generated from opensafely/research-template
/
amoxicillin_percentage_by_age.R
102 lines (86 loc) · 4.06 KB
/
amoxicillin_percentage_by_age.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
library("dplyr")
library("tidyverse")
library("lubridate")
rm(list=ls())
setwd(here::here("output", "measures"))
df1 <- readRDS('ab_type_pre.rds')
df2 <- readRDS('ab_type_2019.rds')
df3 <- readRDS('ab_type_2020.rds')
df4 <- readRDS('ab_type_2021.rds')
df5 <- readRDS('ab_type_2022.rds')
df2 <- bind_rows(df2)
df3 <- bind_rows(df3)
df4 <- bind_rows(df4)
df <- rbind(df1,df2,df3,df4,df5)
rm(df1,df2,df3,df4,df5)
broadtype <- c("Amoxicillin")
df <- df %>% select(patient_id,age,Date,type) %>%
mutate(age_cat= case_when(age>=0&age<=4 ~ "0-4",
age>=5&age<=14 ~ "5-14",
age>=15&age<=24 ~ "15-24",
age>=25&age<=34 ~ "25-34",
age>=35&age<=44 ~ "35-44",
age>=45&age<=54 ~ "45-54",
age>=55&age<=64 ~ "55-64",
age>=65&age<=74 ~ "65-74",
age>=75 ~ "75+"))
df$age_cat <- as.factor(df$age_cat)
df.broad <- df %>% filter(type %in% broadtype )
df.broad_total <- df.broad %>% group_by(Date,age_cat) %>% summarise(
broad_number = n()
)
first_mon=format(min(df.broad_total$Date),"%m-%Y")
last_mon= format(max(df.broad_total$Date),"%m-%Y")
plot.broad_number<- ggplot(df.broad_total, aes(x=Date, y=broad_number ,group=age_cat,color=age_cat))+
annotate(geom = "rect", xmin = as.Date("2021-01-01"),xmax = as.Date("2021-04-01"),ymin = -Inf, ymax = Inf,fill="grey80", alpha=0.5)+
annotate(geom = "rect", xmin = as.Date("2020-11-01"),xmax = as.Date("2020-12-01"),ymin = -Inf, ymax = Inf,fill="grey80", alpha=0.5)+
annotate(geom = "rect", xmin = as.Date("2020-03-01"),xmax = as.Date("2020-06-01"),ymin = -Inf, ymax = Inf,fill="grey80", alpha=0.5)+
geom_line(aes(linetype=age_cat))+
geom_point(aes(shape=age_cat))+
theme(legend.position = "right",legend.title =element_blank())+
labs(
fill = "Age",
title = "The total number of amoxicillin prescriptions by age",
subtitle = paste(first_mon,"-",last_mon),
y = "",
x=""
)+
theme(axis.text.x=element_text(angle=60,hjust=1))+
scale_shape_manual(values = c(rep(1:9))) +
scale_color_manual(values = c("coral2","deeppink3","darkred","darkviolet","brown3","goldenrod2","blue3","green3","forestgreen"))+
scale_x_date(date_labels = "%m-%Y", date_breaks = "1 month")
plot.broad_number
ggsave(
plot= plot.broad_number,
filename="amoxicillin_prescriptions_by_age.jpeg", path=here::here("output"),
)
rm(plot.broad_number,df.broad)
df.all <- df %>% group_by(Date,age_cat) %>% summarise(
ab_number = n()
)
df.prop <- merge(df.broad_total,df.all,by=c("Date","age_cat"))
df.prop$prop <- df.prop$broad_number/df.prop$ab_number
plot.broad_prop<- ggplot(df.prop, aes(x=Date, y=prop ,group=age_cat,color=age_cat))+
annotate(geom = "rect", xmin = as.Date("2021-01-01"),xmax = as.Date("2021-04-01"),ymin = -Inf, ymax = Inf,fill="grey80", alpha=0.5)+
annotate(geom = "rect", xmin = as.Date("2020-11-01"),xmax = as.Date("2020-12-01"),ymin = -Inf, ymax = Inf,fill="grey80", alpha=0.5)+
annotate(geom = "rect", xmin = as.Date("2020-03-01"),xmax = as.Date("2020-06-01"),ymin = -Inf, ymax = Inf,fill="grey80", alpha=0.5)+
geom_line(aes(linetype=age_cat))+
geom_point(aes(shape=age_cat))+
theme(legend.position = "right",legend.title =element_blank())+
labs(
fill = "Age",
title = "Proportion of amoxicillin prescribed by age",
subtitle = paste(first_mon,"-",last_mon),
y = "",
x=""
)+
scale_y_continuous(labels = scales::percent,breaks=seq(0, 1, by = 0.005))+
theme(axis.text.x=element_text(angle=60,hjust=1))+
scale_shape_manual(values = c(rep(1:9))) +
scale_color_manual(values = c("coral2","deeppink3","darkred","darkviolet","brown3","goldenrod2","blue3","green3","forestgreen"))+
scale_x_date(date_labels = "%m-%Y", date_breaks = "1 month")
plot.broad_prop
ggsave(
plot= plot.broad_prop,
filename="amoxicillin_proportion_by_age.jpeg", path=here::here("output"),
)