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CPRD_analysis.R
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CPRD_analysis.R
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#:--------------------------------------------------------
#
# In this file we check the probabilities for CPRD individuals
#
#:--------------------------------------------------------
# load libraries
library(tidyverse)
library(ggplot2)
library(patchwork)
# load data
probabilities_under_30 <- read.delim("data/mody_probabilities_under_30s.txt")
probabilities_under_35 <- read.delim("data/mody_probabilities_under_35s.txt")
## formatted probabilities
probabilities <- probabilities_under_30 %>%
as.data.frame() %>%
## remove the column which the model used
select(-which_equation) %>%
## rename variables
rename("Old Calculator" = "old_prob", "New Calculator" = "new_prob") %>%
## gather in long format
gather("key", "value") %>%
## turn key into factor
mutate(key = factor(key, levels = c("Old Calculator", "New Calculator")))
## divide values by 100 to decimals
# mutate(value = value/100)
plot_cprd_probabilities_density <- patchwork::wrap_plots(
# the first part of the plot
probabilities %>%
filter(key == "New Calculator") %>%
ggplot() +
geom_density(aes(x = value), fill = "grey") +
geom_vline(
data = probabilities %>%
filter(key == "New Calculator") %>%
group_by(key) %>%
mutate(mean = mean(value)) %>%
ungroup() %>%
select(-value) %>%
unique(),
aes(xintercept = mean), linetype = "dashed"
) +
geom_vline(xintercept = 0.036, colour = "black") +
coord_cartesian(xlim = c(0, 0.115), expand = TRUE) +
scale_x_continuous(labels = scales::percent, breaks = c(0, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12)) +
theme_bw() +
theme(
axis.text.x = element_text(size = 22),
axis.title = element_blank(),
axis.text.y = element_blank(),
legend.position = "none",
axis.line = element_line(colour = "black"),
panel.border = element_blank(),
panel.background = element_blank(),
axis.ticks.y = element_blank(),
plot.margin = unit(c(0,0,0,0), "cm")
),
# spacing
plot_spacer(),
# the second part of the plot
probabilities %>%
filter(key == "New Calculator") %>%
ggplot() +
geom_density(aes(x = value), fill = "grey") +
geom_vline(
data = probabilities %>%
filter(key == "New Calculator") %>%
group_by(key) %>%
mutate(mean = mean(value)) %>%
ungroup() %>%
select(-value) %>%
unique(),
aes(xintercept = mean), linetype = "dashed"
) +
geom_vline(xintercept = 0.036, colour = "black") +
coord_cartesian(xlim = c(0.16, 1), expand = TRUE) +
scale_x_continuous(labels = scales::percent, breaks = c(0.12, 0.25, 0.5, 0.75, 1)) +
theme_bw() +
theme(
axis.text.x = element_text(size = 22),
axis.title = element_blank(),
axis.text.y = element_blank(),
legend.position = "none",
axis.line = element_line(colour = "black"),
panel.border = element_blank(),
panel.background = element_blank(),
axis.ticks.y = element_blank(),
axis.line.y = element_blank(),
plot.margin = unit(c(0,0.2,0,0), "cm")
)
) + plot_layout(widths = c(4, -0.17, 4))
plot_cprd_probabilities_boxplot <- patchwork::wrap_plots(
probabilities %>%
ggplot() +
geom_boxplot(aes(x = value, y = key, colour = key)) +
geom_point(
data = probabilities %>%
group_by(key) %>%
mutate(mean = mean(value)) %>%
ungroup() %>%
select(-value) %>%
unique(),
aes(x = mean, y = key, colour = key), shape = "circle", size = 5
) +
geom_vline(xintercept = 0.036, colour = "black") +
scale_colour_manual(values = c("#1B9E77", "#D95F02")) +
coord_cartesian(xlim = c(0, 0.115), expand = TRUE) +
scale_x_continuous(labels = scales::percent, breaks = c(0, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12)) +
theme_bw() +
theme(
axis.text.x = element_text(size = 22),
axis.title = element_blank(),
axis.text.y = element_text(size = 22),
legend.position = "none",
axis.line = element_line(colour = "black"),
panel.border = element_blank(),
panel.background = element_blank(),
axis.ticks.y = element_blank(),
plot.margin = unit(c(0,1.5,0,0), "cm")
),
probabilities %>%
ggplot() +
geom_boxplot(aes(x = value, y = key, colour = key)) +
geom_point(
data = probabilities %>%
group_by(key) %>%
mutate(mean = mean(value)) %>%
ungroup() %>%
select(-value) %>%
unique(),
aes(x = mean, y = key, colour = key), shape = "circle", size = 5
) +
geom_vline(xintercept = 0.036, colour = "black") +
scale_colour_manual(values = c("#1B9E77", "#D95F02")) +
coord_cartesian(xlim = c(0.16, 1), expand = TRUE) +
scale_x_continuous(labels = scales::percent, breaks = c(0.125, 0.25, 0.5, 0.75, 1)) +
theme_bw() +
theme(
axis.text.x = element_text(size = 22),
axis.title = element_blank(),
axis.text.y = element_blank(),
legend.position = "none",
axis.line = element_line(colour = "black"),
panel.border = element_blank(),
panel.background = element_blank(),
axis.ticks.y = element_blank(),
axis.line.y = element_blank(),
plot.margin = unit(c(0,0.5,0,0), "cm")
),
nrow = 1
)
#:-------------------------------------------------------------
# Making plots
pdf("figures/cprd_analysis_density.pdf", width = 11, height = 3)
plot_cprd_probabilities_density
dev.off()