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data_long_process.R
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data_long_process.R
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###############################################################################
# What this script does:
# reads covariate data from eligible individuals
# create long (one-row-per-event) datasets for recurring variables
# saves long datasets
###############################################################################
library(tidyverse)
library(glue)
## preliminaries
# import covariates data
data_covs <- readr::read_rds(
here::here("output", "data", "data_covs.rds"))
# import functions ----
source(here::here("analysis", "lib", "data_process_functions.R"))
###############################################################################
## create one-row-per-event datasets
# shielded
data_pr_shielded <- data_covs %>%
select(patient_id,
matches("^shielded\\_\\d+\\_date")) %>%
pivot_longer(
cols = -patient_id,
names_to = c(NA, "shielded_index"),
names_pattern = "^(.*)_(\\d+)_date",
values_to = "date",
values_drop_na = TRUE
) %>%
arrange(patient_id, date)
readr::write_rds(
data_pr_shielded,
here::here("output", "data", "data_long_shielded_dates.rds"),
compress="gz")
###############################################################################
# nonshielded
data_pr_nonshielded <- data_covs %>%
select(patient_id,
matches("^nonshielded\\_\\d+\\_date")) %>%
pivot_longer(
cols = -patient_id,
names_to = c(NA, "nonshielded_index"),
names_pattern = "^(.*)_(\\d+)_date",
values_to = "date",
values_drop_na = TRUE
) %>%
arrange(patient_id, date)
readr::write_rds(
data_pr_nonshielded,
here::here("output", "data", "data_long_nonshielded_dates.rds"),
compress="gz")
###############################################################################
# bmi
data_pr_bmi <- data_covs %>%
select(patient_id,
matches("^bmi\\_\\d+")) %>%
rename_at(vars(contains("date")),
~ str_c("date_", str_extract(.x, "\\d+"))) %>%
pivot_longer(
cols = -patient_id,
names_sep = "_",
names_to = c(".value", "bmi_index"),
values_drop_na = TRUE) %>%
mutate(bmi = fct_case_when(
bmi < 30 | bmi >=100 ~ "Not obese", # this cat includes missing and clinically implausible values
bmi >= 30 & bmi < 35 ~ "Obese I (30-34.9)",
bmi >= 35 & bmi < 40 ~ "Obese II (35-39.9)",
bmi >= 40 & bmi < 100 ~ "Obese III (40+)",
TRUE ~ NA_character_
)) %>%
arrange(patient_id, date)
readr::write_rds(
data_pr_bmi,
here::here("output", "data", "data_long_bmi_dates.rds"),
compress="gz")
###############################################################################
# suspected covid
data_pr_suspected_covid <- data_covs %>%
select(patient_id,
matches("^primary\\_care\\_suspected\\_covid\\_\\d+\\_date")) %>%
pivot_longer(
cols = -patient_id,
names_to = c(NA, "suspected_index"),
names_pattern = "^(.*)_(\\d+)_date",
values_to = "date",
values_drop_na = TRUE
) %>%
arrange(patient_id, date)
readr::write_rds(
data_pr_suspected_covid,
here::here("output", "data", "data_long_pr_suspected_covid_dates.rds"),
compress="gz")
###############################################################################
# probable covid
data_pr_probable_covid <- data_covs %>%
select(patient_id,
matches("^primary\\_care\\_covid\\_case\\_\\d+\\_date")) %>%
pivot_longer(
cols = -patient_id,
names_to = c(NA, "probable_index"),
names_pattern = "^(.*)_(\\d+)_date",
values_to = "date",
values_drop_na = TRUE
) %>%
arrange(patient_id, date)
readr::write_rds(
data_pr_probable_covid,
here::here("output", "data", "data_long_pr_probable_covid_dates.rds"),
compress="gz")
###############################################################################
# positive test
data_postest <- data_covs %>%
select(patient_id,
matches("^positive\\_test\\_\\d+\\_date")) %>%
pivot_longer(
cols = -patient_id,
names_to = c(NA, "postest_index"),
names_pattern = "^(.*)_(\\d+)_date",
values_to = "date",
values_drop_na = TRUE
) %>%
arrange(patient_id, date)
readr::write_rds(
data_postest,
here::here("output", "data", "data_long_postest_dates.rds"),
compress="gz")
###############################################################################
# covid admission
data_covidadmitted <- data_covs %>%
select(patient_id,
matches("^covidadmitted\\_\\d+\\_date")) %>%
pivot_longer(
cols = -patient_id,
names_to = c(NA, "covidadmitted_index"),
names_pattern = "^(.*)_(\\d+)_date",
values_to = "date",
values_drop_na = TRUE
) %>%
arrange(patient_id, date)
readr::write_rds(
data_covidadmitted,
here::here("output", "data", "data_long_covidadmitted_dates.rds"),
compress="gz")
# ###############################################################################
# # hospital admissions
# data_admissions <- data_covs %>%
# select(patient_id,
# matches("^admitted\\_unplanned\\_\\d+\\_date"),
# matches("^discharged\\_unplanned\\_\\d+\\_date")) %>%
# pivot_longer(
# cols = -patient_id,
# names_to = c(".value", "index"),
# names_pattern = "^(.*)_(\\d+)_date",
# values_drop_na = TRUE
# ) %>%
# select(patient_id, index,
# admitted_date=admitted_unplanned,
# discharged_date = discharged_unplanned) %>%
# arrange(patient_id, admitted_date)
#
# readr::write_rds(
# data_admissions,
# here::here("output", "data", "data_long_admission_dates.rds"),
# compress="gz")
#
# ###############################################################################
# # infectious hospital admissions
# data_admissions_infectious <- data_covs %>%
# select(patient_id,
# matches("^admitted\\_unplanned\\_infectious\\_\\d+\\_date"),
# matches("^discharged\\_unplanned\\_infectious\\_\\d+\\_date")) %>%
# pivot_longer(
# cols = -patient_id,
# names_to = c(".value", "index"),
# names_pattern = "^(.*)_(\\d+)_date",
# values_drop_na = TRUE
# ) %>%
# select(patient_id, index,
# admitted_date=admitted_unplanned_infectious,
# discharged_date = discharged_unplanned_infectious) %>%
# arrange(patient_id, admitted_date)
#
# readr::write_rds(
# data_admissions_infectious,
# here::here("output", "data", "data_long_admission_infectious_dates.rds"),
# compress="gz")
#
# ###############################################################################
# # noninfectious hospital admissions
# #remove infectious admissions from all admissions data
# data_admissions_noninfectious <- anti_join(
# data_admissions,
# data_admissions_infectious,
# by = c("patient_id", "admitted_date", "discharged_date")
# )
#
# readr::write_rds(
# data_admissions_noninfectious,
# here::here("output", "data", "data_long_admission_noninfectious_dates.rds"),
# compress="gz")