overall_ab_boxplot_brit.R

# # # # # # # # # # # # # # # # # # # # #
# This script:
# Generate a plot to show overall antibiotics prescribing rate by month
# By practice, by month, per 1000 patient
# # # # # # # # # # # # # # # # # # # # #

## Import libraries---

library('tidyverse')
library("ggplot2")
library('dplyr')
library('lubridate')

# impoprt data
df <- read_csv(
  here::here("output", "measures", "measure_antibiotics_overall_brit.csv"),
  col_types = cols_only(
    
    # Identifier
    practice = col_integer(),
    
    # Outcomes
    antibacterial_brit  = col_double(),
    population  = col_double(),
    value = col_double(),
    
    # Date
    date = col_date(format="%Y-%m-%d")
    
  ),
  na = character()
  )


# remove last month data
last.date=max(df$date)
df=df%>% filter(date!=last.date)
first_mon <- (format(min(df$date), "%m-%Y"))
last_mon <- (format(max(df$date), "%m-%Y"))

df$date <- as.Date(df$date)
df$cal_mon <- month(df$date)
df$cal_year <- year(df$date)

df_input <- df %>% filter(practice >0)
num_uniq_prac <- as.numeric(dim(table((df_input$practice))))
#line

df_gprate <- df_input %>% group_by(practice, cal_mon, cal_year) %>%
  mutate(ab_rate_1000 = value*1000) 

mean_rate <- df_gprate%>% group_by(cal_mon,cal_year)%>%
  mutate(mean_rate = mean(ab_rate_1000,na.rm=TRUE),
         five=quantile(ab_rate_1000, na.rm=TRUE, c(0.05)),
         ninefive= quantile(ab_rate_1000, na.rm=TRUE, c(0.95)))

#boxplot

overallbox_brit <- ggplot(mean_rate, aes(group=date,x=date,y=ab_rate_1000)) + 
  geom_boxplot(outlier.shape = NA)+
  coord_cartesian(ylim = quantile(mean_rate$ab_rate_1000, c(0.025, 0.975),na.rm=TRUE))+
  geom_vline(xintercept = as.numeric(as.Date("2019-12-31")))+
  geom_vline(xintercept = as.numeric(as.Date("2020-12-31")))+
  labs(
    title = "Overall antibiotics prescribing rate by practice - Brit",
    subtitle = paste(first_mon,"-",last_mon),
    caption = paste("Data from approximately", num_uniq_prac,"TPP Practices"),
    x = "Time",
    y = "Mean Prescribing rate distribution by practice"
  )
overallbox_brit

ggsave(
  plot= overallbox_brit,
  filename="overallbox_brit.jpeg", path=here::here("output"),
)