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cumulative_vax_byage.R
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cumulative_vax_byage.R
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################################################################
# This script:
# - Calculates cumulative uptake of fourth dose/second booster
# COVID-19 vaccine by age
################################################################
# For running locally only #
# setwd("C:/Users/aschaffer/OneDrive - Nexus365/Documents/GitHub/vax-fourth-dose-RD")
# getwd()
# Import libraries #
library('tidyverse')
library('lubridate')
library('arrow')
library('here')
library('reshape2')
library('dplyr')
library('fs')
library('ggplot2')
library('RColorBrewer')
## Create directories
dir_create(here::here("output", "cumulative_rates"), showWarnings = FALSE, recurse = TRUE)
# Custom functions
# Factorise ----
fct_case_when <- function(...) {
# uses dplyr::case_when but converts the output to a factor,
# with factors ordered as they appear in the case_when's ... argument
args <- as.list(match.call())
levels <- sapply(args[-1], function(f) f[[3]]) # extract RHS of formula
levels <- levels[!is.na(levels)]
factor(dplyr::case_when(...), levels=levels)
}
# Read in data
fourth <- arrow::read_feather(here::here("output", "input_fourth.feather")) %>%
mutate_at(c(vars(c(contains("_date")))), as.Date, format = "%Y-%m-%d") %>%
arrange(age_cat, desc(covid_vax_4_date)) %>%
dplyr::select(!c(sex,imd,ethnicity,region))
###########################
### By 5-year age group ###
###########################
### Calculate cumulative proportion of people receiving fourth dose
fourth_age5_byday <- fourth %>%
group_by(age_cat) %>%
mutate(total = n()) %>% # Calculate denominator (total count per age category)
ungroup() %>%
subset(!is.na(covid_vax_4_date)) %>% # Remove people with no 4th vax
group_by(age_cat, total, covid_vax_4_date) %>%
summarise(vax_4_n = n()) %>% # Num vaccinated each day
ungroup() %>%
arrange(age_cat, covid_vax_4_date) %>%
group_by(age_cat, total) %>%
mutate(vax_4_sum = cumsum(vax_4_n), # Cumulative num vaccinated each day
#vax_4_sum = case_when(vax_4_sum > 5 ~ vax_4_sum), # Redaction
vax_4_sum = round(vax_4_sum / 7) * 7, # Rounding
rate = vax_4_sum / total * 100) %>% # Cumulative % vaccinated each day
complete(covid_vax_4_date = seq(min(as.Date(covid_vax_4_date)),
max(as.Date("2022-11-30")), by = '1 day')) %>%
fill(c(vax_4_sum, rate)) %>% # Create rows for days with zero vaccinations
ungroup() %>%
select(!vax_4_n)
# Save
fourth_age5_byday <- fourth_age5_byday %>% subset(covid_vax_4_date >= as.Date("2022-09-01"))
write.csv(fourth_age5_byday,
here::here("output", "cumulative_rates", "final_dose4_cum_byage5.csv"), row.names = FALSE)
### Plot cumulative fourth dose over time
ggplot(subset(fourth_age5_byday, age_cat != "Missing" &
covid_vax_4_date >= "2022-09-01" &
covid_vax_4_date < "2022-12-01")) +
geom_line(aes(x = covid_vax_4_date, y = rate/100, group = age_cat, col = age_cat),
size = 1.25) +
geom_vline(aes(xintercept = as.Date("2022-10-14")), linetype = "longdash") +
scale_colour_manual(values = c('#00496f', '#0f85a0', '#edd746', '#dd4124'))+
scale_y_continuous(labels = scales::percent, limits = c(0, 1)) +
scale_x_continuous(breaks = c(as.Date("2022-09-01"), as.Date("2022-10-01"),
as.Date("2022-10-14"), as.Date("2022-11-01"),
as.Date("2022-12-01")),
labels = c("Sep 1", "Oct 1", "Oct 14", "Nov 1", "Dec 1")) +
xlab(NULL) + ylab("Received second booster") +
theme_bw() +
theme(panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))
ggsave(here::here("output", "cumulative_rates", "plot_dose4_cum_age5.png"),
dpi = 300, units = "in", width = 6, height = 3.25)
###########################
### By 1-year age group ###
###########################
### Calculate cumulative proportion of people receiving fourth dose
fourth_age1_byday <- fourth %>%
subset(age < 54 & age > 45) %>% # Restrict to 4 years before/after cutoff
group_by(age) %>%
mutate(total = n()) %>% # Calculate denominator (total count per age category)
ungroup() %>%
subset(!is.na(covid_vax_4_date)) %>% # Remove people with no 4th vax
group_by(age, total, covid_vax_4_date) %>%
summarise(vax_4_n = n()) %>% # Num vaccinated each day
ungroup() %>%
arrange(age, covid_vax_4_date) %>%
group_by(age, total) %>%
mutate(vax_4_sum = cumsum(vax_4_n), # Cumulative num vaccinated each day
#vax_4_sum = case_when(vax_4_sum > 5 ~ vax_4_sum), # Redaction
vax_4_sum = round(vax_4_sum / 7) * 7, # Rounding
total = round(total / 7) * 7, # Rounding
rate = vax_4_sum / total * 100) %>% # Cumulative % vaccinated each day
complete(covid_vax_4_date = seq(min(as.Date(covid_vax_4_date)),
max(as.Date("2022-11-30")), by = '1 day')) %>%
fill(c(vax_4_sum, rate)) %>% # Create rows for days with zero vaccinations
ungroup() %>%
select(!vax_4_n) %>%
mutate(age = as.character(age))
# Save
fourth_age1_byday <- fourth_age1_byday %>% subset(covid_vax_4_date >= as.Date("2022-09-01"))
write.csv(fourth_age1_byday,
here::here("output", "cumulative_rates", "final_dose4_cum_byage1.csv"), row.names = FALSE)
### Plot cumulative fourth dose over time
ggplot(subset(fourth_age1_byday,
covid_vax_4_date >= "2022-09-01" &
covid_vax_4_date < "2022-12-01")) +
geom_line(aes(x = covid_vax_4_date, y = rate/100, group = age, col = age),
size = 1.25) +
geom_vline(aes(xintercept = as.Date("2022-10-14")), linetype = "longdash") +
scale_color_brewer(palette = "RdBu") +
scale_y_continuous(labels = scales::percent, limits = c(0, 1)) +
scale_x_continuous(breaks = c(as.Date("2022-09-01"), as.Date("2022-10-01"),
as.Date("2022-10-14"), as.Date("2022-11-01"),
as.Date("2022-12-01")),
labels = c("Sep 1", "Oct 1", "Oct 14", "Nov 1", "Dec 1")) +
xlab(NULL) + ylab("Received second booster") +
theme_bw() +
theme(panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))
ggsave(here::here("output", "cumulative_rates", "plot_dose4_cum_age1.png"),
dpi = 300, units = "in", width = 6, height = 3.25)
###################
##### Checks ######
###################
# Proportion with each number of doses on Nov 1
dose_counts <- fourth %>%
mutate(# Count receiving each dose
first_dose = ifelse(is.na(covid_vax_1_date)|covid_vax_1_date > "2022-11-01", 0, 1),
second_dose = ifelse(is.na(covid_vax_2_date)|covid_vax_2_date > "2022-11-01", 0, 1),
third_dose = ifelse(is.na(covid_vax_3_date)|covid_vax_3_date > "2022-11-01", 0, 1),
fourth_dose = ifelse(is.na(covid_vax_4_date)|covid_vax_4_date > "2022-11-01", 0, 1),
no_dose = ifelse(is.na(covid_vax_1_date), 1, 0),
# Variable representing number of doses
num_dose = case_when(fourth_dose == 1 ~ 4,
third_dose == 1 ~ 3,
second_dose == 1 ~ 2,
first_dose == 1~ 1,
TRUE ~ 0)
)
write.csv(dose_counts,
here::here("output", "cumulative_rates", "doses_at_nov1.csv"), row.names = FALSE)
# Plot of when people received each dose (see if it makes sense)
doses_by_day <- fourth %>%
select(!c(age_cat, age, sex, imd, region, ethnicity)) %>%
melt(id = c("patient_id")) %>%
rename(vax = variable, date = value) %>%
mutate(vax = fct_case_when(
vax == "covid_vax_1_date" ~ "First dose",
vax == "covid_vax_2_date" ~ "Second dose",
vax == "covid_vax_3_date" ~ "Third dose",
vax == "covid_vax_4_date" ~ "Fourth dose"
)) %>%
subset(!is.na(date)) %>%
group_by(vax, date) %>%
summarise(vax_n = n()) %>%
group_by(vax) %>%
complete(date = seq(min(as.Date(date)),
max(as.Date("2022-11-30")),
by = '1 day')) %>%
fill(vax_n) %>% # Create rows for days with zero vaccinations
ungroup()
ggplot(doses_by_day, aes(x = date, y = vax_n)) +
geom_line(aes(col = vax)) +
geom_ribbon(aes(group = vax, fill = vax, ymax = vax_n), ymin = 0, alpha = 0.5) +
xlab("") + ylab("Received vaccine (n)") +
scale_colour_manual(values = c('#00496f', '#0f85a0', '#edd746', '#dd4124'))+
scale_fill_manual(values = c('#00496f', '#0f85a0', '#edd746', '#dd4124')) +
scale_x_continuous(breaks = c(as.Date("2021-01-01"), as.Date("2021-07-01"),
as.Date("2022-01-01"), as.Date("2022-07-01")),
labels = c("Jan 2021", "Jul 2021", "Jan 2022", "Jul 2022")) +
theme_bw() +
theme(panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))
ggsave(here::here("output", "cumulative_rates", "plot_all_doses_over_time.png"),
dpi = 300, units = "in", width = 6, height = 3.25)