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report.R
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report.R
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library(tidyverse)
library(lubridate)
#Compliance ratios from Section 1 of NG188 guidance
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(),
patient_id = col_double()),
na = c("", "NA", "0"))
#generate number of NAs
#debug_ac <- cohort_any_acute_covid_recorded %>% is.na() %>% colSums()
#debug_ac <- map(cohort_any_acute_covid_recorded, class)
debug_ac <- cohort_any_acute_covid_recorded %>% group_by(year(acute_diag_dat)) %>% summarise(n = n())
write.csv(debug_ac, 'output/debug_ac.csv')
Rec_1_1_denom <- nrow(cohort_any_acute_covid_recorded)
Rec_1_1_num <- sum((cohort_any_acute_covid_recorded$advice_given - cohort_any_acute_covid_recorded$acute_diag_dat > 0), na.rm = TRUE)
Rec_1_1_ratio <- Rec_1_1_num / Rec_1_1_denom
Rec_1_8_denom <- cohort_any_acute_covid_recorded %>% filter(interpreter_needed > ymd("20190101")) %>% nrow()
Rec_1_8_num <- cohort_any_acute_covid_recorded %>% filter(interpreter_needed > ymd("20190101"),
interpreter_booked > ymd("20190101")) %>% nrow()
Rec_1_8_ratio <- Rec_1_8_num / Rec_1_8_denom
#Leaving Rec 1_10 until outpatient linkage is carried out
#Compliance ratios from Section 2 of NG188 guidance
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"),
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(),
patient_id = col_double()),
na = c("", "NA", "0"))
#debug_oc <- cohort_ongoing_or_post_covid %>% is.na() %>% colSums()
#debug_oc <- map(cohort_ongoing_or_post_covid, class)
debug_oc <- cohort_ongoing_or_post_covid %>% group_by(year(pc_or_oc_diag_dat)) %>% summarise(n = n())
write.csv(debug_oc, 'output/debug_oc.csv')
Rec_2_4_denom <- nrow(cohort_ongoing_or_post_covid)
Rec_2_4_num <- cohort_ongoing_or_post_covid %>% filter(discussion_about_daily_living > ymd("20190101")) %>% nrow()
Rec_2_4_ratio <- Rec_2_4_num / Rec_2_4_denom
#Compliance ratios from Section 3 of NG188 guidance
#Rec_3_1 abandoned as not sure what 'relevant acute services' ought to be, vagueness as to what
#3 diagnostic tests
Rec_3_4_denom <- Rec_2_4_denom
Rec_3_4_num <- cohort_ongoing_or_post_covid %>% filter(diagnostic_bloods > ymd("20190101")) %>% nrow()
Rec_3_4_ratio <- Rec_3_4_num / Rec_3_4_denom
Rec_3_5_denom <- Rec_2_4_denom
Rec_3_5_num <- cohort_ongoing_or_post_covid %>% filter(diagnostic_sit_stand > ymd("20190101")) %>% nrow()
Rec_3_5_ratio <- Rec_3_5_num / Rec_3_5_denom
Rec_3_6_denom <- Rec_2_4_denom
Rec_3_6_num <- cohort_ongoing_or_post_covid %>% filter(diagnostic_bp_test > 0) %>% nrow()
Rec_3_6_ratio <- Rec_3_6_num / Rec_3_6_denom
Rec_3_7_denom <- Rec_2_4_denom
Rec_3_7_num <- cohort_ongoing_or_post_covid %>% filter(diagnostic_chest_xray > ymd("20190101")) %>% nrow()
Rec_3_7_ratio <- Rec_3_7_num / Rec_3_7_denom
Rec_3_8_denom <- cohort_ongoing_or_post_covid %>% filter(risk_of_self_harm > ymd("20190101")) %>% nrow()
Rec_3_8_num <- cohort_ongoing_or_post_covid %>% filter(risk_of_self_harm > ymd("20190101"),
referral_psych > ymd("20190101")) %>% nrow()
Rec_3_8_ratio <- Rec_3_8_num / Rec_3_8_denom
Rec_3_9_denom <- cohort_ongoing_or_post_covid %>% filter(mild_anxiety_or_depression > ymd("20190101")) %>% nrow()
Rec_3_9_num <- cohort_ongoing_or_post_covid %>% filter(mild_anxiety_or_depression > ymd("20190101"),
referral_psych_iapt > ymd("20190101")) %>% nrow()
Rec_3_9_ratio <- Rec_3_9_num / Rec_3_9_denom
Rec_3_10_denom <- Rec_2_4_denom
Rec_3_10_num <- cohort_ongoing_or_post_covid %>% filter(referral_pc_clinic > ymd("20190101")) %>% nrow()
Rec_3_10_ratio <- Rec_3_10_num / Rec_3_10_denom
#3 referral patterns, self-care, secondary care, treated in primary care
Rec_3_11_denom <- Rec_2_4_denom
Rec_3_11_num_self_management <- cohort_ongoing_or_post_covid %>% filter(self_care_advise_or_support > ymd("20190101")) %>% nrow()
Rec_3_11_num_community_referral <- cohort_ongoing_or_post_covid %>% filter(community_care > ymd("20190101")) %>% nrow()
Rec_3_11_prim_care <- cohort_ongoing_or_post_covid %>% filter(primary_care_managment > ymd("20190101")) %>% nrow()
#other referral destinations - would they go direct from primary care or be cross-referred from PC clinic (or both? - maybe needs thinking about)
#4 long covid rates by practice - need
#5 variation in long covid rates
#variables
#demographic - age, ethnicity, health worker?, socioeconomic deprivation
#comorbidities
rm(cohort_any_acute_covid_recorded, cohort_ongoing_or_post_covid, debug_ac, debug_oc)
mget(ls()) %>% bind_rows() %>% write_csv('output/ratios.csv')