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debug_script.R
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debug_script.R
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library(tidyverse)
library(lubridate)
cohort_any_acute_covid_recorded <- read_csv("output/input_any_acute_covid_pri_care.csv",
col_types = cols(
acute_diag_dat = col_date(format = "%Y-%m-%d"),
advice_given = col_date(format = "%Y-%m-%d"),
interpreter_needed = col_date(format = "%Y-%m-%d"),
interpreter_booked = col_date(format = "%Y-%m-%d"),
age_at_diag = col_double(),
prac_id = col_double(),
prac_msoa = col_character(),
sex = col_character(),
msoa = col_character(),
imd = col_character(),
age_group = col_character(),
ethnicity = col_double(),
patient_id = col_double()),
na = c("", "NA", "0"))
cohort_ongoing_or_post_covid <- read_csv('output/input_ongoing_post_covid.csv',
col_types = cols(
pc_or_oc_diag_dat = col_date(format = "%Y-%m-%d"),
diag_ongoing_covid = col_date(format = "%Y-%m-%d"),
diag_post_covid = col_date(format = "%Y-%m-%d"),
diagnostic_bloods = col_date(format = "%Y-%m-%d"),
diagnostic_sit_stand = col_date(format = "%Y-%m-%d"),
diagnostic_chest_xray = col_date(format = "%Y-%m-%d"),
referral_paed = col_date(format = "%Y-%m-%d"),
referral_psych = col_date(format = "%Y-%m-%d"),
referral_psych_iapt = col_date(format = "%Y-%m-%d"),
referral_respiratory = col_date(format = "%Y-%m-%d"),
referral_cardiology = col_date(format = "%Y-%m-%d"),
referral_pain = col_date(format = "%Y-%m-%d"),
referral_gastro = col_date(format = "%Y-%m-%d"),
referral_endocrinology = col_date(format = "%Y-%m-%d"),
referral_neurology = col_date(format = "%Y-%m-%d"),
referral_rheumatology = col_date(format = "%Y-%m-%d"),
referral_dermatology = col_date(format = "%Y-%m-%d"),
referral_ent = col_date(format = "%Y-%m-%d"),
referral_inf_diseases = col_date(format = "%Y-%m-%d"),
referral_pc_clinic = col_date(format = "%Y-%m-%d"),
referral_pc_clinic_counts = col_number(),
#referral_social_worker = col_date(format = "%Y-%m-%d"),
risk_of_self_harm = col_date(format = "%Y-%m-%d"),
mild_anxiety_or_depression = col_date(format = "%Y-%m-%d"),
psych_referral = col_date(format = "%Y-%m-%d"),
psych_referral_iapt = col_date(format = "%Y-%m-%d"),
discussion_about_daily_living = col_date(format = "%Y-%m-%d"),
#self_care_advise_or_support = col_date(format = "%Y-%m-%d"),
primary_care_managment = col_date(format = "%Y-%m-%d"),
community_care = col_date(format = "%Y-%m-%d"),
age_at_diag = col_double(),
prac_id = col_double(),
prac_msoa = col_character(),
diagnostic_bp_test = col_double(),
sex = col_character(),
msoa = col_character(),
imd = col_factor(),
age_group = col_character(),
ethnicity = col_double(),
patient_id = col_double()),
na = c("", "NA", "0"))
cohort_all <- read_csv('output/input_all.csv',
col_types = cols(.default = col_date(),
sex = col_factor(),
msoa = col_factor(),
imd = col_factor(),
age_group = col_factor(),
ethnicity = col_factor(),
patient_id = col_guess())
)
MSOA_Region_Lookup <- read_csv("analysis/MSOA_Region_Lookup.csv")
cohort_any_acute_covid_recorded <- cohort_any_acute_covid_recorded %>%
left_join(MSOA_Region_Lookup,
by = c("msoa" = "MSOA11CD")) %>%
rename("region" = "RGN11NM")
cohort_ongoing_or_post_covid <- cohort_ongoing_or_post_covid %>%
left_join(MSOA_Region_Lookup,
by = c("msoa" = "MSOA11CD")) %>%
rename("region" = "RGN11NM")
cohort_all <- cohort_all %>%
left_join(MSOA_Region_Lookup,
by = c("msoa" = "MSOA11CD")) %>%
rename("region" = "RGN11NM")
debug_all_counts <- cohort_all %>% summarise(across(.fns = ~sum(!is.na(.x))))
debug_all_crosstab <- table(!is.na(cohort_all$diag_any_lc_diag), !is.na(cohort_all$referral_pc_clinic))
write_csv(debug_all_counts, 'output/debug_all_counts.csv')
write.table(debug_all_crosstab, 'output/debug_all_diag_refer_crosstab.csv', sep = ",")
debug_ac_count <- tibble(nrow(cohort_any_acute_covid_recorded))
write_csv(debug_ac_count, 'output/debug_ac_counts.csv')
debug_oc_count <- tibble(nrow(cohort_ongoing_or_post_covid))
write_csv(debug_oc_count, 'output/debug_oc_counts.csv')
debug_referral_count <- cohort_ongoing_or_post_covid %>% summarise(ref_total = sum(referral_pc_clinic_counts, na.rm = TRUE))
write_csv(debug_referral_count, 'output/debug_referral_count.csv')
debug_nuts_1_region <- cohort_all %>% group_by(region) %>% summarise(n = n())
write_csv(debug_nuts_1_region, 'output/debug_nuts_1_region.csv')