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BMI_median_summary_stats.R
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BMI_median_summary_stats.R
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##########################################################
# Author: Miriam Samuel
# Input: BMI_complete_median.feather
# Output:
# Last modified: 9th March 2022
###########################################################
# >> Read in packages
## packages
library(broom)
library(purrr)
library(dplyr)
library(janitor)
library(tidyverse)
library(here)
library(arrow)
# >> Read in file
BMI_complete_categories <- read_feather (here::here ("output/data", "BMI_complete_median.feather"))
# >> Start analysis
BMI_complete_categories_2 <- BMI_complete_categories
# names(BMI_complete_categories_2)
##### Change all exposure variables to characters to allow appending of summary tables
BMI_complete_categories_2 <- BMI_complete_categories_2 %>%
dplyr::mutate(
sex = as.character(sex),
age_group = as.character(age_group),
ethnic_no_miss = as.character(ethnic_no_miss),
eth_group_16 = as.character(eth_group_16),
imd = as.character(imd),
region = as.character (region),
) %>%
dplyr::mutate(across(starts_with("comorbid_"), as.character))
BMI_complete_categories_2
## Have changed to characters- need to bind the reframed data sets
## Yearly summary statistics of median BMI
median_bmi_all <- BMI_complete_categories_2 %>%
dplyr::group_by(year) %>%
summarise(
average_bmi = median (median_bmi, na.rm = TRUE)) %>%
pivot_wider(names_from = year, values_from = average_bmi)
median_bmi_all <- median_bmi_all %>%
dplyr::mutate(covariate = "all", category = "all")
## Function to calculate average BMI
average_bmi_function <- function(data, var) {
tab1 <- data %>%
dplyr::group_by(year, {{var}}) %>%
summarise(
average_bmi = median(median_bmi, na.rm=TRUE)
) %>%
pivot_wider(names_from = year, values_from = average_bmi)
tab1 %>%
dplyr::rename( "category" = {{var}})
}
median_bmi_age_group <- average_bmi_function(BMI_complete_categories_2, age_group) %>%
dplyr::mutate(covariate="age_group")
median_bmi_imd <- average_bmi_function(BMI_complete_categories_2, imd) %>%
dplyr::mutate(covariate="imd")
median_bmi_sex <- average_bmi_function(BMI_complete_categories_2, sex) %>%
dplyr::mutate(covariate="sex")
median_bmi_region <- average_bmi_function(BMI_complete_categories_2, region) %>%
dplyr::mutate(covariate="region")
median_bmi_ethnic_no_miss <- average_bmi_function(BMI_complete_categories_2, ethnic_no_miss) %>%
dplyr::mutate(covariate="ethnic_no_miss")
median_bmi_eth_group_16 <- average_bmi_function(BMI_complete_categories_2, eth_group_16) %>%
dplyr::mutate(covariate="eth_group_16")
median_bmi_comorbid_learning_disability <- average_bmi_function(BMI_complete_categories_2, comorbid_learning_disability) %>%
dplyr::mutate(covariate="comorbid_learning_disability")
median_bmi_comorbid_depression <- average_bmi_function(BMI_complete_categories_2, comorbid_depression) %>%
dplyr::mutate(covariate="comorbid_depression")
median_bmi_comorbid_dementia <- average_bmi_function(BMI_complete_categories_2, comorbid_dementia) %>%
dplyr::mutate(covariate="comorbid_dementia")
median_bmi_comorbid_psychosis_schiz_bipolar <- average_bmi_function(BMI_complete_categories_2, comorbid_psychosis_schiz_bipolar ) %>%
dplyr::mutate(covariate="comorbid_psychosis_schiz_bipolar ")
median_bmi_comorbid_diabetes_type <- average_bmi_function(BMI_complete_categories_2, comorbid_diabetes_type) %>%
dplyr::mutate(covariate="comorbid_diabetes_type")
median_bmi_comorbid_diabetes_t1 <- average_bmi_function(BMI_complete_categories_2, comorbid_diabetes_t1) %>%
dplyr::mutate(covariate="comorbid_diabetes_t1")
median_bmi_comorbid_diabetes_t2 <- average_bmi_function(BMI_complete_categories_2, comorbid_diabetes_t2) %>%
dplyr::mutate(covariate="comorbid_diabetes_t2")
median_bmi_comorbid_asthma <- average_bmi_function(BMI_complete_categories_2, comorbid_asthma) %>%
dplyr::mutate(covariate="comorbid_asthma")
median_bmi_comorbid_COPD <- average_bmi_function(BMI_complete_categories_2, comorbid_COPD) %>%
dplyr::mutate(covariate="comorbid_COPD")
median_bmi_comorbid_stroke_and_TIA <- average_bmi_function(BMI_complete_categories_2, comorbid_stroke_and_TIA) %>%
dplyr::mutate(covariate="comorbid_stroke_and_TIA")
median_bmi_comorbid_chronic_cardiac <- average_bmi_function(BMI_complete_categories_2, comorbid_chronic_cardiac) %>%
dplyr::mutate(covariate="comorbid_chronic_cardiac")
median_bmi_comorbid_hypertension <- average_bmi_function(BMI_complete_categories_2, comorbid_hypertension) %>%
dplyr::mutate(covariate="comorbid_hypertension")
median_bmi_comorbid_all_cancer <- average_bmi_function(BMI_complete_categories_2, comorbid_all_cancer) %>%
dplyr::mutate(covariate="comorbid_all_cancer")
###############
## append the data sets to create a single summary table
median_bmi_summary_demographic <- median_bmi_all %>%
dplyr::bind_rows(median_bmi_age_group,
median_bmi_sex,
median_bmi_ethnic_no_miss,
median_bmi_eth_group_16,
median_bmi_imd,
median_bmi_region) %>%
dplyr::select(covariate, category, "2015","2016","2017","2018","2019","2020", "2021")
# Summary of covariates
median_bmi_summary_covariates <- median_bmi_all %>%
dplyr::bind_rows(
median_bmi_comorbid_learning_disability,
median_bmi_comorbid_depression,
median_bmi_comorbid_dementia,
median_bmi_comorbid_psychosis_schiz_bipolar,
median_bmi_comorbid_diabetes_t2,
median_bmi_comorbid_diabetes_t1,
median_bmi_comorbid_asthma,
median_bmi_comorbid_COPD,
median_bmi_comorbid_stroke_and_TIA,
median_bmi_comorbid_chronic_cardiac,
median_bmi_comorbid_hypertension,
median_bmi_comorbid_all_cancer
)%>%
dplyr::select(covariate,category, "2015","2016","2017","2018","2019","2020", "2021")
#####################################################################################
# define outputs
write.csv (median_bmi_summary_demographic, here::here ("output/data","median_bmi_summary_table_demographic.csv"))
write.csv (median_bmi_summary_covariates, here::here ("output/data","median_bmi_summary_table_covariates.csv"))