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asthma_other.R
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asthma_other.R
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#### asthma_other ####
#### This is not a final list, it is just used as a lookup when read codes or terms are missing.
# Description: read codes corresponding to asthma that are not included in:
# asthma_review, RCGP3Q, asthma_plan, exacerbation, emergency
# cat1: asthma_other
# cat2: NA; asthma_control_step; trigger; health education
# score: NA
source('setup.R')
asthma_V3 <- read_csv("lists_in/OpenSafely/opensafely-asthma-diagnosis-2020-04-15.csv") %>%
filter(CTV3Source == 'CTV3Map_Code_Only' |
CTV3Source == 'CTV3Map_Code_And_Term') %>%
select(read_code = CTV3ID, read_term = CTV3PreferredTermDesc) %>%
mutate_at('read_code', list(~ str_extract(., pattern = '^.{5}'))) %>%
mutate(cat1 = 'asthma_other',
cat2 = NA_character_) %>%
distinct()
CPRD_asthma <- read_cprd('asthma') %>%
mutate(cat1 = 'asthma_other',
cat2 = NA_character_)
asthma_other <- bind_rows(asthma_V3, CPRD_asthma) %>%
add_row(read_code = '38DL.',
read_term = 'Asthma control test') %>%
add_row(read_code = '679J.',
read_term = 'Health education - asthma') %>%
add_row(read_code = '1789.',
read_term = 'Asthma trigger - respiratory infection') %>%
add_row(read_code = '1788.',
read_term = 'Asthma trigger - cold air') %>%
add_row(read_code = '178B.',
read_term = 'Asthma trigger - exercise') %>%
add_row(read_code = 'XaIww',
read_term = 'Asthma trigger') %>%
add_row(read_code = '178..',
read_term = 'Asthma trigger') %>%
add_row(read_code = '1781.',
read_term = 'Asthma trigger - pollen') %>%
add_row(read_code = '1787.',
read_term = 'Asthma trigger - seasonal') %>%
add_row(read_code = '1786.',
read_term = 'Asthma trigger - animals') %>%
add_row(read_code = '178A.',
read_term = 'Asthma trigger - airborne dust') %>%
add_row(read_code = 'XaIer',
read_term = 'Asthma follow-up') %>%
add_row(read_code = '1785.',
read_term = 'Asthma trigger - damp') %>%
add_row(read_code = '1784.',
read_term = 'Asthma trigger - emotion') %>%
add_row(read_code = '663j.',
read_term = 'Asthma - currently active') %>%
add_row(read_code = '1783.',
read_term = 'Asthma trigger - warm air') %>%
add_row(read_code = '1782.',
read_term = 'Asthma trigger - tobacco smoke') %>%
anti_join(read_csv('lists_out/asthma_review.csv') %>%
rename(read_code = `Read code`),
by = 'read_code') %>%
anti_join(read_csv('lists_out/asthma_plan.csv') %>%
rename(read_code = `Read code`), by = 'read_code') %>%
anti_join(read_csv('lists_out/RCP3Q.csv') %>%
rename(read_code = `Read code`), by = 'read_code') %>%
anti_join(read_csv('lists_out/exacerbation.csv') %>%
rename(read_code = `Read code`), by = 'read_code') %>%
anti_join(read_csv('lists_out/emergency.csv') %>%
rename(read_code = `Read code`), by = 'read_code') %>%
# get rid of 'asthma resolved'
filter(!(read_term %in% 'Asthma resolved')) %>%
# tidy up duplicate read_code with different read_term
mutate_at('read_term', list(~ case_when(read_code %in% 'H330.' ~ 'Extrinsic (atopic) asthma',
read_code %in% 'H3300' ~ 'Extrinsic asthma without status asthmaticus',
read_code %in% 'H331.' ~ 'Intrinsic asthma',
read_code %in% 'H33zz' ~ 'Asthma NOS',
. %in% 'Exercise induced asthma' ~ 'Exercise-induced asthma',
. %in% 'Aspirin induced asthma' ~ 'Aspirin-induced asthma',
. %in% 'Late onset asthma' ~ 'Late-onset asthma',
TRUE~ .))) %>%
mutate_at('cat2', list(~ case_when(str_detect(read_term, 'Asthma control step') ~ 'asthma_control_step',
str_detect(read_term, 'trigger') ~ 'trigger',
str_detect(read_term, 'Health education') ~ 'health_education',
TRUE ~ NA_character_))) %>%
mutate(cat1 = 'asthma_other',
score = NA_real_) %>%
select(read_code, read_term) %>%
distinct()
# check for duplicates in read_code
asthma_other$read_code[duplicated(asthma_other$read_code)]
# sort duplicates
asthma_other <- asthma_other %>%
mutate_at('read_term', list(~ case_when(read_code %in% 'H33z.' ~'Asthma unspecified',
read_code %in% 'H33..' ~ 'Asthma',
TRUE ~ .))) %>%
mutate_at('read_term', tolower) %>%
select(read_code, read_term) %>%
distinct()
# make sure all Read codes are 5 characters and fix if not
asthma_other %>%
filter(str_length(read_code)<5)
asthma_other <- asthma_other %>%
mutate_at('read_code', list(~ str_pad(., width=5, side='right', pad='.')))
write_csv(asthma_other, path = 'lists_out/asthma_other.csv')