
missing_pfizer_3 = rbernoulli(nrow(.), p=0.9),
missing_az_3 = rbernoulli(nrow(.), p=0.9),
missing_moderna_3 = rbernoulli(nrow(.), p=0.9)
) %>%
mutate(across(covid_vax_pfizer_1_date,
~if_else(
vaccine_1_type %in% "pfizer",
.x,
NA_Date_))) %>%
mutate(across(covid_vax_az_1_date,
~if_else(
vaccine_1_type %in% "az",
.x,
NA_Date_))) %>%
mutate(across(covid_vax_moderna_1_date,
~if_else(
vaccine_1_type %in% "moderna",
.x,
NA_Date_))) %>%
mutate(across(matches("covid_vax_\\w+_1_date"),
~ if_else(
vaccine_1_type %in% "none",
NA_Date_,
.x
))) %>%
mutate(
covid_vax_pfizer_2_date = covid_vax_pfizer_1_date + days(round(rnorm(nrow(.), mean = 10*7, sd = 3))),
covid_vax_az_2_date = covid_vax_az_1_date + days(round(rnorm(nrow(.), mean = 10*7, sd = 3))),
covid_vax_moderna_2_date = covid_vax_moderna_1_date + days(round(rnorm(nrow(.), mean = 10*7, sd = 3))),
) %>%
mutate(across(covid_vax_pfizer_2_date,
~if_else(
missing_pfizer_2,
NA_Date_,
.x))) %>%
mutate(across(covid_vax_az_2_date,
~if_else(
missing_az_2,
NA_Date_,
.x))) %>%
mutate(across(covid_vax_moderna_2_date,
~if_else(
missing_moderna_2,
NA_Date_,
.x))) %>%
mutate(
covid_vax_pfizer_3_date = covid_vax_pfizer_2_date + days(round(rnorm(nrow(.), mean = 6*4*7, sd = 7))),
covid_vax_az_3_date = covid_vax_az_2_date + days(round(rnorm(nrow(.), mean = 6*4*7, sd = 7))),
covid_vax_moderna_3_date = covid_vax_moderna_2_date + days(round(rnorm(nrow(.), mean = 6*4*7, sd = 7))),
) %>%
select(-starts_with("missing"), -vaccine_1_type)
### from dummy_data_covs
dummy_data_covs <- dummy_data_vax %>%
# indicator for flu vaccine in past 5 years
# mutate(flu_vaccine = rbernoulli(n = nrow(.), p=0.3)) %>%
# date vars ever
bind_cols(
pmap(
list(a = date_vars_ever,
b = rep(0.2, length(date_vars_ever))),
function(a,b)
var_date(
.data = .,
name = !! a,
incidence = b,
keep_vars = FALSE
))) %>%
# date vars recent
bind_cols(
pmap(
list(a = date_vars_recent,
b = rep(0.2, length(date_vars_recent))),
function(a,b)
var_date(
.data = .,
name = !! a,
incidence = b,
earliest="2020-11-01",
latest="2021-12-31",
keep_vars = FALSE
))) %>%
# add death_date if coviddeath_date
mutate(across(death_date,
~if_else(
!is.na(coviddeath_date),
coviddeath_date,
NA_Date_))) %>%
# add recurrent bmi vars
bind_cols(vars_bmi_recurrent(.data = ., r = study_parameters$recur_bmi)) %>%
# add recurrent shielded vars
bind_cols(
var_date_recurrent(
.data = .,
name_string = "shielded",
incidence = 0.2,
r = study_parameters$recur_shielded)) %>%
bind_cols(
var_date_recurrent(
.data = .,
name_string = "nonshielded",
incidence = 0.1,
r = study_parameters$recur_shielded)) %>%
# add recurrent hospital admission vars
# bind_cols(
# var_date_recurrent(
# .data = .,
# name_string = "admitted_unplanned",
# incidence = 0.1,
# r = study_parameters$recur_admissions)) %>%
# bind_cols(
# var_date_recurrent(
# .data = .,
# name_string = "admitted_unplanned_infectious",
# incidence = 0.1,
# r = study_parameters$recur_admissions)) %>%
# add dob
mutate(
dob = as.POSIXct(
# floor_date as all 1st of the month as dob YYYY-MM in OpenSAFELY
# then add days(31) to make sure no ages are below 16 because of floor_date
floor_date(as.Date(study_parameters$ref_age_2) - years(age_2) + days(31), unit = "months"))
) %>%
# add efi
# mutate(
# efi = if_else(
# rbernoulli(n = nrow(.), p = 0.99),
# rnorm(n = nrow(.), mean = 0.2, sd = 0.09),
# NA_real_)) %>%
mutate(across(contains("_date"), as.POSIXct)) %>%
mutate(across(ends_with("date"), as.POSIXct)) %>%
mutate(across(c(ethnicity_6, ethnicity_6_sus, jcvi_group, region_0, sex),
as.factor)) %>%
droplevels()
# final dummy data
dummy_data <- dummy_data_covs
arrow::write_feather(dummy_data, here::here("analysis", "dummy_data.feather"))
#
# # checks
# # all names there and the same?
# all(sort(names(dummy_data)) == sort(names(input_vax)))
# # any different types
# classes_input_vax <- sapply(
# sort(names(input_vax)),
# function(x)
# class(input_vax[[x]]))
# classes_dummy_data <- sapply(
# sort(names(dummy_data)),
# function(x)
# class(dummy_data[[x]]))
# classes_match <- sapply(
# names(classes_input_vax),
# function(x)
# all(classes_input_vax[[x]] == classes_dummy_data[[x]]))
#
# sort(names(dummy_data))[!classes_match]